DOI: 10.5281/zenodo.15794524
title: Fermented Foods Microbial Genomes Database

description: Fermented Foods Microbial Genomes Database

This database contains 13,850 microbial genomes assembled from various fermented foods and associated curated metadata. 

We have also clustered the database at 95% identity for creating a species-representative database, and at 99% identity for creating a "strain"-representative database, since we hypothesize that many bioactivities and phenotypes for fermented food microbes are important at the strain-level.

This GitHub repository documents how publicly available genomes and metagenome-assembled genomes were sourced and curated. This GitHub repository documents how the associated metadata was curated. 

This database largely pulls from existing genome resources, and we curated this database specifically for fermented foods. If you use this database, please cite the following genome databases/resources: 



MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics. Elisa B. Caffrey, Matthew R. Olm, Caroline Isabel Kothe, Joshua Evans, Justin L. Sonnenburg . bioRxiv 2024.03.29.587370; doi: https://doi.org/10.1101/2024.03.29.587370

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Carlino, Niccolo Alvarez-Ordonez, Avelino et al. Cell, Volume 187, Issue 20, 5775-5795.e15 AND the associated Zenodo release: Master Consortium. (2024). Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. Zenodo. https://doi.org/10.5281/zenodo.13285428


We are incredibly grateful for these groups and countless others taking the time to make their data publicly available. Included in the metadata is the original DOI and study link from which the genome was generated, in addition to if they were collated into one of the above two larger databases. If you specifically use/analyze a subset of genomes, please cite those studies to credit those that generate data and make it publicly available.

Subsetting the Database to Species/Strain-Resolved Representatives or a Custom Set

We have provided the entire set of 13,850 microbial genomes in a single tar archive for download. We have also provided tar archives of the genomes clustered at 95% and 99% identity. If you wish to download the entire database and then only use a subset of the database, such as species-representative (clustered at 95% ANI) or "strain-representative" (clustered at 99% ANI) genomes after downloading the entire database, you can use our helper script for subsetting genomes that are representatives or a custom list that you provide.

 

usage: subset_genomes.py [-h] [--rep-column {rep_95id,rep_99id}]                         [--id-column ID_COLUMN] [--dry-run]                         [--genome-list GENOME_LIST]                         metadata_tsv all_genomes_dir output_dir

Subset representative genomes (species/strain) from a genome set usingmetadata.

positional arguments:  metadata_tsv          Path to metadata TSV file  all_genomes_dir       Directory containing all .fa genome files  output_dir            Directory to copy representative genomes to

optional arguments:  -h, --help            show this help message and exit  --rep-column {rep_95id,rep_99id}                        Column in metadata to use for representatives (e.g.,                        rep_95id or rep_99id)  --id-column ID_COLUMN                        Column in metadata with genome file IDs (default:                        mag_id)  --dry-run             Only print what would be copied, don't actually copy  --genome-list GENOME_LIST                        Optional: Path to file with list of genome IDs or                        filenames to subset (one per line)

KBase Fermented Foods Microbial Genomes Database Narrative

We have uploaded the "strain-representative" set of ~4300 genomes to KBase as a public narrative. 



KBase is a community-driven platform for facilitating open science research in systems biology. KBase allows you to run bioinformatics tools on large datasets using freely available Department of Energy high-perofrmance computing resources, allowing for open-sharing of research outputs and collaborative work. You can sign-up for a KBase account with any email account. You are not required to be affiliated with an academic institution or government organization to use KBase, and you can reside outside of the United States.

 

This platform not only allows additional access to the Fermented Foods Microbial Genomes Database, but access to open-source bioinformatics tools and high-performance computing resources through the DOE to run reproducible analyses. You can use this narrative for exploring the database, incorporating your own genomes to compare against genomes in the database, and/or using as a teaching resource.