{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T20:31:37Z","timestamp":1775680297198,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T00:00:00Z","timestamp":1665360000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U19AG063744-01"],"award-info":[{"award-number":["1U19AG063744-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000196","name":"Canada Foundation for Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 \u2018omes\u2019 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.<\/jats:p>","DOI":"10.1093\/nar\/gkac868","type":"journal-article","created":{"date-parts":[[2022,10,10]],"date-time":"2022-10-10T20:26:07Z","timestamp":1665433567000},"page":"D611-D620","source":"Crossref","is-referenced-by-count":100,"title":["MiMeDB: the Human Microbial Metabolome Database"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3207-2434","authenticated-orcid":false,"given":"David S","family":"Wishart","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"},{"name":"Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8, Canada"},{"name":"Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton T6G 2B7, AB, Canada"},{"name":"Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta , Edmonton, AB T6G 2H7, Canada"}]},{"given":"Eponine","family":"Oler","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"Harrison","family":"Peters","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"AnChi","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8667-0907","authenticated-orcid":false,"given":"Sagan","family":"Girod","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"Scott","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"Sukanta","family":"Saha","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"},{"name":"Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8, Canada"}]},{"given":"Vicki\u00a0W","family":"Lui","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"Marcia","family":"LeVatte","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"given":"Vasuk","family":"Gautam","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1858-5732","authenticated-orcid":false,"given":"Rima","family":"Kaddurah-Daouk","sequence":"additional","affiliation":[{"name":"Department of Medicine, Duke University School of Medicine , Durham, NC 27710, USA"}]},{"given":"Naama","family":"Karu","sequence":"additional","affiliation":[{"name":"Leiden Academic Centre for Drug Research, Leiden University , Leiden\u00a02333 CC, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2022,10,10]]},"reference":[{"key":"2023010804233009800_B1","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"2023010804233009800_B2","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1097\/MOG.0000000000000139","article-title":"The gut microbiome in health and in disease","volume":"31","author":"Shreiner","year":"2015","journal-title":"Curr. Opin. Gastroenterol."},{"key":"2023010804233009800_B3","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1097\/NT.0000000000000167","article-title":"The gut microbiome and its role in obesity","volume":"51","author":"Davis","year":"2016","journal-title":"Nutr. Today"},{"key":"2023010804233009800_B4","doi-asserted-by":"crossref","first-page":"98","DOI":"10.3389\/fgene.2019.00098","article-title":"Current understanding of gut microbiota in mood disorders: an update of human studies","volume":"10","author":"Huang","year":"2019","journal-title":"Front. Genet."},{"key":"2023010804233009800_B5","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.cell.2014.03.011","article-title":"Role of the microbiota in immunity and inflammation","volume":"157","author":"Belkaid","year":"2014","journal-title":"Cell"},{"key":"2023010804233009800_B6","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.mrrev.2009.04.001","article-title":"Mechanisms of primary cancer prevention by butyrate and other products formed during gut flora-mediated fermentation of dietary fibre","volume":"682","author":"Scharlau","year":"2009","journal-title":"Mutat. Res. Mutat. Res."},{"key":"2023010804233009800_B7","doi-asserted-by":"crossref","first-page":"1897","DOI":"10.1681\/ASN.2013101062","article-title":"The uremic toxicity of indoxyl sulfate and p-cresyl sulfate: a systematic review","volume":"25","author":"Vanholder","year":"2014","journal-title":"J. Am. Soc. Nephrol."},{"key":"2023010804233009800_B8","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.2215\/CJN.03980609","article-title":"Serum indoxyl sulfate is associated with vascular disease and mortality in chronic kidney disease patients","volume":"4","author":"Barreto","year":"2009","journal-title":"Clin. J. Am. Soc. Nephrol."},{"key":"2023010804233009800_B9","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.neuro.2016.01.006","article-title":"Indoxyl sulfate, not p-cresyl sulfate, is associated with cognitive impairment in early-stage chronic kidney disease","volume":"53","author":"Yeh","year":"2016","journal-title":"Neurotoxicology"},{"key":"2023010804233009800_B10","doi-asserted-by":"crossref","first-page":"370","DOI":"10.3389\/fphar.2017.00370","article-title":"Indoxyl sulfate affects glial function increasing oxidative stress and neuroinflammation in chronic kidney disease: interaction between astrocytes and microglia","volume":"8","author":"Adesso","year":"2017","journal-title":"Front. Pharmacol."},{"key":"2023010804233009800_B11","doi-asserted-by":"crossref","first-page":"365","DOI":"10.3390\/jcm7100365","article-title":"AST-120 reduces neuroinflammation induced by indoxyl sulfate in glial cells","volume":"7","author":"Adesso","year":"2018","journal-title":"J. Clin. Med."