tutorial_mock.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# RExMap tutorial: mock community data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RExMap v1.0 loaded.\n"
     ]
    }
   ],
   "source": [
    "library(rexmap)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Specify full main path and load raw FASTQ files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "out_path = path.expand('~/data/zheng_2015_tutorial')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "fastq_path = file.path(out_path, 'fastq')\n",
    "fq_fwd = read_files(fastq_path, 'R1')\n",
    "fq_rev = read_files(fastq_path, 'R2')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Generate output files for the pre-processing part of the pipeline:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "sample_ids = sampleids_from_filenames(fq_fwd, separator='_')\n",
    "fq_mer = file.path(out_path, 'rexmap_merged', paste0(sample_ids, '.fastq'))\n",
    "fq_pcr = file.path(out_path, 'rexmap_trimmed', paste0(sample_ids, '.fastq'))\n",
    "fq_fil = file.path(out_path, 'rexmap_filtered', paste0(sample_ids, '.fastq'))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Pre-processing\n",
    "Merge reads, remove PCR primers and perform quality control and fixed-length trimming."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Loading FASTQ reads: V3V4Rep1_R1.fastq, V3V4Rep1_R2.fastq ... OK.\n",
      "Merging pairs... OK.\n",
      "Writing output files... OK.\n"
     ]
    }
   ],
   "source": [
    "mergestats = merge_pairs(fq_fwd, fq_rev, fq_mer, verbose=T)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>/Users/igor/data/zheng_2015_tutorial/fastq/V3V4Rep1_R1.fastq</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>total</th><td>25600</td></tr>\n",
       "\t<tr><th scope=row>low_pct_sim</th><td>1355</td></tr>\n",
       "\t<tr><th scope=row>low_aln_len</th><td>2</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|l}\n",
       "  & /Users/igor/data/zheng\\_2015\\_tutorial/fastq/V3V4Rep1\\_R1.fastq\\\\\n",
       "\\hline\n",
       "\ttotal & 25600\\\\\n",
       "\tlow\\_pct\\_sim & 1355\\\\\n",
       "\tlow\\_aln\\_len & 2\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | /Users/igor/data/zheng_2015_tutorial/fastq/V3V4Rep1_R1.fastq | \n",
       "|---|---|---|\n",
       "| total | 25600 | \n",
       "| low_pct_sim | 1355 | \n",
       "| low_aln_len | 2 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "            /Users/igor/data/zheng_2015_tutorial/fastq/V3V4Rep1_R1.fastq\n",
       "total       25600                                                       \n",
       "low_pct_sim 1355                                                        \n",
       "low_aln_len 2                                                           "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "mergestats"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Primer set used for amplifying V3-V4 region was 341F and 805R, which are labelled as 'V3-V4-2' in our reference table:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>Primer1</th><th scope=col>Primer2</th><th scope=col>Primer1_sequence_5to3</th><th scope=col>Primer2_sequence_3to5</th><th scope=col>Hypervariable_region</th><th scope=col>DB</th><th scope=col>table</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>341F                                                      </td><td>805R                                                      </td><td>GACAGCCTACGGGNGGCWGCAG                                    </td><td>GACTACHVGGGTATCTAATCC                                     </td><td>V3-V4-2                                                   </td><td>V3-V4_337F-805R_hang21_wrefseq_sequences_unique_variants  </td><td>V3-V4_337F-805R_hang21_wrefseq_table_unique_variants_R.txt</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllllll}\n",
       " Primer1 & Primer2 & Primer1\\_sequence\\_5to3 & Primer2\\_sequence\\_3to5 & Hypervariable\\_region & DB & table\\\\\n",
       "\\hline\n",
       "\t 341F                                                                     & 805R                                                                     & GACAGCCTACGGGNGGCWGCAG                                                   & GACTACHVGGGTATCTAATCC                                                    & V3-V4-2                                                                  & V3-V4\\_337F-805R\\_hang21\\_wrefseq\\_sequences\\_unique\\_variants     & V3-V4\\_337F-805R\\_hang21\\_wrefseq\\_table\\_unique\\_variants\\_R.txt\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "Primer1 | Primer2 | Primer1_sequence_5to3 | Primer2_sequence_3to5 | Hypervariable_region | DB | table | \n",
       "|---|\n",
       "| 341F                                                       | 805R                                                       | GACAGCCTACGGGNGGCWGCAG                                     | GACTACHVGGGTATCTAATCC                                      | V3-V4-2                                                    | V3-V4_337F-805R_hang21_wrefseq_sequences_unique_variants   | V3-V4_337F-805R_hang21_wrefseq_table_unique_variants_R.txt | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "  Primer1 Primer2 Primer1_sequence_5to3  Primer2_sequence_3to5\n",
       "1 341F    805R    GACAGCCTACGGGNGGCWGCAG GACTACHVGGGTATCTAATCC\n",
       "  Hypervariable_region DB                                                      \n",
       "1 V3-V4-2              V3-V4_337F-805R_hang21_wrefseq_sequences_unique_variants\n",
       "  table                                                     \n",
       "1 V3-V4_337F-805R_hang21_wrefseq_table_unique_variants_R.txt"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "rexmap_option('blast_dbs')[6]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* PCR trimmer mode: region V3-V4-2 \n",
      "(fwd: GACAGCCTACGGGNGGCWGCAG, rev: GGATTAGATACCCBDGTAGTC)\n",
      "* loading file...OK.\n",
      "* trimming...OK.\n",
      "* saving output...OK.\n"
     ]
    }
   ],
   "source": [
    "trimstats = remove_pcr_primers(fq_mer, fq_pcr, region='V3-V4-2', verbose=T)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>/Users/igor/data/zheng_2015_tutorial/rexmap_merged/V3V4Rep1.fastq</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>fwd_trim</th><td>24219</td></tr>\n",
       "\t<tr><th scope=row>rev_trim</th><td>24127</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|l}\n",
       "  & /Users/igor/data/zheng\\_2015\\_tutorial/rexmap\\_merged/V3V4Rep1.fastq\\\\\n",
       "\\hline\n",
       "\tfwd\\_trim & 24219\\\\\n",
       "\trev\\_trim & 24127\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | /Users/igor/data/zheng_2015_tutorial/rexmap_merged/V3V4Rep1.fastq | \n",
       "|---|---|\n",
       "| fwd_trim | 24219 | \n",
       "| rev_trim | 24127 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "         /Users/igor/data/zheng_2015_tutorial/rexmap_merged/V3V4Rep1.fastq\n",
       "fwd_trim 24219                                                           \n",
       "rev_trim 24127                                                           "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "trimstats"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now find a length to trim all reads before passing them to DADA2 denoising. A good rule of thumb is length above which we have 99% of the reads:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "402"
      ],
      "text/latex": [
       "402"
      ],
      "text/markdown": [
       "402"
      ],
      "text/plain": [
       "[1] 402"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "seqlen.ft = sequence_length_table(fq_pcr)\n",
    "trim_length = ftquantile(seqlen.ft, 0.01)\n",
    "trim_length"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Trim reads to this length and then filter out the remaining reads with too many (> 2) expected errors:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "filtstats = filter_and_trim(fq_pcr, fq_fil, truncLen=trim_length)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th></th><th scope=col>reads.in</th><th scope=col>reads.out</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><th scope=row>V3V4Rep1.fastq</th><td>24244</td><td>22070</td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|ll}\n",
       "  & reads.in & reads.out\\\\\n",
       "\\hline\n",
       "\tV3V4Rep1.fastq & 24244 & 22070\\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "| <!--/--> | reads.in | reads.out | \n",
       "|---|\n",
       "| V3V4Rep1.fastq | 24244 | 22070 | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "               reads.in reads.out\n",
       "V3V4Rep1.fastq 24244    22070    "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "filtstats"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## DADA2 denoising\n",
    "Denoise these filter and trimmed reads, then pass on the pre-trimmed reads (`fq_tri`) to retrieve back full-length sequences before we align them vs a reference database:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* learn errors...8872140 total bases in 22070 reads from 1 samples will be used for learning the error rates.\n",
      "Initializing error rates to maximum possible estimate.\n",
      "selfConsist step 1 .\n",
      "   selfConsist step 2\n",
      "   selfConsist step 3\n",
      "   selfConsist step 4\n",
      "   selfConsist step 5\n",
      "Convergence after  5  rounds.\n",
      " OK.\n",
      "* processing  V3V4Rep1.fastq\n",
      "Sample 1 - 22070 reads in 14060 unique sequences.\n",
      "Trimmed length:  402  nt.\n",
      "Retrieving full-length sequences...\n",
      "Sample  1 . Load...OK. Consensus...OK. Update...OK.\n"
     ]
    }
   ],
   "source": [
    "dada_result = dada_denoise(fq_fil, fq_pcr, verbose=T)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Extract sequence abundance from DADA2 output:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* generating sequence table..."
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "The sequences being tabled vary in length.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " OK.\n",
      "* removing bimeras..."
