Database Commons

a catalog of worldwide biological databases

The Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, freely accessible resource linking human-associated microbes to the metabolites they produce, along with their connections to human health, disease, and diet. Since the release of MiMeDB 1.0 in 2023, the database has been substantially expanded and redesigned. Major updates include the systematic addition of millions of newly annotated genes and pathways, thousands of new metabolites, significantly expanded pathway and reaction coverage, along with broader representation of eukaryotic gut microbes. MiMeDB 2.0 now contains >12.9 million annotated microbial genes, over 23.1 million microbial pathways, 29 295 metabolites, 21 829 metabolic reactions, 3725 microbial species and strains, and 514 076 new experimental and predicted nuclear magnetic resonance and mass spectrometry spectra of microbial metabolites. New features, such as detailed microbial descriptions, metabolite origin tags, refined search filters, and species-specific reaction queries, have been added to enhance usability. Likewise, redesigned network and genome viewers have been implemented to support more comprehensive, intuitive, and integrated visualization of complex, multi-omic relationships. The significant addition of more metabolite spectral data and improved spectral search capabilities further strengthen metabolite identification and discovery. Together, these improvements make MiMeDB 2.0 one of the most comprehensive and user-friendly platforms for investigating the human microbiome at a molecular level and exploring the roles of microbes and microbial metabolites in human health, diet, and disease.

The Human Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, multi-omic, microbiome resource that connects: (i) microbes to microbial genomes; (ii) microbial genomes to microbial metabolites; (iii) microbial metabolites to the human exposome and (iv) all of these 'omes' to human health. MiMeDB was established to consolidate the growing body of data connecting the human microbiome and the chemicals it produces to both health and disease. MiMeDB contains detailed taxonomic, microbiological and body-site location data on most known human microbes (bacteria and fungi). This microbial data is linked to extensive genomic and proteomic sequence data that is closely coupled to colourful interactive chromosomal maps. The database also houses detailed information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that ultimately lead to the observed microbial metabolites in humans. Additional, extensively referenced data about the known or presumptive health effects, measured biosample concentrations and human protein targets for these compounds is provided. All of this information is housed in richly annotated, highly interactive, visually pleasing database that has been designed to be easy to search, easy to browse and easy to navigate. Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases. We believe that MiMeDB represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.