MiMeDB: the Human Microbial Metabolome Database
Nucleic Acids Research, vol. 51, pp. D611–D620
Abstract
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.
Authors 12
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David Scott Wishart corresponding
Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8, Canada
Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton T6G 2B7, AB, Canada
Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta , Edmonton, AB T6G 2H7, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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Affiliation as printed
Department of Medicine, Duke University School of Medicine , Durham, NC 27710, USA
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Affiliation as printed
Leiden Academic Centre for Drug Research, Leiden University , Leiden 2333 CC, The Netherlands
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