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Identified 28 bimeras out of 45 input sequences.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " OK.\n",
      "* adding together sequences that differ in shifts on lengths...collapse:\n",
      "* generating temporary files...OK.\n",
      "* blast word size: 322 \n",
      "* running blast...blast status:  0\n",
      "OK.\n",
      "* selecting ends-free alignments...OK.\n",
      "* no sequences need collapsing.\n",
      "* cleaning up temporary files...OK.\n",
      "* returning input.\n",
      " OK.\n"
     ]
    }
   ],
   "source": [
    "ab.dt = sequence_abundance(dada_result)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## BLAST\n",
    "Align the un-trimmed sequences to the RExMap reference database for V3-V4 region:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "* blast input type: abundance table\n",
      "* blast out: OK. blast best: OK. copy number table: OK.\n",
      "merge: OK. Fix overhang differences:..OK. OK.\n"
     ]
    }
   ],
   "source": [
    "blast_output = blast(ab.dt, region='V3-V4-2', verbose=T)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## OSU abundance table\n",
    "From sequence abundance table and BLAST output, estimate the abundance of each Operational Strain Unit (OSU):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "osu_ab.dt = abundance(ab.dt, blast_output)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>sample_id</th><th scope=col>osu_id</th><th scope=col>osu_count</th><th scope=col>pctsim</th><th scope=col>species</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1074                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>2813                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Streptococcus_mutans_[106]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>    206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>2436                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Escherichia_coli_[7164],Shigella_sonnei_[854],Shigella_flexneri_[67],Shigella_boydii_[32],Escherichia_fergusonii_[7],Escherichia_albertii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1093                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td> 946                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Staphylococcus_epidermidis_RP62A,Staphylococcus_epidermidis_ET-024,Staphylococcus_epidermidis_FDAARGOS_157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   2440                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Rhodobacter_sphaeroides_[11],Rhodobacter_johrii_JA192,Rhodobacter_megalophilus_DSM_18937,Rhodobacter_sp._AKP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>     68                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Bacillus_cereus_[887],Bacillus_thuringiensis_[413],Bacillus_toyonensis_[198],Bacillus_wiedmannii_[131],Bacillus_anthracis_[118],Bacillus_pseudomycoides_[103],Bacillus_mycoides_[55],Bacillus_gaemokensis_[2],Bacillus_weihenstephanensis_[2],Bacillus_bingmayongensis_FJAT-13831,Bacillus_bombysepticus_Wang,Bacillus_licheniformis_V30,Bacillus_sp._0711P9-1,Bacillus_sp._100374,Bacillus_sp._4048,Bacillus_sp._4049,Bacillus_sp._7_6_55CFAA_CT2,Bacillus_sp._AFS012607,Bacillus_sp._AFS014408,Bacillus_sp._AFS015896,Bacillus_sp._AFS019443,Bacillus_sp._AFS023182,Bacillus_sp._AFS029637,Bacillus_sp._AFS033286,Bacillus_sp._AFS051223,Bacillus_sp._AFS054943,Bacillus_sp._AFS059628,Bacillus_sp._AFS075034,Bacillus_sp._AFS075960,Bacillus_sp._AFS094611,Bacillus_sp._AFS098217,Bacillus_sp._AKBS9,Bacillus_sp._BI3,Bacillus_sp._EB422,Bacillus_sp._FDAARGOS_235,Bacillus_sp._G3(2015),Bacillus_sp._GeD10,Bacillus_sp._H1a,Bacillus_sp._H1m,Bacillus_sp._HMSC036E02,Bacillus_sp._JH7,Bacillus_sp._K2I17,Bacillus_sp._KbaB1,Bacillus_sp._KbaL1,Bacillus_sp._L_1B0_5,Bacillus_sp._L_1B0_8,Bacillus_sp._L27,Bacillus_sp._LK2,Bacillus_sp._M13(2017),Bacillus_sp._MB353a,Bacillus_sp._MB366,Bacillus_sp._MN5_Mn5,Bacillus_sp._N24,Bacillus_sp._N35-10-2,Bacillus_sp._N35-10-4,Bacillus_sp._NH11B,Bacillus_sp._NH24A2,Bacillus_sp._Root11,Bacillus_sp._Root131,Bacillus_sp._RUTrin4,Bacillus_sp._RZ2MS9,Bacillus_sp._S1-R1J2-FB,Bacillus_sp._S1-R2T1-FB,Bacillus_sp._S1-R4H1-FB,Bacillus_sp._S1-R5C1-FB,Bacillus_sp._TD41,Bacillus_sp._TD42,Bacillus_sp._UAEU-H3K6M1,Bacillus_sp._UMTAT18,Bacillus_sp._YF23</td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1056                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td> 324                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Streptococcus_agalactiae_[466],Streptococcus_sp._HMSC036H09,Streptococcus_sp._HMSC056B03,Streptococcus_sp._HMSC056D01,Streptococcus_sp._HMSC063D10,Streptococcus_sp._HMSC064H02,Streptococcus_sp._HMSC065G04,Streptococcus_sp._HMSC068H01,Streptococcus_sp._HMSC069D09,Streptococcus_sp._HMSC070A10,Streptococcus_sp._HMSC070B09,Streptococcus_sp._HMSC072E12,Streptococcus_sp._HMSC072G02,Streptococcus_sp._HMSC074F09,Streptococcus_sp._HMSC074F10,Streptococcus_sp._HMSC075A03,Streptococcus_sp._HMSC076D11,Streptococcus_sp._HMSC076H07,Streptococcus_sp._HMSC076H08,Streptococcus_sp._HMSC076H09,Streptococcus_sp._HMSC076H10,Streptococcus_sp._HMSC078D02,Streptococcus_sp._HMSC078E03,Streptococcus_sp._HMSC078E08,Streptococcus_sp._HMSC11C05                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   2715                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td> 287                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Clostridium_beijerinckii_[13],Clostridium_saccharoperbutylacetonicum_[4],Clostridium_diolis_[2],Clostridium_sp._BL-8,Clostridium_sp._DL-VIII,Clostridium_sp._LS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>    754                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td> 264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Pseudomonas_aeruginosa_[1853],Candidatus_Hepatobacter_penaei_NHPB,Pseudomonas_denitrificans_(nomen_rejiciendum),Pseudomonas_otitidis_LNU-E-001,Pseudomonas_sp._2_1_26,Pseudomonas_sp._HMSC057H01,Pseudomonas_sp._HMSC058A10,Pseudomonas_sp._HMSC058B07,Pseudomonas_sp._HMSC058C05,Pseudomonas_sp._HMSC059F05,Pseudomonas_sp._HMSC05H02,Pseudomonas_sp._HMSC060F12,Pseudomonas_sp._HMSC060G01,Pseudomonas_sp._HMSC060G02,Pseudomonas_sp._HMSC061A10,Pseudomonas_sp._HMSC063H08,Pseudomonas_sp._HMSC064G05,Pseudomonas_sp._HMSC065H01,Pseudomonas_sp._HMSC065H02,Pseudomonas_sp._HMSC066A08,Pseudomonas_sp._HMSC066B03,Pseudomonas_sp._HMSC067D05,Pseudomonas_sp._HMSC067F09,Pseudomonas_sp._HMSC067G02,Pseudomonas_sp._HMSC069G05,Pseudomonas_sp._HMSC070B12,Pseudomonas_sp._HMSC071F02,Pseudomonas_sp._HMSC072F09,Pseudomonas_sp._HMSC073F05,Pseudomonas_sp._HMSC075A08,Pseudomonas_sp._HMSC076A11,Pseudomonas_sp._HMSC076A12,Pseudomonas_sp._HMSC16B01,Pseudomonas_sp._P179,Pseudomonas_sp._YS-1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1309                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td> 242                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Staphylococcus_aureus_[7702],Staphylococcus_argenteus_[81],Staphylococcus_schweitzeri_[2],Staphylococcus_simiae_[2],Pararheinheimera_mesophila_IITR-13,Staphylococcus_sp._HMSC035F01,Staphylococcus_sp._HMSC035F11,Staphylococcus_sp._HMSC055H04,Staphylococcus_sp._HMSC055H07,Staphylococcus_sp._HMSC057B01,Staphylococcus_sp._HMSC058E01,Staphylococcus_sp._HMSC060D01,Staphylococcus_sp._HMSC060D12,Staphylococcus_sp._HMSC063G01,Staphylococcus_sp._HMSC063H12,Staphylococcus_sp._HMSC067F10,Staphylococcus_sp._HMSC075C08,Staphylococcus_sp._HMSC34D01,Staphylococcus_sp._HMSC34H10,Staphylococcus_sp._HMSC35D08,Staphylococcus_sp._HMSC36A10,Staphylococcus_sp._HMSC36C03,Staphylococcus_sp._HMSC36D07,Staphylococcus_sp._HMSC36D12,Staphylococcus_sp._HMSC36F05,Staphylococcus_sp._HMSC36G04,Staphylococcus_sp._HMSC55F09,Staphylococcus_sp._HMSC56B09,Staphylococcus_sp._HMSC57A07,Staphylococcus_sp._HMSC57B03,Staphylococcus_sp._HMSC58A02,Staphylococcus_sp._HMSC58B01,Staphylococcus_sp._HMSC58E11,Staphylococcus_sp._HMSC64F10,Staphylococcus_sp._HMSC66A04,Staphylococcus_sp._HMSC66C11,Staphylococcus_sp._HMSC70F07,Staphylococcus_sp._HMSC72E08,Staphylococcus_sp._HMSC73A05,Staphylococcus_sp._HMSC74D05,Staphylococcus_sp._HMSC74G01,Staphylococcus_sp._HMSC74G05,Staphylococcus_sp._HMSC76G03,Staphylococcus_sp._HMSC77A05,Streptococcus_sobrinus_TCI-345                                                                                                                                                                                                                               </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   2336                                                                                                                                                                                                                                                                                                                                                                                                                                     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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Helicobacter_pylori_[587]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   2525                                                                                                                                                                                                                                                                                                                                                                                                                                     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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Lactobacillus_gasseri_[25]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   2887                                                                                                                                                                                                                                                                                                                                                                                                                                     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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Acinetobacter_baumannii_[1910],Acinetobacter_calcoaceticus/baumannii_complex_sp._ABNIH27,Acinetobacter_nosocomialis_ABBL048,Acinetobacter_sp._1396970,Acinetobacter_sp._AKBS16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1263                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>  32                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            </td><td>Neisseria_meningitidis_[455],Neisseria_animalis_Neisseria_meningitidis,Neisseria_canis_Neisseria_meningitidis,Psychrobacter_immobilis_Neisseria_meningitidis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>  24                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Listeria_monocytogenes_[2023],Listeria_ivanovii_[10],Listeria_innocua_[6],Listeria_seeligeri_[4],Listeria_welshimeri_[4],Listeria_marthii_NR_9579                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>   1467                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>   9                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td>100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Staphylococcus_aureus_SA3-LAU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </td></tr>\n",
       "\t<tr><td>V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   </td><td>1000017                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    </td><td>   6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       </td><td> 99.29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     </td><td>Escherichia_coli_[7871],Shigella_sonnei_[856],Shigella_flexneri_[67],Shigella_boydii_[33],Escherichia_fergusonii_[7],Escherichia_albertii_[5],Acinetobacter_baumannii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE172,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666,Lactobacillus_acidophilus_KLDS_1.0901,Shigella_sp._PAMC_28760                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllll}\n",
       " sample\\_id & osu\\_id & osu\\_count & pctsim & species\\\\\n",
