Skip to content

Latest commit

 

History

History
30 lines (26 loc) · 4.22 KB

README.md

File metadata and controls

30 lines (26 loc) · 4.22 KB

FS9

This repo includes all data, code, and relevant results for the study "Route of oxytetracycline administration differentially impacts the growth and gut microbiome of pigs co-infected with Bordetella bronchiseptica and Pasteurella multocida"

Table of contents

Chapter Description
data Includes data files needed to carry out R analysis. Also includes mock_community_16S3.fna file listing expected mock community sequences for mock sample Mock5
scripts R scripts for 16S data, qPCR, and other pig sample analyses. AbxConcWeightADGLungLesion.R and AMR_qPCR.R can be run anytime. Only fecal 16S data-related scripts are numbered and must be run in that order.
mothur.md Commands used in mothur to process FS9 16S data, additional notes
Notes.md To-do list for FS9, BioProject PRJNA693865 notes

Scripts description and the order to run them

Order Script file name Description
1a mothur.md First run mothur.md to process 16S sequence data and generate output for R scripts.
1b 1_OTUtable.R Generate OTU table from mothur output to use for creating phyloseq objects
2a 2a_phyloseq_NONINFnm_INFnm.R Generate phyloseq object to use for 3a_alpha_beta_diversity_NONINFnm_INFnm.R. Run adonis function with distance matrices to assess how variation is attributed to different experimental treatments or uncontrolled covariates.
2b 2b_phyloseq_INFnmfeedinject.R Generate phyloseq object to use for 3b_alpha_beta_diversity_INFnmfeedinject.R. Run adonis function with distance matrices to assess how variation is attributed to different experimental treatments or uncontrolled covariates.
3a 3a_alpha_beta_diversity_NONINFnm_INFnm.R Run alpha (Shannon, Inverse Simpson) and beta diversity (generating NMDS, pairwise comparisons) analyses, data visualization
3b 3b_alpha_beta_diversity_INFnmfeedinject.R Run alpha (Shannon, Inverse Simpson) and beta diversity (generating NMDS, pairwise comparisons) analyses, data visualization
4a 4a_DeSeq2_NONINFnm_INFnm.R Identify differentially abundant bacterial taxa (order and genus levels) between groups within each day, data visualization
4b 4b_DeSeq2_INFnmfeedinject.R Identify differentially abundant bacterial taxa (order level) between groups within each day, data visualization
5b 5b_NMDS_DeSeq2_INFnmfeedinject.R Combined steps 2b, 3b, and 4b into one script to generate figure for manuscript
Anytime AbxConcWeightADGLungLesion.R Data visualization of oxytet concentration in various tissue sites, correlation between oxytet concentration and weight for each tissue site, average daily gain, and lung lesion severity
Anytime AMR_qPCR.R Data visualization of relative abundance (log10) of each AMR gene using scatter point box plots; and box plots of total abundance of each AMR gene using AULC calculation
  • Annotation Notes
    • (1/2/3/4)a = NONINFnm vs INFnm
    • (1/2/3/4/5)b = INFnm vs INFfeed vs INFinject.