},{"key":"2023010804233009800_B12","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/s41575-019-0258-z","article-title":"Gut microbiota-derived metabolites as key actors in inflammatory bowel disease","volume":"17","author":"Lavelle","year":"2020","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"2023010804233009800_B13","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1136\/gutjnl-2020-323071","article-title":"Gut microbiota-derived metabolites as central regulators in metabolic disorders","volume":"70","author":"Agus","year":"2021","journal-title":"Gut"},{"key":"2023010804233009800_B14","doi-asserted-by":"crossref","first-page":"100138","DOI":"10.1016\/j.xcrm.2020.100138","article-title":"Metabolic network analysis reveals altered bile acid synthesis and metabolism in Alzheimer's disease","volume":"1","author":"Baloni","year":"2020","journal-title":"Cell Reports Med"},{"key":"2023010804233009800_B15","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B16","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/bib\/bbx085","article-title":"The biocyc collection of microbial genomes and metabolic pathways","volume":"20","author":"Karp","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2023010804233009800_B17","doi-asserted-by":"crossref","first-page":"D614","DOI":"10.1093\/nar\/gky992","article-title":"The virtual metabolic human database: integrating human and gut microbiome metabolism with nutrition and disease","volume":"47","author":"Noronha","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B18","doi-asserted-by":"crossref","first-page":"D25","DOI":"10.1093\/nar\/gkm929","article-title":"GenBank","volume":"36","author":"Benson","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B19","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkh131","article-title":"UniProt: the universal protein knowledgebase","volume":"32","author":"Apweiler","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B20","doi-asserted-by":"crossref","first-page":"D599","DOI":"10.1093\/nar\/gkr1105","article-title":"BacMap: an up-to-date electronic atlas of annotated bacterial genomes","volume":"40","author":"Cruz","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B21","doi-asserted-by":"crossref","first-page":"1286","DOI":"10.3945\/ajcn.113.076133","article-title":"The food metabolome: a window over dietary exposure","volume":"99","author":"Scalbert","year":"2014","journal-title":"Am. J. Clin. Nutr."},{"key":"2023010804233009800_B22","first-page":"D908","article-title":"Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk","volume":"48","author":"Neveu","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B23","doi-asserted-by":"crossref","first-page":"D622","DOI":"10.1093\/nar\/gkab1062","article-title":"HMDB 5.0: the human metabolome database for 2022","volume":"50","author":"Wishart","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B24","doi-asserted-by":"crossref","first-page":"D495","DOI":"10.1093\/nar\/gkv1060","article-title":"ECMDB 2.0: a richer resource for understanding the biochemistry of e. coli","volume":"44","author":"Sajed","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B25","doi-asserted-by":"crossref","first-page":"D665","DOI":"10.1093\/nar\/gkab1052","article-title":"NP-MRD: the natural products magnetic resonance database","volume":"50","author":"Wishart","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B26","doi-asserted-by":"crossref","first-page":"W165","DOI":"10.1093\/nar\/gkac383","article-title":"CFM-ID 4.0 \u2013 a web server for accurate MS-based metabolite identification","volume":"50","author":"Wang","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B27","doi-asserted-by":"crossref","first-page":"D440","DOI":"10.1093\/nar\/gkw1058","article-title":"YMDB 2.0: a significantly expanded version of the yeast metabolome database","volume":"45","author":"Ramirez-Gaona","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B28","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13321-016-0174-y","article-title":"ClassyFire: automated chemical classification with a comprehensive, computable taxonomy","volume":"8","author":"Djoumbou\u00a0Feunang","year":"2016","journal-title":"J. Cheminform."},{"key":"2023010804233009800_B29","doi-asserted-by":"crossref","first-page":"W20","DOI":"10.1093\/nar\/gkh435","article-title":"BLAST: at the core of a powerful and diverse set of sequence analysis tools","volume":"32","author":"McGinnis","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B30","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1093\/bib\/bbx081","article-title":"Visualizing and comparing circular genomes using the CGView family of tools","volume":"20","author":"Stothard","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2023010804233009800_B31","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the drugbank database for 2018","volume":"46","author":"Wishart","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B32","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2023010804233009800_B33","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkac313","article-title":"BioTransformer 3.0\u2014a web server for accurately predicting metabolic transformation products","volume":"50","author":"Wishart","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023010804233009800_B34","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/s13321-015-0087-1","article-title":"MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics","volume":"7","author":"Jeffryes","year":"2015","journal-title":"J. Cheminform."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D611\/48440796\/gkac868.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/D1\/D611\/48440796\/gkac868.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:24:23Z","timestamp":1673151863000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/D1\/D611\/6754917"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,10]]},"references-count":34,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2022,10,10]]},"published-print":{"date-parts":[[2023,1,6]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac868","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1,6]]},"published":{"date-parts":[[2022,10,10]]}}}