{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:41:50Z","timestamp":1783489310042,"version":"3.55.0"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2021,10,28]],"date-time":"2021-10-28T00:00:00Z","timestamp":1635379200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0905600"],"award-info":[{"award-number":["2019YFA0905600"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0712403"],"award-info":[{"award-number":["2020YFA0712403"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61932008"],"award-info":[{"award-number":["61932008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61772368"],"award-info":[{"award-number":["61772368"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Science and Technology Innovation Fund","award":["19511101404"],"award-info":[{"award-number":["19511101404"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>mBodyMap is a curated database for microbes across the human body and their associations with health and diseases. Its primary aim is to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes by consistently annotating the microbial contents of collected samples using state-of-the-art toolsets and manually curating the meta-data of corresponding human hosts. mBodyMap organizes collected samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison. To help users find microbes of interest and visualize and compare their distributions and abundances\/prevalence within different body sites and various diseases, the mBodyMap database is equipped with an intuitive interface and extensive graphical representations of the collected data. So far, it contains a total of 63 148 runs, including 14 401 metagenomes and 48 747 amplicons related to health and 56 human diseases, from within 22 human body sites across 136 projects. Also available in the database are pre-computed abundances and prevalence of 6247 species (belonging to 1645 genera) stratified by body sites and diseases. mBodyMap can be accessed at: https:\/\/mbodymap.microbiome.cloud.<\/jats:p>","DOI":"10.1093\/nar\/gkab973","type":"journal-article","created":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T06:13:08Z","timestamp":1633587188000},"page":"D808-D816","source":"Crossref","is-referenced-by-count":59,"title":["mBodyMap: a curated database for microbes across human body and their associations with health and diseases"],"prefix":"10.1093","volume":"50","author":[{"given":"Hanbo","family":"Jin","sequence":"first","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoru","family":"Hu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuqing","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiqian","family":"Duan","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenmo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4531-3970","authenticated-orcid":false,"given":"Xing-Ming","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China"},{"name":"Research Institute of Intelligent Complex System, Fudan University, Shanghai 200433, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5160-4398","authenticated-orcid":false,"given":"Wei-Hua","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China"},{"name":"Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai\u00a0264003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,28]]},"reference":[{"key":"2022010507421167500_B1","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature08821","article-title":"A human gut microbial gene catalogue established by metagenomic sequencing","volume":"464","author":"Qin","year":"2010","journal-title":"Nature"},{"key":"2022010507421167500_B2","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nature05414","article-title":"An obesity-associated gut microbiome with increased capacity for energy harvest","volume":"444","author":"Turnbaugh","year":"2006","journal-title":"Nature"},{"key":"2022010507421167500_B3","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.pharmthera.2015.11.012","article-title":"Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases","volume":"158","author":"Ghaisas","year":"2016","journal-title":"Pharmacol. Ther."},{"key":"2022010507421167500_B4","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrg3182","article-title":"The human microbiome: at the interface of health and disease","volume":"13","author":"Cho","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"2022010507421167500_B5","doi-asserted-by":"crossref","first-page":"15163","DOI":"10.3748\/wjg.v20.i41.15163","article-title":"Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis","volume":"20","author":"Tojo","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"2022010507421167500_B6","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/s41586-019-1238-8","article-title":"The integrative human microbiome project","volume":"569","author":"The Integrative HMP (iHMP) Research Network Consortium.","year":"2019","journal-title":"Nature"},{"key":"2022010507421167500_B7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"Human Microbiome Project Consortium.","year":"2012","journal-title":"Nature"},{"key":"2022010507421167500_B8","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1016\/j.jaci.2012.03.010","article-title":"The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites","volume":"129","author":"Ursell","year":"2012","journal-title":"J. Allergy Clin. Immunol."