- [GTDB] - [Genomes, vR220, 2024.04] - [2022.1, Nucleic Acids Res] - [GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.]
- [GlobDB] - [Genomes, 220, NA] - [A collection from Daan Septh.]
- [proGenomes] - [Genomes, v3, NA]
- [cFMD] - [Food Microbial Genomes, v1.2.0, 2024.08] - [2024.08, cell] - [Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.]
- [GOMC] - [Genomes, NA, 2024.09] - [2024.09, Nature] - [Global marine microbial diversity and its potential in bioprospecting.]
- [Ocean Microbiomics Database (OMD)] - [Genomes, v1.1, NA] - [2022.06, Nature] - [Biosynthetic potential of the global ocean microbiome.]
- [OceanDNA] - [Genomes, v2022-05, 2022.05] - [2022.05, figshare] - [The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments.]
- [AllTheBacteria] - [Genomes, v2024-08, 2024.08] - [2024.03, bioRxiv] - [AllTheBacteria - all bacterial genomes assembled, available and searchable.]
- [MGnify] - [Genomes, ftp, 2023.09] - [2022.12, Nucleic Acids Res] - [[MGnify: the microbiome sequence data analysis resource in 2023.](https://doi.org/10.1093/nar/gkac1080] - [MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues]
- [Logan] - [Unitigs/Contigs, NA, AWS]
- [BakRep] - [2024.10, Microbial Genomics] - [BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata.]
- [BacDive] - [Online database] - [2024.10, Nucleic Acids Res] - [BacDive in 2025: the core database for prokaryotic strain data.]
- [GROWdb] - NMDC data portal - with KBase - GROWdb Explorer - [2024.11, Nature] - A functional microbiome catalogue crowdsourced from North American rivers.