       "\\hline\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            &    1074                                                                                                                                                                                                                                                                                                                                                                                                                                          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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              & Streptococcus\\_mutans\\_{[}106{]}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      &     206                                                                                                                                                                                                                                                                                                                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                                            & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        & Escherichia\\_coli\\_{[}7164{]},Shigella\\_sonnei\\_{[}854{]},Shigella\\_flexneri\\_{[}67{]},Shigella\\_boydii\\_{[}32{]},Escherichia\\_fergusonii\\_{[}7{]},Escherichia\\_albertii\\_{[}2{]},Shigella\\_dysenteriae\\_{[}2{]},Achromobacter\\_sp.\\_ATCC35328,Brenneria\\_alni\\_pvfi20,Citrobacter\\_braakii\\_SCC4,Escherichia\\_sp.\\_1\\_1\\_43,Escherichia\\_sp.\\_3\\_2\\_53FAA,Escherichia\\_sp.\\_4\\_1\\_40B,Escherichia\\_sp.\\_B1147,Escherichia\\_sp.\\_KTE11,Escherichia\\_sp.\\_KTE159,Escherichia\\_sp.\\_KTE52,Escherichia\\_sp.\\_KTE96,Escherichia\\_sp.\\_TW09308,Escherichia\\_sp.\\_TW15838,Escherichia\\_vulneris\\_ATCC\\_33821,Klebsiella\\_oxytoca\\_2880STDY5682666                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  &    1093                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Staphylococcus\\_epidermidis\\_RP62A,Staphylococcus\\_epidermidis\\_ET-024,Staphylococcus\\_epidermidis\\_FDAARGOS\\_157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          &    2440                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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                                                                                                                                                                                                                                                                                                   & Rhodobacter\\_sphaeroides\\_{[}11{]},Rhodobacter\\_johrii\\_JA192,Rhodobacter\\_megalophilus\\_DSM\\_18937,Rhodobacter\\_sp.\\_AKP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  &      68                                                                                                    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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          & Bacillus\\_cereus\\_{[}887{]},Bacillus\\_thuringiensis\\_{[}413{]},Bacillus\\_toyonensis\\_{[}198{]},Bacillus\\_wiedmannii\\_{[}131{]},Bacillus\\_anthracis\\_{[}118{]},Bacillus\\_pseudomycoides\\_{[}103{]},Bacillus\\_mycoides\\_{[}55{]},Bacillus\\_gaemokensis\\_{[}2{]},Bacillus\\_weihenstephanensis\\_{[}2{]},Bacillus\\_bingmayongensis\\_FJAT-13831,Bacillus\\_bombysepticus\\_Wang,Bacillus\\_licheniformis\\_V30,Bacillus\\_sp.\\_0711P9-1,Bacillus\\_sp.\\_100374,Bacillus\\_sp.\\_4048,Bacillus\\_sp.\\_4049,Bacillus\\_sp.\\_7\\_6\\_55CFAA\\_CT2,Bacillus\\_sp.\\_AFS012607,Bacillus\\_sp.\\_AFS014408,Bacillus\\_sp.\\_AFS015896,Bacillus\\_sp.\\_AFS019443,Bacillus\\_sp.\\_AFS023182,Bacillus\\_sp.\\_AFS029637,Bacillus\\_sp.\\_AFS033286,Bacillus\\_sp.\\_AFS051223,Bacillus\\_sp.\\_AFS054943,Bacillus\\_sp.\\_AFS059628,Bacillus\\_sp.\\_AFS075034,Bacillus\\_sp.\\_AFS075960,Bacillus\\_sp.\\_AFS094611,Bacillus\\_sp.\\_AFS098217,Bacillus\\_sp.\\_AKBS9,Bacillus\\_sp.\\_BI3,Bacillus\\_sp.\\_EB422,Bacillus\\_sp.\\_FDAARGOS\\_235,Bacillus\\_sp.\\_G3(2015),Bacillus\\_sp.\\_GeD10,Bacillus\\_sp.\\_H1a,Bacillus\\_sp.\\_H1m,Bacillus\\_sp.\\_HMSC036E02,Bacillus\\_sp.\\_JH7,Bacillus\\_sp.\\_K2I17,Bacillus\\_sp.\\_KbaB1,Bacillus\\_sp.\\_KbaL1,Bacillus\\_sp.\\_L\\_1B0\\_5,Bacillus\\_sp.\\_L\\_1B0\\_8,Bacillus\\_sp.\\_L27,Bacillus\\_sp.\\_LK2,Bacillus\\_sp.\\_M13(2017),Bacillus\\_sp.\\_MB353a,Bacillus\\_sp.\\_MB366,Bacillus\\_sp.\\_MN5\\_Mn5,Bacillus\\_sp.\\_N24,Bacillus\\_sp.\\_N35-10-2,Bacillus\\_sp.\\_N35-10-4,Bacillus\\_sp.\\_NH11B,Bacillus\\_sp.\\_NH24A2,Bacillus\\_sp.\\_Root11,Bacillus\\_sp.\\_Root131,Bacillus\\_sp.\\_RUTrin4,Bacillus\\_sp.\\_RZ2MS9,Bacillus\\_sp.\\_S1-R1J2-FB,Bacillus\\_sp.\\_S1-R2T1-FB,Bacillus\\_sp.\\_S1-R4H1-FB,Bacillus\\_sp.\\_S1-R5C1-FB,Bacillus\\_sp.\\_TD41,Bacillus\\_sp.\\_TD42,Bacillus\\_sp.\\_UAEU-H3K6M1,Bacillus\\_sp.\\_UMTAT18,Bacillus\\_sp.\\_YF23\\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            &    1056                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Streptococcus\\_agalactiae\\_{[}466{]},Streptococcus\\_sp.\\_HMSC036H09,Streptococcus\\_sp.\\_HMSC056B03,Streptococcus\\_sp.\\_HMSC056D01,Streptococcus\\_sp.\\_HMSC063D10,Streptococcus\\_sp.\\_HMSC064H02,Streptococcus\\_sp.\\_HMSC065G04,Streptococcus\\_sp.\\_HMSC068H01,Streptococcus\\_sp.\\_HMSC069D09,Streptococcus\\_sp.\\_HMSC070A10,Streptococcus\\_sp.\\_HMSC070B09,Streptococcus\\_sp.\\_HMSC072E12,Streptococcus\\_sp.\\_HMSC072G02,Streptococcus\\_sp.\\_HMSC074F09,Streptococcus\\_sp.\\_HMSC074F10,Streptococcus\\_sp.\\_HMSC075A03,Streptococcus\\_sp.\\_HMSC076D11,Streptococcus\\_sp.\\_HMSC076H07,Streptococcus\\_sp.\\_HMSC076H08,Streptococcus\\_sp.\\_HMSC076H09,Streptococcus\\_sp.\\_HMSC076H10,Streptococcus\\_sp.\\_HMSC078D02,Streptococcus\\_sp.\\_HMSC078E03,Streptococcus\\_sp.\\_HMSC078E08,Streptococcus\\_sp.\\_HMSC11C05                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        &    2715                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Clostridium\\_beijerinckii\\_{[}13{]},Clostridium\\_saccharoperbutylacetonicum\\_{[}4{]},Clostridium\\_diolis\\_{[}2{]},Clostridium\\_sp.\\_BL-8,Clostridium\\_sp.\\_DL-VIII,Clostridium\\_sp.\\_LS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            &     754                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             &  264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              & Pseudomonas\\_aeruginosa\\_{[}1853{]},Candidatus\\_Hepatobacter\\_penaei\\_NHPB,Pseudomonas\\_denitrificans\\_(nomen\\_rejiciendum),Pseudomonas\\_otitidis\\_LNU-E-001,Pseudomonas\\_sp.\\_2\\_1\\_26,Pseudomonas\\_sp.\\_HMSC057H01,Pseudomonas\\_sp.\\_HMSC058A10,Pseudomonas\\_sp.\\_HMSC058B07,Pseudomonas\\_sp.\\_HMSC058C05,Pseudomonas\\_sp.\\_HMSC059F05,Pseudomonas\\_sp.\\_HMSC05H02,Pseudomonas\\_sp.\\_HMSC060F12,Pseudomonas\\_sp.\\_HMSC060G01,Pseudomonas\\_sp.\\_HMSC060G02,Pseudomonas\\_sp.\\_HMSC061A10,Pseudomonas\\_sp.\\_HMSC063H08,Pseudomonas\\_sp.\\_HMSC064G05,Pseudomonas\\_sp.\\_HMSC065H01,Pseudomonas\\_sp.\\_HMSC065H02,Pseudomonas\\_sp.\\_HMSC066A08,Pseudomonas\\_sp.\\_HMSC066B03,Pseudomonas\\_sp.\\_HMSC067D05,Pseudomonas\\_sp.\\_HMSC067F09,Pseudomonas\\_sp.\\_HMSC067G02,Pseudomonas\\_sp.\\_HMSC069G05,Pseudomonas\\_sp.\\_HMSC070B12,Pseudomonas\\_sp.\\_HMSC071F02,Pseudomonas\\_sp.\\_HMSC072F09,Pseudomonas\\_sp.\\_HMSC073F05,Pseudomonas\\_sp.\\_HMSC075A08,Pseudomonas\\_sp.\\_HMSC076A11,Pseudomonas\\_sp.\\_HMSC076A12,Pseudomonas\\_sp.\\_HMSC16B01,Pseudomonas\\_sp.\\_P179,Pseudomonas\\_sp.\\_YS-1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        &    1309                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       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                                                                                                                                                                                                                                                  & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          & Staphylococcus\\_aureus\\_{[}7702{]},Staphylococcus\\_argenteus\\_{[}81{]},Staphylococcus\\_schweitzeri\\_{[}2{]},Staphylococcus\\_simiae\\_{[}2{]},Pararheinheimera\\_mesophila\\_IITR-13,Staphylococcus\\_sp.\\_HMSC035F01,Staphylococcus\\_sp.\\_HMSC035F11,Staphylococcus\\_sp.\\_HMSC055H04,Staphylococcus\\_sp.\\_HMSC055H07,Staphylococcus\\_sp.\\_HMSC057B01,Staphylococcus\\_sp.\\_HMSC058E01,Staphylococcus\\_sp.\\_HMSC060D01,Staphylococcus\\_sp.\\_HMSC060D12,Staphylococcus\\_sp.\\_HMSC063G01,Staphylococcus\\_sp.\\_HMSC063H12,Staphylococcus\\_sp.\\_HMSC067F10,Staphylococcus\\_sp.\\_HMSC075C08,Staphylococcus\\_sp.\\_HMSC34D01,Staphylococcus\\_sp.\\_HMSC34H10,Staphylococcus\\_sp.\\_HMSC35D08,Staphylococcus\\_sp.\\_HMSC36A10,Staphylococcus\\_sp.\\_HMSC36C03,Staphylococcus\\_sp.\\_HMSC36D07,Staphylococcus\\_sp.\\_HMSC36D12,Staphylococcus\\_sp.\\_HMSC36F05,Staphylococcus\\_sp.\\_HMSC36G04,Staphylococcus\\_sp.\\_HMSC55F09,Staphylococcus\\_sp.\\_HMSC56B09,Staphylococcus\\_sp.\\_HMSC57A07,Staphylococcus\\_sp.\\_HMSC57B03,Staphylococcus\\_sp.\\_HMSC58A02,Staphylococcus\\_sp.\\_HMSC58B01,Staphylococcus\\_sp.\\_HMSC58E11,Staphylococcus\\_sp.\\_HMSC64F10,Staphylococcus\\_sp.\\_HMSC66A04,Staphylococcus\\_sp.\\_HMSC66C11,Staphylococcus\\_sp.\\_HMSC70F07,Staphylococcus\\_sp.\\_HMSC72E08,Staphylococcus\\_sp.\\_HMSC73A05,Staphylococcus\\_sp.\\_HMSC74D05,Staphylococcus\\_sp.\\_HMSC74G01,Staphylococcus\\_sp.\\_HMSC74G05,Staphylococcus\\_sp.\\_HMSC76G03,Staphylococcus\\_sp.\\_HMSC77A05,Streptococcus\\_sobrinus\\_TCI-345                                                                                                                                                                                                                               \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            &    2336                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Helicobacter\\_pylori\\_{[}587{]}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            &    2525                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Lactobacillus\\_gasseri\\_{[}25{]}                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                &    2887                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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                                                                                                                                                                                                                                                                                                                           & Acinetobacter\\_baumannii\\_{[}1910{]},Acinetobacter\\_calcoaceticus/baumannii\\_complex\\_sp.\\_ABNIH27,Acinetobacter\\_nosocomialis\\_ABBL048,Acinetobacter\\_sp.\\_1396970,Acinetobacter\\_sp.\\_AKBS16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              &    1263                                                                                                                                                                                                                                                                                                                                                                                                                        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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                & Neisseria\\_meningitidis\\_{[}455{]},Neisseria\\_animalis\\_Neisseria\\_meningitidis,Neisseria\\_canis\\_Neisseria\\_meningitidis,Psychrobacter\\_immobilis\\_Neisseria\\_meningitidis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  &    1185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    & Listeria\\_monocytogenes\\_{[}2023{]},Listeria\\_ivanovii\\_{[}10{]},Listeria\\_innocua\\_{[}6{]},Listeria\\_seeligeri\\_{[}4{]},Listeria\\_welshimeri\\_{[}4{]},Listeria\\_marthii\\_NR\\_9579                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        &    1467                                                                                                                                                                                                                                                                                                                                                                                                                                              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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           & 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          & Staphylococcus\\_aureus\\_SA3-LAU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \\\\\n",
       "\t V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              & 1000017                                                                                                                                                                                                                                                                                        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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   & Escherichia\\_coli\\_{[}7871{]},Shigella\\_sonnei\\_{[}856{]},Shigella\\_flexneri\\_{[}67{]},Shigella\\_boydii\\_{[}33{]},Escherichia\\_fergusonii\\_{[}7{]},Escherichia\\_albertii\\_{[}5{]},Acinetobacter\\_baumannii\\_{[}2{]},Shigella\\_dysenteriae\\_{[}2{]},Achromobacter\\_sp.\\_ATCC35328,Brenneria\\_alni\\_pvfi20,Citrobacter\\_braakii\\_SCC4,Escherichia\\_sp.\\_1\\_1\\_43,Escherichia\\_sp.\\_3\\_2\\_53FAA,Escherichia\\_sp.\\_4\\_1\\_40B,Escherichia\\_sp.\\_B1147,Escherichia\\_sp.\\_KTE11,Escherichia\\_sp.\\_KTE159,Escherichia\\_sp.\\_KTE172,Escherichia\\_sp.\\_KTE52,Escherichia\\_sp.\\_KTE96,Escherichia\\_sp.\\_TW09308,Escherichia\\_sp.\\_TW15838,Escherichia\\_vulneris\\_ATCC\\_33821,Klebsiella\\_oxytoca\\_2880STDY5682666,Lactobacillus\\_acidophilus\\_KLDS\\_1.0901,Shigella\\_sp.