Database#
The mOTUs-db (see website) is an open-access collection of prokaryotic genomes designed to help researchers map the vast and often hidden diversity of microbial life.
Why should you use mOTUs-db?#
🌍 Extensive species and habitat coverage
The database covers ~4 million genomes clustered into 124,295 species-level taxonomic units (mOTUs), accounting for 16,994 genera and 164 phyla (see Database statistics). Our analysis suggests that around 50% of these species-level clusters are complementary to major repositories like the Genome Taxonomy Database (GTDB).
Genomes included within mOTUs-db have been recovered from 120,769 metagenomic samples spanning over a hundred diverse ecosystems beyond the human gut or ocean, for example, animal-associated microbiomes, freshwater, or wetlands. You can view and search all environment categories here .
🔒 Consistent data quality
The mOTUs-db consists of 3.90 million prokaryotic genomes from two main sources:
919,090 genomes from existing public repositories to provide a reliable taxonomic foundation for well-characterized species.
2.98 million metagenome-assembled genomes (MAGs) recovered from over 120,769 metagenomic samples using a standardized workflow that has been shown to yield more and higher-quality MAGs per sample (see Paoli et al. (2022), Nature and Mattock and Watson (2023), Nat Methods).
Each genome in the database is accompanied by completeness and contamination scores, allowing users to filter and select genomes that best fit their specific research needs.
🏞️ Seamless access to environment and functional information
Every MAG in the database retains its association to the metagenomic sample it was recovered from (see Naming conventions). As each metagenomic sample has an environmental annotation, exploring the differences in genomes recovered from different environments is straightforward.
Every genome in the database has been annotated with KEGG, Pfam, and eggNOG. Users can download annotation files through the genome pages, the API, or the motus download command of the mOTUs tool. Moreover, users can search for genomes containing a functional gene group of interest using the motus genomes command of the mOTUs tool.
🛠️ Direct integration with the mOTUs tool
The database directly interfaces with the mOTUs tool. The user can therefore access available genomic context for every species profiled with mOTUs in their metagenomic sample.
The complete content of the database is available within the tool through the motus genomes and motus download commands (see tutorial).
Moreover, the mOTUs profiler has been run on the same collection of metagenomic samples as the MAG recovery workflow. The resulting prevalence and abundance distributions can be seen on an interactive map available on each individual mOTUs page on the database website. These pre-generated taxonomic profiles are also available for download from Zenodo.
💻 Intuitive web interface
The website enables users to search and filter all 3.9 million genomes by taxonomy, mOTU identifier, or basic quality metrics. Users can interactively browse metagenomic studies, explore individual samples, and inspect biosynthetic gene clusters (BGCs) across the database.
mOTUs is part of SIB's portfolio of open tools and databases.
mOTUs is part of the ELIXIR-CH Service Delivery Plan.