ODFM, an omics data resource from microorganisms associated with fermented foods

Abstract

ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.

Fermented Foods, Health and the Gut Microbiome

“…However, a diverse range of non-starter microbes are associated with most fermented foods, the full extent of which is only now becoming apparent with the application of high-throughput DNA sequencing technologies [ 4 ]. Recently, a freely accessible online database has been established that functions as an archive for the annotated genomic, metagenomic, transcriptomic, and metataxonomic information of microbes associated with fermented foods, enabling evaluation of individual strains as potential starter cultures [ 183 ]. This tool has the potential to reveal the full diversity of fermented food-associated microbes, and has useful practical applications in the fermented food industry.…”

MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics

“…MAGs assembled from the 90 samples were collated with genomes from previous fermented food sequencing to create a high quality reference database of relevant genomes. These sources include the ODFM database 18 (205 genomes), three dairy ferment metagenomic surveys 20,21,28 (539, 62, and 64 respectively), a large metagenomic survey of substrate-associated differences in fermented food MAGs 19 (477 genomes), and three studies of novel fermented foods 24,23,22 (19, 100, 11 genomes respectively). Due to the central role members of the Lactobacillus genus play in lactic acid fermentation, 320 Lactobacillus NCBI reference genomes reported in the literature were included 29 .…”

“…However, no such resource is available for fermented foods. Other databases for fermented food sequence analysis are not compatible with large-scale metagenomic data and are not suitable for identification of novel MAGs 18 . Here we present MiFoDB (Microbial Food DataBase), a workflow for the identification of bacterial and eukaryotic genomes in fermented foods, with an accompanying customizable database.…”

FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota

“…Omics Database of Fermentative Microbes (ODFM) is an integrated data management system containing information on genome, metagenome, metataxonome, metatranscriptome, and metabolome of fermentative microorganisms associated with various foods. Within this database, food sources are expressed as samples and include kimchi, fermented seafoods, soybean paste, solar salt, vinegar, and alcohol fermentation starter [ 29 ]. The Probiotic Database collects probiotics from several fermented foods, including traditional dairy products, providing biological information for use in humans, animals, and plants [ 30 ].…”