\\_PAMC\\_28760                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "sample_id | osu_id | osu_count | pctsim | species | \n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1074                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | 2813                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Streptococcus_mutans_[106]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |     206                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Escherichia_coli_[7164],Shigella_sonnei_[854],Shigella_flexneri_[67],Shigella_boydii_[32],Escherichia_fergusonii_[7],Escherichia_albertii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1093                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                          | Staphylococcus_epidermidis_RP62A,Staphylococcus_epidermidis_ET-024,Staphylococcus_epidermidis_FDAARGOS_157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    2440                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                          | Rhodobacter_sphaeroides_[11],Rhodobacter_johrii_JA192,Rhodobacter_megalophilus_DSM_18937,Rhodobacter_sp._AKP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |      68                                                                                                                                                                                                                                                                                                                                                                                                                                                   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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Bacillus_cereus_[887],Bacillus_thuringiensis_[413],Bacillus_toyonensis_[198],Bacillus_wiedmannii_[131],Bacillus_anthracis_[118],Bacillus_pseudomycoides_[103],Bacillus_mycoides_[55],Bacillus_gaemokensis_[2],Bacillus_weihenstephanensis_[2],Bacillus_bingmayongensis_FJAT-13831,Bacillus_bombysepticus_Wang,Bacillus_licheniformis_V30,Bacillus_sp._0711P9-1,Bacillus_sp._100374,Bacillus_sp._4048,Bacillus_sp._4049,Bacillus_sp._7_6_55CFAA_CT2,Bacillus_sp._AFS012607,Bacillus_sp._AFS014408,Bacillus_sp._AFS015896,Bacillus_sp._AFS019443,Bacillus_sp._AFS023182,Bacillus_sp._AFS029637,Bacillus_sp._AFS033286,Bacillus_sp._AFS051223,Bacillus_sp._AFS054943,Bacillus_sp._AFS059628,Bacillus_sp._AFS075034,Bacillus_sp._AFS075960,Bacillus_sp._AFS094611,Bacillus_sp._AFS098217,Bacillus_sp._AKBS9,Bacillus_sp._BI3,Bacillus_sp._EB422,Bacillus_sp._FDAARGOS_235,Bacillus_sp._G3(2015),Bacillus_sp._GeD10,Bacillus_sp._H1a,Bacillus_sp._H1m,Bacillus_sp._HMSC036E02,Bacillus_sp._JH7,Bacillus_sp._K2I17,Bacillus_sp._KbaB1,Bacillus_sp._KbaL1,Bacillus_sp._L_1B0_5,Bacillus_sp._L_1B0_8,Bacillus_sp._L27,Bacillus_sp._LK2,Bacillus_sp._M13(2017),Bacillus_sp._MB353a,Bacillus_sp._MB366,Bacillus_sp._MN5_Mn5,Bacillus_sp._N24,Bacillus_sp._N35-10-2,Bacillus_sp._N35-10-4,Bacillus_sp._NH11B,Bacillus_sp._NH24A2,Bacillus_sp._Root11,Bacillus_sp._Root131,Bacillus_sp._RUTrin4,Bacillus_sp._RZ2MS9,Bacillus_sp._S1-R1J2-FB,Bacillus_sp._S1-R2T1-FB,Bacillus_sp._S1-R4H1-FB,Bacillus_sp._S1-R5C1-FB,Bacillus_sp._TD41,Bacillus_sp._TD42,Bacillus_sp._UAEU-H3K6M1,Bacillus_sp._UMTAT18,Bacillus_sp._YF23 | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1056                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |  324                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Streptococcus_agalactiae_[466],Streptococcus_sp._HMSC036H09,Streptococcus_sp._HMSC056B03,Streptococcus_sp._HMSC056D01,Streptococcus_sp._HMSC063D10,Streptococcus_sp._HMSC064H02,Streptococcus_sp._HMSC065G04,Streptococcus_sp._HMSC068H01,Streptococcus_sp._HMSC069D09,Streptococcus_sp._HMSC070A10,Streptococcus_sp._HMSC070B09,Streptococcus_sp._HMSC072E12,Streptococcus_sp._HMSC072G02,Streptococcus_sp._HMSC074F09,Streptococcus_sp._HMSC074F10,Streptococcus_sp._HMSC075A03,Streptococcus_sp._HMSC076D11,Streptococcus_sp._HMSC076H07,Streptococcus_sp._HMSC076H08,Streptococcus_sp._HMSC076H09,Streptococcus_sp._HMSC076H10,Streptococcus_sp._HMSC078D02,Streptococcus_sp._HMSC078E03,Streptococcus_sp._HMSC078E08,Streptococcus_sp._HMSC11C05                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    2715                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Clostridium_beijerinckii_[13],Clostridium_saccharoperbutylacetonicum_[4],Clostridium_diolis_[2],Clostridium_sp._BL-8,Clostridium_sp._DL-VIII,Clostridium_sp._LS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |     754                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |  264                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Pseudomonas_aeruginosa_[1853],Candidatus_Hepatobacter_penaei_NHPB,Pseudomonas_denitrificans_(nomen_rejiciendum),Pseudomonas_otitidis_LNU-E-001,Pseudomonas_sp._2_1_26,Pseudomonas_sp._HMSC057H01,Pseudomonas_sp._HMSC058A10,Pseudomonas_sp._HMSC058B07,Pseudomonas_sp._HMSC058C05,Pseudomonas_sp._HMSC059F05,Pseudomonas_sp._HMSC05H02,Pseudomonas_sp._HMSC060F12,Pseudomonas_sp._HMSC060G01,Pseudomonas_sp._HMSC060G02,Pseudomonas_sp._HMSC061A10,Pseudomonas_sp._HMSC063H08,Pseudomonas_sp._HMSC064G05,Pseudomonas_sp._HMSC065H01,Pseudomonas_sp._HMSC065H02,Pseudomonas_sp._HMSC066A08,Pseudomonas_sp._HMSC066B03,Pseudomonas_sp._HMSC067D05,Pseudomonas_sp._HMSC067F09,Pseudomonas_sp._HMSC067G02,Pseudomonas_sp._HMSC069G05,Pseudomonas_sp._HMSC070B12,Pseudomonas_sp._HMSC071F02,Pseudomonas_sp._HMSC072F09,Pseudomonas_sp._HMSC073F05,Pseudomonas_sp._HMSC075A08,Pseudomonas_sp._HMSC076A11,Pseudomonas_sp._HMSC076A12,Pseudomonas_sp._HMSC16B01,Pseudomonas_sp._P179,Pseudomonas_sp._YS-1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1309                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |  242                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        | 100.00                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Staphylococcus_aureus_[7702],Staphylococcus_argenteus_[81],Staphylococcus_schweitzeri_[2],Staphylococcus_simiae_[2],Pararheinheimera_mesophila_IITR-13,Staphylococcus_sp._HMSC035F01,Staphylococcus_sp._HMSC035F11,Staphylococcus_sp._HMSC055H04,Staphylococcus_sp._HMSC055H07,Staphylococcus_sp._HMSC057B01,Staphylococcus_sp._HMSC058E01,Staphylococcus_sp._HMSC060D01,Staphylococcus_sp._HMSC060D12,Staphylococcus_sp._HMSC063G01,Staphylococcus_sp._HMSC063H12,Staphylococcus_sp._HMSC067F10,Staphylococcus_sp._HMSC075C08,Staphylococcus_sp._HMSC34D01,Staphylococcus_sp._HMSC34H10,Staphylococcus_sp._HMSC35D08,Staphylococcus_sp._HMSC36A10,Staphylococcus_sp._HMSC36C03,Staphylococcus_sp._HMSC36D07,Staphylococcus_sp._HMSC36D12,Staphylococcus_sp._HMSC36F05,Staphylococcus_sp._HMSC36G04,Staphylococcus_sp._HMSC55F09,Staphylococcus_sp._HMSC56B09,Staphylococcus_sp._HMSC57A07,Staphylococcus_sp._HMSC57B03,Staphylococcus_sp._HMSC58A02,Staphylococcus_sp._HMSC58B01,Staphylococcus_sp._HMSC58E11,Staphylococcus_sp._HMSC64F10,Staphylococcus_sp._HMSC66A04,Staphylococcus_sp._HMSC66C11,Staphylococcus_sp._HMSC70F07,Staphylococcus_sp._HMSC72E08,Staphylococcus_sp._HMSC73A05,Staphylococcus_sp._HMSC74D05,Staphylococcus_sp._HMSC74G01,Staphylococcus_sp._HMSC74G05,Staphylococcus_sp._HMSC76G03,Staphylococcus_sp._HMSC77A05,Streptococcus_sobrinus_TCI-345                                                                                                                                                                                                                                | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    2336                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Helicobacter_pylori_[587]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    2525                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Lactobacillus_gasseri_[25]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    2887                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Acinetobacter_baumannii_[1910],Acinetobacter_calcoaceticus/baumannii_complex_sp._ABNIH27,Acinetobacter_nosocomialis_ABBL048,Acinetobacter_sp._1396970,Acinetobacter_sp._AKBS16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1263                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Neisseria_meningitidis_[455],Neisseria_animalis_Neisseria_meningitidis,Neisseria_canis_Neisseria_meningitidis,Psychrobacter_immobilis_Neisseria_meningitidis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1185                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Listeria_monocytogenes_[2023],Listeria_ivanovii_[10],Listeria_innocua_[6],Listeria_seeligeri_[4],Listeria_welshimeri_[4],Listeria_marthii_NR_9579                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |    1467                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Staphylococcus_aureus_SA3-LAU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | \n",
       "| V3V4Rep1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | 1000017                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |  99.29                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | Escherichia_coli_[7871],Shigella_sonnei_[856],Shigella_flexneri_[67],Shigella_boydii_[33],Escherichia_fergusonii_[7],Escherichia_albertii_[5],Acinetobacter_baumannii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE172,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666,Lactobacillus_acidophilus_KLDS_1.0901,Shigella_sp._PAMC_28760                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "   sample_id osu_id  osu_count pctsim\n",
       "1  V3V4Rep1     1074 2813      100.00\n",
       "2  V3V4Rep1      206 2436      100.00\n",
       "3  V3V4Rep1     1093  946      100.00\n",
       "4  V3V4Rep1     2440  920      100.00\n",
       "5  V3V4Rep1       68  596      100.00\n",
       "6  V3V4Rep1     1056  324      100.00\n",
       "7  V3V4Rep1     2715  287      100.00\n",
       "8  V3V4Rep1      754  264      100.00\n",
       "9  V3V4Rep1     1309  242      100.00\n",
       "10 V3V4Rep1     2336   90      100.00\n",
       "11 V3V4Rep1     2525   34      100.00\n",
       "12 V3V4Rep1     2887   33      100.00\n",
       "13 V3V4Rep1     1263   32      100.00\n",
       "14 V3V4Rep1     1185   24      100.00\n",
       "15 V3V4Rep1     1467    9      100.00\n",
       "16 V3V4Rep1  1000017    6       99.29\n",
       "   species                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    \n",
       "1  Streptococcus_mutans_[106]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \n",
       "2  Escherichia_coli_[7164],Shigella_sonnei_[854],Shigella_flexneri_[67],Shigella_boydii_[32],Escherichia_fergusonii_[7],Escherichia_albertii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               \n",
       "3  Staphylococcus_epidermidis_RP62A,Staphylococcus_epidermidis_ET-024,Staphylococcus_epidermidis_FDAARGOS_157                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \n",
       "4  Rhodobacter_sphaeroides_[11],Rhodobacter_johrii_JA192,Rhodobacter_megalophilus_DSM_18937,Rhodobacter_sp._AKP1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "5  Bacillus_cereus_[887],Bacillus_thuringiensis_[413],Bacillus_toyonensis_[198],Bacillus_wiedmannii_[131],Bacillus_anthracis_[118],Bacillus_pseudomycoides_[103],Bacillus_mycoides_[55],Bacillus_gaemokensis_[2],Bacillus_weihenstephanensis_[2],Bacillus_bingmayongensis_FJAT-13831,Bacillus_bombysepticus_Wang,Bacillus_licheniformis_V30,Bacillus_sp._0711P9-1,Bacillus_sp._100374,Bacillus_sp._4048,Bacillus_sp._4049,Bacillus_sp._7_6_55CFAA_CT2,Bacillus_sp._AFS012607,Bacillus_sp._AFS014408,Bacillus_sp._AFS015896,Bacillus_sp._AFS019443,Bacillus_sp._AFS023182,Bacillus_sp._AFS029637,Bacillus_sp._AFS033286,Bacillus_sp._AFS051223,Bacillus_sp._AFS054943,Bacillus_sp._AFS059628,Bacillus_sp._AFS075034,Bacillus_sp._AFS075960,Bacillus_sp._AFS094611,Bacillus_sp._AFS098217,Bacillus_sp._AKBS9,Bacillus_sp._BI3,Bacillus_sp._EB422,Bacillus_sp._FDAARGOS_235,Bacillus_sp._G3(2015),Bacillus_sp._GeD10,Bacillus_sp._H1a,Bacillus_sp._H1m,Bacillus_sp._HMSC036E02,Bacillus_sp._JH7,Bacillus_sp._K2I17,Bacillus_sp._KbaB1,Bacillus_sp._KbaL1,Bacillus_sp._L_1B0_5,Bacillus_sp._L_1B0_8,Bacillus_sp._L27,Bacillus_sp._LK2,Bacillus_sp._M13(2017),Bacillus_sp._MB353a,Bacillus_sp._MB366,Bacillus_sp._MN5_Mn5,Bacillus_sp._N24,Bacillus_sp._N35-10-2,Bacillus_sp._N35-10-4,Bacillus_sp._NH11B,Bacillus_sp._NH24A2,Bacillus_sp._Root11,Bacillus_sp._Root131,Bacillus_sp._RUTrin4,Bacillus_sp._RZ2MS9,Bacillus_sp._S1-R1J2-FB,Bacillus_sp._S1-R2T1-FB,Bacillus_sp._S1-R4H1-FB,Bacillus_sp._S1-R5C1-FB,Bacillus_sp._TD41,Bacillus_sp._TD42,Bacillus_sp._UAEU-H3K6M1,Bacillus_sp._UMTAT18,Bacillus_sp._YF23\n",
       "6  Streptococcus_agalactiae_[466],Streptococcus_sp._HMSC036H09,Streptococcus_sp._HMSC056B03,Streptococcus_sp._HMSC056D01,Streptococcus_sp._HMSC063D10,Streptococcus_sp._HMSC064H02,Streptococcus_sp._HMSC065G04,Streptococcus_sp._HMSC068H01,Streptococcus_sp._HMSC069D09,Streptococcus_sp._HMSC070A10,Streptococcus_sp._HMSC070B09,Streptococcus_sp._HMSC072E12,Streptococcus_sp._HMSC072G02,Streptococcus_sp._HMSC074F09,Streptococcus_sp._HMSC074F10,Streptococcus_sp._HMSC075A03,Streptococcus_sp._HMSC076D11,Streptococcus_sp._HMSC076H07,Streptococcus_sp._HMSC076H08,Streptococcus_sp._HMSC076H09,Streptococcus_sp._HMSC076H10,Streptococcus_sp._HMSC078D02,Streptococcus_sp._HMSC078E03,Streptococcus_sp._HMSC078E08,Streptococcus_sp._HMSC11C05                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      \n",
       "7  Clostridium_beijerinckii_[13],Clostridium_saccharoperbutylacetonicum_[4],Clostridium_diolis_[2],Clostridium_sp._BL-8,Clostridium_sp._DL-VIII,Clostridium_sp._LS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            \n",
       "8  Pseudomonas_aeruginosa_[1853],Candidatus_Hepatobacter_penaei_NHPB,Pseudomonas_denitrificans_(nomen_rejiciendum),Pseudomonas_otitidis_LNU-E-001,Pseudomonas_sp._2_1_26,Pseudomonas_sp._HMSC057H01,Pseudomonas_sp._HMSC058A10,Pseudomonas_sp._HMSC058B07,Pseudomonas_sp._HMSC058C05,Pseudomonas_sp._HMSC059F05,Pseudomonas_sp._HMSC05H02,Pseudomonas_sp._HMSC060F12,Pseudomonas_sp._HMSC060G01,Pseudomonas_sp._HMSC060G02,Pseudomonas_sp._HMSC061A10,Pseudomonas_sp._HMSC063H08,Pseudomonas_sp._HMSC064G05,Pseudomonas_sp._HMSC065H01,Pseudomonas_sp._HMSC065H02,Pseudomonas_sp._HMSC066A08,Pseudomonas_sp._HMSC066B03,Pseudomonas_sp._HMSC067D05,Pseudomonas_sp._HMSC067F09,Pseudomonas_sp._HMSC067G02,Pseudomonas_sp._HMSC069G05,Pseudomonas_sp._HMSC070B12,Pseudomonas_sp._HMSC071F02,Pseudomonas_sp._HMSC072F09,Pseudomonas_sp._HMSC073F05,Pseudomonas_sp._HMSC075A08,Pseudomonas_sp._HMSC076A11,Pseudomonas_sp._HMSC076A12,Pseudomonas_sp._HMSC16B01,Pseudomonas_sp._P179,Pseudomonas_sp._YS-1p                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         \n",
       "9  Staphylococcus_aureus_[7702],Staphylococcus_argenteus_[81],Staphylococcus_schweitzeri_[2],Staphylococcus_simiae_[2],Pararheinheimera_mesophila_IITR-13,Staphylococcus_sp._HMSC035F01,Staphylococcus_sp._HMSC035F11,Staphylococcus_sp._HMSC055H04,Staphylococcus_sp._HMSC055H07,Staphylococcus_sp._HMSC057B01,Staphylococcus_sp._HMSC058E01,Staphylococcus_sp._HMSC060D01,Staphylococcus_sp._HMSC060D12,Staphylococcus_sp._HMSC063G01,Staphylococcus_sp._HMSC063H12,Staphylococcus_sp._HMSC067F10,Staphylococcus_sp._HMSC075C08,Staphylococcus_sp._HMSC34D01,Staphylococcus_sp._HMSC34H10,Staphylococcus_sp._HMSC35D08,Staphylococcus_sp._HMSC36A10,Staphylococcus_sp._HMSC36C03,Staphylococcus_sp._HMSC36D07,Staphylococcus_sp._HMSC36D12,Staphylococcus_sp._HMSC36F05,Staphylococcus_sp._HMSC36G04,Staphylococcus_sp._HMSC55F09,Staphylococcus_sp._HMSC56B09,Staphylococcus_sp._HMSC57A07,Staphylococcus_sp._HMSC57B03,Staphylococcus_sp._HMSC58A02,Staphylococcus_sp._HMSC58B01,Staphylococcus_sp._HMSC58E11,Staphylococcus_sp._HMSC64F10,Staphylococcus_sp._HMSC66A04,Staphylococcus_sp._HMSC66C11,Staphylococcus_sp._HMSC70F07,Staphylococcus_sp._HMSC72E08,Staphylococcus_sp._HMSC73A05,Staphylococcus_sp._HMSC74D05,Staphylococcus_sp._HMSC74G01,Staphylococcus_sp._HMSC74G05,Staphylococcus_sp._HMSC76G03,Staphylococcus_sp._HMSC77A05,Streptococcus_sobrinus_TCI-345                                                                                                                                                                                                                               \n",
       "10 Helicobacter_pylori_[587]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  \n",
       "11 Lactobacillus_gasseri_[25]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 \n",
       "12 Acinetobacter_baumannii_[1910],Acinetobacter_calcoaceticus/baumannii_complex_sp._ABNIH27,Acinetobacter_nosocomialis_ABBL048,Acinetobacter_sp._1396970,Acinetobacter_sp._AKBS16                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             \n",
       "13 Neisseria_meningitidis_[455],Neisseria_animalis_Neisseria_meningitidis,Neisseria_canis_Neisseria_meningitidis,Psychrobacter_immobilis_Neisseria_meningitidis                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               \n",
       "14 Listeria_monocytogenes_[2023],Listeria_ivanovii_[10],Listeria_innocua_[6],Listeria_seeligeri_[4],Listeria_welshimeri_[4],Listeria_marthii_NR_9579                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          \n",
       "15 Staphylococcus_aureus_SA3-LAU                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              \n",
       "16 Escherichia_coli_[7871],Shigella_sonnei_[856],Shigella_flexneri_[67],Shigella_boydii_[33],Escherichia_fergusonii_[7],Escherichia_albertii_[5],Acinetobacter_baumannii_[2],Shigella_dysenteriae_[2],Achromobacter_sp._ATCC35328,Brenneria_alni_pvfi20,Citrobacter_braakii_SCC4,Escherichia_sp._1_1_43,Escherichia_sp._3_2_53FAA,Escherichia_sp._4_1_40B,Escherichia_sp._B1147,Escherichia_sp._KTE11,Escherichia_sp._KTE159,Escherichia_sp._KTE172,Escherichia_sp._KTE52,Escherichia_sp._KTE96,Escherichia_sp._TW09308,Escherichia_sp._TW15838,Escherichia_vulneris_ATCC_33821,Klebsiella_oxytoca_2880STDY5682666,Lactobacillus_acidophilus_KLDS_1.0901,Shigella_sp._PAMC_28760                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              "
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "osu_ab.dt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Taxonomy\n",
    "Assign NCBI taxonomy classification for each OSU:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "osu_tax.dt = taxonomy(osu_ab.dt)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<table>\n",
       "<thead><tr><th scope=col>osu_id</th><th scope=col>pctsim</th><th scope=col>phylum</th><th scope=col>class</th><th scope=col>order</th><th scope=col>family</th><th scope=col>genus</th></tr></thead>\n",
       "<tbody>\n",
       "\t<tr><td>    206                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[8143]                                                                                                               </td><td>Gammaproteobacteria_[8142],Betaproteobacteria_[1]                                                                                   </td><td>Enterobacterales_[8142],Burkholderiales_[1]                                                                                         </td><td>Enterobacteriaceae_[8141],Alcaligenaceae_[1],Pectobacteriaceae_[1]                                                                  </td><td>Escherichia_[7184],Shigella_[955],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1]                                    </td></tr>\n",
       "\t<tr><td>1000017                                                                                                                             </td><td> 99.29                                                                                                                              </td><td>Proteobacteria_[8860],Firmicutes_[1]                                                                                                </td><td>Gammaproteobacteria_[8859],Betaproteobacteria_[1],Bacilli_[1]                                                                       </td><td>Enterobacterales_[8857],Pseudomonadales_[2],Burkholderiales_[1],Lactobacillales_[1]                                                 </td><td>Enterobacteriaceae_[8856],Moraxellaceae_[2],Alcaligenaceae_[1],Pectobacteriaceae_[1],Lactobacillaceae_[1]                           </td><td>Escherichia_[7895],Shigella_[959],Acinetobacter_[2],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1],Lactobacillus_[1]</td></tr>\n",
       "\t<tr><td>   2887                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[1914]                                                                                                               </td><td>Gammaproteobacteria_[1914]                                                                                                          </td><td>Pseudomonadales_[1914]                                                                                                              </td><td>Moraxellaceae_[1914]                                                                                                                </td><td>Acinetobacter_[1914]                                                                                                                </td></tr>\n",
       "\t<tr><td>     68                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[1970]                                                                                                                   </td><td>Bacilli_[1970]                                                                                                                      </td><td>Bacillales_[1970]                                                                                                                   </td><td>Bacillaceae_[1970]                                                                                                                  </td><td>Bacillus_[1970]                                                                                                                     </td></tr>\n",
       "\t<tr><td>   2715                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[22]                                                                                                                     </td><td>Clostridia_[22]                                                                                                                     </td><td>Clostridiales_[22]                                                                                                                  </td><td>Clostridiaceae_[22]                                                                                                                 </td><td>Clostridium_[22]                                                                                                                    </td></tr>\n",
       "\t<tr><td>   2336                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[587]                                                                                                                </td><td>Epsilonproteobacteria_[587]                                                                                                         </td><td>Campylobacterales_[587]                                                                                                             </td><td>Helicobacteraceae_[587]                                                                                                             </td><td>Helicobacter_[587]                                                                                                                  </td></tr>\n",
       "\t<tr><td>    754                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[1886]                                                                                                               </td><td>Gammaproteobacteria_[1886]                                                                                                          </td><td>Pseudomonadales_[1886]                                                                                                              </td><td>Pseudomonadaceae_[1886]                                                                                                             </td><td>Pseudomonas_[1886],Hepatobacter_[1]                                                                                                 </td></tr>\n",
       "\t<tr><td>   2525                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[25]                                                                                                                     </td><td>Bacilli_[25]                                                                                                                        </td><td>Lactobacillales_[25]                                                                                                                </td><td>Lactobacillaceae_[25]                                                                                                               </td><td>Lactobacillus_[25]                                                                                                                  </td></tr>\n",
       "\t<tr><td>   1185                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[2048]                                                                                                                   </td><td>Bacilli_[2048]                                                                                                                      </td><td>Bacillales_[2048]                                                                                                                   </td><td>Listeriaceae_[2048]                                                                                                                 </td><td>Listeria_[2048]                                                                                                                     </td></tr>\n",
       "\t<tr><td>   1263                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[458]                                                                                                                </td><td>Betaproteobacteria_[457],Gammaproteobacteria_[1]                                                                                    </td><td>Neisseriales_[457],Pseudomonadales_[1]                                                                                              </td><td>Neisseriaceae_[457],Moraxellaceae_[1]                                                                                               </td><td>Neisseria_[457],Psychrobacter_[1]                                                                                                   </td></tr>\n",
       "\t<tr><td>   1309                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[7827]                                                                                                                   </td><td>Bacilli_[7827]                                                                                                                      </td><td>Bacillales_[7826],Lactobacillales_[1]                                                                                               </td><td>Staphylococcaceae_[7826],Streptococcaceae_[1]                                                                                       </td><td>Staphylococcus_[7826],Pararheinheimera_[1],Streptococcus_[1]                                                                        </td></tr>\n",
       "\t<tr><td>   2440                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Proteobacteria_[14]                                                                                                                 </td><td>Alphaproteobacteria_[14]                                                                                                            </td><td>Rhodobacterales_[14]                                                                                                                </td><td>Rhodobacteraceae_[14]                                                                                                               </td><td>Rhodobacter_[14]                                                                                                                    </td></tr>\n",
       "\t<tr><td>   1093                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[3]                                                                                                                      </td><td>Bacilli_[3]                                                                                                                         </td><td>Bacillales_[3]                                                                                                                      </td><td>Staphylococcaceae_[3]                                                                                                               </td><td>Staphylococcus_[3]                                                                                                                  </td></tr>\n",
       "\t<tr><td>   1467                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[1]                                                                                                                      </td><td>Bacilli_[1]                                                                                                                         </td><td>Bacillales_[1]                                                                                                                      </td><td>Staphylococcaceae_[1]                                                                                                               </td><td>Staphylococcus_[1]                                                                                                                  </td></tr>\n",
       "\t<tr><td>   1074                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[106]                                                                                                                    </td><td>Bacilli_[106]                                                                                                                       </td><td>Lactobacillales_[106]                                                                                                               </td><td>Streptococcaceae_[106]                                                                                                              </td><td>Streptococcus_[106]                                                                                                                 </td></tr>\n",
       "\t<tr><td>   1056                                                                                                                             </td><td>100.00                                                                                                                              </td><td>Firmicutes_[490]                                                                                                                    </td><td>Bacilli_[490]                                                                                                                       </td><td>Lactobacillales_[490]                                                                                                               </td><td>Streptococcaceae_[490]                                                                                                              </td><td>Streptococcus_[490]                                                                                                                 </td></tr>\n",
       "</tbody>\n",
       "</table>\n"
      ],
      "text/latex": [
       "\\begin{tabular}{r|lllllll}\n",
       " osu\\_id & pctsim & phylum & class & order & family & genus\\\\\n",
       "\\hline\n",
       "\t     206                                                                                                                                                                  & 100.00                                                                                                                                                                   & Proteobacteria\\_{[}8143{]}                                                                                                                                              & Gammaproteobacteria\\_{[}8142{]},Betaproteobacteria\\_{[}1{]}                                                                                                            & Enterobacterales\\_{[}8142{]},Burkholderiales\\_{[}1{]}                                                                                                                  & Enterobacteriaceae\\_{[}8141{]},Alcaligenaceae\\_{[}1{]},Pectobacteriaceae\\_{[}1{]}                                                                                     & Escherichia\\_{[}7184{]},Shigella\\_{[}955{]},Achromobacter\\_{[}1{]},Brenneria\\_{[}1{]},Citrobacter\\_{[}1{]},Klebsiella\\_{[}1{]}                                    \\\\\n",
       "\t 1000017                                                                                                                                                                              &  99.29                                                                                                                                                                               & Proteobacteria\\_{[}8860{]},Firmicutes\\_{[}1{]}                                                                                                                                     & Gammaproteobacteria\\_{[}8859{]},Betaproteobacteria\\_{[}1{]},Bacilli\\_{[}1{]}                                                                                                      & Enterobacterales\\_{[}8857{]},Pseudomonadales\\_{[}2{]},Burkholderiales\\_{[}1{]},Lactobacillales\\_{[}1{]}                                                                          & Enterobacteriaceae\\_{[}8856{]},Moraxellaceae\\_{[}2{]},Alcaligenaceae\\_{[}1{]},Pectobacteriaceae\\_{[}1{]},Lactobacillaceae\\_{[}1{]}                                              & Escherichia\\_{[}7895{]},Shigella\\_{[}959{]},Acinetobacter\\_{[}2{]},Achromobacter\\_{[}1{]},Brenneria\\_{[}1{]},Citrobacter\\_{[}1{]},Klebsiella\\_{[}1{]},Lactobacillus\\_{[}1{]}\\\\\n",
       "\t    2887                                                                                                                                    & 100.00                                                                                                                                     & Proteobacteria\\_{[}1914{]}                                                                                                                & Gammaproteobacteria\\_{[}1914{]}                                                                                                           & Pseudomonadales\\_{[}1914{]}                                                                                                               & Moraxellaceae\\_{[}1914{]}                                                                                                                 & Acinetobacter\\_{[}1914{]}                                                                                                                \\\\\n",
       "\t      68                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}1970{]}                                                                                                                    & Bacilli\\_{[}1970{]}                                                                                                                       & Bacillales\\_{[}1970{]}                                                                                                                    & Bacillaceae\\_{[}1970{]}                                                                                                                   & Bacillus\\_{[}1970{]}                                                                                                                     \\\\\n",
       "\t    2715                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}22{]}                                                                                                                      & Clostridia\\_{[}22{]}                                                                                                                      & Clostridiales\\_{[}22{]}                                                                                                                   & Clostridiaceae\\_{[}22{]}                                                                                                                  & Clostridium\\_{[}22{]}                                                                                                                    \\\\\n",
       "\t    2336                                                                                                                                    & 100.00                                                                                                                                     & Proteobacteria\\_{[}587{]}                                                                                                                 & Epsilonproteobacteria\\_{[}587{]}                                                                                                          & Campylobacterales\\_{[}587{]}                                                                                                              & Helicobacteraceae\\_{[}587{]}                                                                                                              & Helicobacter\\_{[}587{]}                                                                                                                  \\\\\n",
       "\t     754                                                                                                                                          & 100.00                                                                                                                                           & Proteobacteria\\_{[}1886{]}                                                                                                                      & Gammaproteobacteria\\_{[}1886{]}                                                                                                                 & Pseudomonadales\\_{[}1886{]}                                                                                                                     & Pseudomonadaceae\\_{[}1886{]}                                                                                                                    & Pseudomonas\\_{[}1886{]},Hepatobacter\\_{[}1{]}                                                                                                 \\\\\n",
       "\t    2525                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}25{]}                                                                                                                      & Bacilli\\_{[}25{]}                                                                                                                         & Lactobacillales\\_{[}25{]}                                                                                                                 & Lactobacillaceae\\_{[}25{]}                                                                                                                & Lactobacillus\\_{[}25{]}                                                                                                                  \\\\\n",
       "\t    1185                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}2048{]}                                                                                                                    & Bacilli\\_{[}2048{]}                                                                                                                       & Bacillales\\_{[}2048{]}                                                                                                                    & Listeriaceae\\_{[}2048{]}                                                                                                                  & Listeria\\_{[}2048{]}                                                                                                                     \\\\\n",
       "\t    1263                                                                                                                                          & 100.00                                                                                                                                           & Proteobacteria\\_{[}458{]}                                                                                                                       & Betaproteobacteria\\_{[}457{]},Gammaproteobacteria\\_{[}1{]}                                                                                     & Neisseriales\\_{[}457{]},Pseudomonadales\\_{[}1{]}                                                                                               & Neisseriaceae\\_{[}457{]},Moraxellaceae\\_{[}1{]}                                                                                                & Neisseria\\_{[}457{]},Psychrobacter\\_{[}1{]}                                                                                                   \\\\\n",
       "\t    1309                                                                                                                                                & 100.00                                                                                                                                                 & Firmicutes\\_{[}7827{]}                                                                                                                                & Bacilli\\_{[}7827{]}                                                                                                                                   & Bacillales\\_{[}7826{]},Lactobacillales\\_{[}1{]}                                                                                                      & Staphylococcaceae\\_{[}7826{]},Streptococcaceae\\_{[}1{]}                                                                                              & Staphylococcus\\_{[}7826{]},Pararheinheimera\\_{[}1{]},Streptococcus\\_{[}1{]}                                                                        \\\\\n",
       "\t    2440                                                                                                                                    & 100.00                                                                                                                                     & Proteobacteria\\_{[}14{]}                                                                                                                  & Alphaproteobacteria\\_{[}14{]}                                                                                                             & Rhodobacterales\\_{[}14{]}                                                                                                                 & Rhodobacteraceae\\_{[}14{]}                                                                                                                & Rhodobacter\\_{[}14{]}                                                                                                                    \\\\\n",
       "\t    1093                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}3{]}                                                                                                                       & Bacilli\\_{[}3{]}                                                                                                                          & Bacillales\\_{[}3{]}                                                                                                                       & Staphylococcaceae\\_{[}3{]}                                                                                                                & Staphylococcus\\_{[}3{]}                                                                                                                  \\\\\n",
       "\t    1467                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}1{]}                                                                                                                       & Bacilli\\_{[}1{]}                                                                                                                          & Bacillales\\_{[}1{]}                                                                                                                       & Staphylococcaceae\\_{[}1{]}                                                                                                                & Staphylococcus\\_{[}1{]}                                                                                                                  \\\\\n",
       "\t    1074                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}106{]}                                                                                                                     & Bacilli\\_{[}106{]}                                                                                                                        & Lactobacillales\\_{[}106{]}                                                                                                                & Streptococcaceae\\_{[}106{]}                                                                                                               & Streptococcus\\_{[}106{]}                                                                                                                 \\\\\n",
       "\t    1056                                                                                                                                    & 100.00                                                                                                                                     & Firmicutes\\_{[}490{]}                                                                                                                     & Bacilli\\_{[}490{]}                                                                                                                        & Lactobacillales\\_{[}490{]}                                                                                                                & Streptococcaceae\\_{[}490{]}                                                                                                               & Streptococcus\\_{[}490{]}                                                                                                                 \\\\\n",
       "\\end{tabular}\n"
      ],
      "text/markdown": [
       "\n",
       "osu_id | pctsim | phylum | class | order | family | genus | \n",
       "|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
       "|     206                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[8143]                                                                                                                | Gammaproteobacteria_[8142],Betaproteobacteria_[1]                                                                                    | Enterobacterales_[8142],Burkholderiales_[1]                                                                                          | Enterobacteriaceae_[8141],Alcaligenaceae_[1],Pectobacteriaceae_[1]                                                                   | Escherichia_[7184],Shigella_[955],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1]                                     | \n",
       "| 1000017                                                                                                                              |  99.29                                                                                                                               | Proteobacteria_[8860],Firmicutes_[1]                                                                                                 | Gammaproteobacteria_[8859],Betaproteobacteria_[1],Bacilli_[1]                                                                        | Enterobacterales_[8857],Pseudomonadales_[2],Burkholderiales_[1],Lactobacillales_[1]                                                  | Enterobacteriaceae_[8856],Moraxellaceae_[2],Alcaligenaceae_[1],Pectobacteriaceae_[1],Lactobacillaceae_[1]                            | Escherichia_[7895],Shigella_[959],Acinetobacter_[2],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1],Lactobacillus_[1] | \n",
       "|    2887                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[1914]                                                                                                                | Gammaproteobacteria_[1914]                                                                                                           | Pseudomonadales_[1914]                                                                                                               | Moraxellaceae_[1914]                                                                                                                 | Acinetobacter_[1914]                                                                                                                 | \n",
       "|      68                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[1970]                                                                                                                    | Bacilli_[1970]                                                                                                                       | Bacillales_[1970]                                                                                                                    | Bacillaceae_[1970]                                                                                                                   | Bacillus_[1970]                                                                                                                      | \n",
       "|    2715                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[22]                                                                                                                      | Clostridia_[22]                                                                                                                      | Clostridiales_[22]                                                                                                                   | Clostridiaceae_[22]                                                                                                                  | Clostridium_[22]                                                                                                                     | \n",
       "|    2336                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[587]                                                                                                                 | Epsilonproteobacteria_[587]                                                                                                          | Campylobacterales_[587]                                                                                                              | Helicobacteraceae_[587]                                                                                                              | Helicobacter_[587]                                                                                                                   | \n",
       "|     754                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[1886]                                                                                                                | Gammaproteobacteria_[1886]                                                                                                           | Pseudomonadales_[1886]                                                                                                               | Pseudomonadaceae_[1886]                                                                                                              | Pseudomonas_[1886],Hepatobacter_[1]                                                                                                  | \n",
       "|    2525                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[25]                                                                                                                      | Bacilli_[25]                                                                                                                         | Lactobacillales_[25]                                                                                                                 | Lactobacillaceae_[25]                                                                                                                | Lactobacillus_[25]                                                                                                                   | \n",
       "|    1185                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[2048]                                                                                                                    | Bacilli_[2048]                                                                                                                       | Bacillales_[2048]                                                                                                                    | Listeriaceae_[2048]                                                                                                                  | Listeria_[2048]                                                                                                                      | \n",
       "|    1263                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[458]                                                                                                                 | Betaproteobacteria_[457],Gammaproteobacteria_[1]                                                                                     | Neisseriales_[457],Pseudomonadales_[1]                                                                                               | Neisseriaceae_[457],Moraxellaceae_[1]                                                                                                | Neisseria_[457],Psychrobacter_[1]                                                                                                    | \n",
       "|    1309                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[7827]                                                                                                                    | Bacilli_[7827]                                                                                                                       | Bacillales_[7826],Lactobacillales_[1]                                                                                                | Staphylococcaceae_[7826],Streptococcaceae_[1]                                                                                        | Staphylococcus_[7826],Pararheinheimera_[1],Streptococcus_[1]                                                                         | \n",
       "|    2440                                                                                                                              | 100.00                                                                                                                               | Proteobacteria_[14]                                                                                                                  | Alphaproteobacteria_[14]                                                                                                             | Rhodobacterales_[14]                                                                                                                 | Rhodobacteraceae_[14]                                                                                                                | Rhodobacter_[14]                                                                                                                     | \n",
       "|    1093                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[3]                                                                                                                       | Bacilli_[3]                                                                                                                          | Bacillales_[3]                                                                                                                       | Staphylococcaceae_[3]                                                                                                                | Staphylococcus_[3]                                                                                                                   | \n",
       "|    1467                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[1]                                                                                                                       | Bacilli_[1]                                                                                                                          | Bacillales_[1]                                                                                                                       | Staphylococcaceae_[1]                                                                                                                | Staphylococcus_[1]                                                                                                                   | \n",
       "|    1074                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[106]                                                                                                                     | Bacilli_[106]                                                                                                                        | Lactobacillales_[106]                                                                                                                | Streptococcaceae_[106]                                                                                                               | Streptococcus_[106]                                                                                                                  | \n",
       "|    1056                                                                                                                              | 100.00                                                                                                                               | Firmicutes_[490]                                                                                                                     | Bacilli_[490]                                                                                                                        | Lactobacillales_[490]                                                                                                                | Streptococcaceae_[490]                                                                                                               | Streptococcus_[490]                                                                                                                  | \n",
       "\n",
       "\n"
      ],
      "text/plain": [
       "   osu_id  pctsim phylum                              \n",
       "1      206 100.00 Proteobacteria_[8143]               \n",
       "2  1000017  99.29 Proteobacteria_[8860],Firmicutes_[1]\n",
       "3     2887 100.00 Proteobacteria_[1914]               \n",
       "4       68 100.00 Firmicutes_[1970]                   \n",
       "5     2715 100.00 Firmicutes_[22]                     \n",
       "6     2336 100.00 Proteobacteria_[587]                \n",
       "7      754 100.00 Proteobacteria_[1886]               \n",
       "8     2525 100.00 Firmicutes_[25]                     \n",
       "9     1185 100.00 Firmicutes_[2048]                   \n",
       "10    1263 100.00 Proteobacteria_[458]                \n",
       "11    1309 100.00 Firmicutes_[7827]                   \n",
       "12    2440 100.00 Proteobacteria_[14]                 \n",
       "13    1093 100.00 Firmicutes_[3]                      \n",
       "14    1467 100.00 Firmicutes_[1]                      \n",
       "15    1074 100.00 Firmicutes_[106]                    \n",
       "16    1056 100.00 Firmicutes_[490]                    \n",
       "   class                                                        \n",
       "1  Gammaproteobacteria_[8142],Betaproteobacteria_[1]            \n",
       "2  Gammaproteobacteria_[8859],Betaproteobacteria_[1],Bacilli_[1]\n",
       "3  Gammaproteobacteria_[1914]                                   \n",
       "4  Bacilli_[1970]                                               \n",
       "5  Clostridia_[22]                                              \n",
       "6  Epsilonproteobacteria_[587]                                  \n",
       "7  Gammaproteobacteria_[1886]                                   \n",
       "8  Bacilli_[25]                                                 \n",
       "9  Bacilli_[2048]                                               \n",
       "10 Betaproteobacteria_[457],Gammaproteobacteria_[1]             \n",
       "11 Bacilli_[7827]                                               \n",
       "12 Alphaproteobacteria_[14]                                     \n",
       "13 Bacilli_[3]                                                  \n",
       "14 Bacilli_[1]                                                  \n",
       "15 Bacilli_[106]                                                \n",
       "16 Bacilli_[490]                                                \n",
       "   order                                                                              \n",
       "1  Enterobacterales_[8142],Burkholderiales_[1]                                        \n",
       "2  Enterobacterales_[8857],Pseudomonadales_[2],Burkholderiales_[1],Lactobacillales_[1]\n",
       "3  Pseudomonadales_[1914]                                                             \n",
       "4  Bacillales_[1970]                                                                  \n",
       "5  Clostridiales_[22]                                                                 \n",
       "6  Campylobacterales_[587]                                                            \n",
       "7  Pseudomonadales_[1886]                                                             \n",
       "8  Lactobacillales_[25]                                                               \n",
       "9  Bacillales_[2048]                                                                  \n",
       "10 Neisseriales_[457],Pseudomonadales_[1]                                             \n",
       "11 Bacillales_[7826],Lactobacillales_[1]                                              \n",
       "12 Rhodobacterales_[14]                                                               \n",
       "13 Bacillales_[3]                                                                     \n",
       "14 Bacillales_[1]                                                                     \n",
       "15 Lactobacillales_[106]                                                              \n",
       "16 Lactobacillales_[490]                                                              \n",
       "   family                                                                                                   \n",
       "1  Enterobacteriaceae_[8141],Alcaligenaceae_[1],Pectobacteriaceae_[1]                                       \n",
       "2  Enterobacteriaceae_[8856],Moraxellaceae_[2],Alcaligenaceae_[1],Pectobacteriaceae_[1],Lactobacillaceae_[1]\n",
       "3  Moraxellaceae_[1914]                                                                                     \n",
       "4  Bacillaceae_[1970]                                                                                       \n",
       "5  Clostridiaceae_[22]                                                                                      \n",
       "6  Helicobacteraceae_[587]                                                                                  \n",
       "7  Pseudomonadaceae_[1886]                                                                                  \n",
       "8  Lactobacillaceae_[25]                                                                                    \n",
       "9  Listeriaceae_[2048]                                                                                      \n",
       "10 Neisseriaceae_[457],Moraxellaceae_[1]                                                                    \n",
       "11 Staphylococcaceae_[7826],Streptococcaceae_[1]                                                            \n",
       "12 Rhodobacteraceae_[14]                                                                                    \n",
       "13 Staphylococcaceae_[3]                                                                                    \n",
       "14 Staphylococcaceae_[1]                                                                                    \n",
       "15 Streptococcaceae_[106]                                                                                   \n",
       "16 Streptococcaceae_[490]                                                                                   \n",
       "   genus                                                                                                                               \n",
       "1  Escherichia_[7184],Shigella_[955],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1]                                    \n",
       "2  Escherichia_[7895],Shigella_[959],Acinetobacter_[2],Achromobacter_[1],Brenneria_[1],Citrobacter_[1],Klebsiella_[1],Lactobacillus_[1]\n",
       "3  Acinetobacter_[1914]                                                                                                                \n",
       "4  Bacillus_[1970]                                                                                                                     \n",
       "5  Clostridium_[22]                                                                                                                    \n",
       "6  Helicobacter_[587]                                                                                                                  \n",
       "7  Pseudomonas_[1886],Hepatobacter_[1]                                                                                                 \n",
       "8  Lactobacillus_[25]                                                                                                                  \n",
       "9  Listeria_[2048]                                                                                                                     \n",
       "10 Neisseria_[457],Psychrobacter_[1]                                                                                                   \n",
       "11 Staphylococcus_[7826],Pararheinheimera_[1],Streptococcus_[1]                                                                        \n",
       "12 Rhodobacter_[14]                                                                                                                    \n",
       "13 Staphylococcus_[3]                                                                                                                  \n",
       "14 Staphylococcus_[1]                                                                                                                  \n",
       "15 Streptococcus_[106]                                                                                                                 \n",
       "16 Streptococcus_[490]                                                                                                                 "
      ]
     },
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     "output_type": "display_data"
    }
   ],
   "source": [
    "osu_tax.dt"
   ]
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   "source": [
    "The numbers in brackets show the number of strains belonging to the specific taxonomic rank."
   ]
  },
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   "cell_type": "code",
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