},{"key":"2022010507421167500_B9","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1136\/gutjnl-2018-316106","article-title":"Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota","volume":"68","author":"Tito","year":"2019","journal-title":"Gut"},{"key":"2022010507421167500_B10","doi-asserted-by":"crossref","first-page":"2105","DOI":"10.1136\/gutjnl-2020-323314","article-title":"Human and preclinical studies of the host\u2013gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health","volume":"70","author":"Brial","year":"2021","journal-title":"Gut"},{"key":"2022010507421167500_B11","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nature15766","article-title":"Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota","volume":"528","author":"Forslund","year":"2015","journal-title":"Nature"},{"key":"2022010507421167500_B12","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/s41586-020-2269-x","article-title":"Statin therapy is associated with lower prevalence of gut microbiota dysbiosis","volume":"581","author":"Vieira-Silva","year":"2020","journal-title":"Nature"},{"key":"2022010507421167500_B13","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1038\/nm.4345","article-title":"Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug","volume":"23","author":"Wu","year":"2017","journal-title":"Nat. Med."},{"key":"2022010507421167500_B14","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1016\/j.cmet.2021.02.012","article-title":"Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis","volume":"33","author":"Wu","year":"2021","journal-title":"Cell Metab."},{"key":"2022010507421167500_B15","doi-asserted-by":"crossref","first-page":"e00630-19","DOI":"10.1128\/mSystems.00630-19","article-title":"Human skin, oral, and gut microbiomes predict chronological age","volume":"5","author":"Huang","year":"2020","journal-title":"Msystems"},{"key":"2022010507421167500_B16","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol."},{"key":"2022010507421167500_B17","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1126\/science.aad3369","article-title":"Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity","volume":"352","author":"Zhernakova","year":"2016","journal-title":"Science"},{"key":"2022010507421167500_B18","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/s41579-020-0368-1","article-title":"Diversity within species: interpreting strains in microbiomes","volume":"18","author":"Van\u00a0Rossum","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"2022010507421167500_B19","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1136\/gutjnl-2018-317715","article-title":"Antibiotics-induced monodominance of a novel gut bacterial order","volume":"68","author":"Hildebrand","year":"2019","journal-title":"Gut"},{"key":"2022010507421167500_B20","doi-asserted-by":"crossref","first-page":"50S","DOI":"10.1097\/PRS.0000000000007621","article-title":"Temporal variation of the facial skin microbiome: a 2-year longitudinal study in healthy adults","volume":"147","author":"Hillebrand","year":"2021","journal-title":"Plast. Reconstr. Surg."},{"key":"2022010507421167500_B21","doi-asserted-by":"crossref","first-page":"565549","DOI":"10.3389\/fmicb.2020.565549","article-title":"New insights into the skin microbial communities and skin aging","volume":"11","author":"Li","year":"2020","journal-title":"Front. Microbiol."},{"key":"2022010507421167500_B22","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/s12866-018-1197-5","article-title":"Disbiome database: linking the microbiome to disease","volume":"18","author":"Janssens","year":"2018","journal-title":"BMC Microbiol."},{"key":"2022010507421167500_B23","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.ebiom.2016.01.032","article-title":"Gut microbiota linked to sexual preference and HIV infection","volume":"5","author":"Noguera-Julian","year":"2016","journal-title":"EBioMedicine"},{"key":"2022010507421167500_B24","doi-asserted-by":"crossref","first-page":"e021682","DOI":"10.1136\/bmjopen-2018-021682","article-title":"Metagenomic analysis of gut microbial communities from a Central Asian population","volume":"8","author":"Kushugulova","year":"2018","journal-title":"BMJ Open"},{"key":"2022010507421167500_B25","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3390\/microorganisms7010014","article-title":"What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases","volume":"7","author":"Rinninella","year":"2019","journal-title":"Microorganisms"},{"key":"2022010507421167500_B26","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1038\/d41586-020-00193-3","article-title":"The hunt for a healthy microbiome","volume":"577","author":"Eisenstein","year":"2020","journal-title":"Nature"},{"key":"2022010507421167500_B27","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"2022010507421167500_B28","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.cmet.2020.06.011","article-title":"The gut microbiota in prediabetes and diabetes: a population-based cross-sectional study","volume":"32","author":"Wu","year":"2020","journal-title":"Cell Metab."},{"key":"2022010507421167500_B29","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biol."},{"key":"2022010507421167500_B30","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13073-017-0490-5","article-title":"A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients","volume":"9","author":"Hall","year":"2017","journal-title":"Genome Medicine"},{"key":"2022010507421167500_B31","doi-asserted-by":"crossref","first-page":"e00112-21","DOI":"10.1128\/mSystems.00112-21","article-title":"Metagenomic analysis of common intestinal diseases reveals relationships among microbial signatures and powers multidisease diagnostic models","volume":"6","author":"Jiang","year":"2021","journal-title":"Msystems"},{"key":"2022010507421167500_B32","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1186\/s12864-020-6749-z","article-title":"Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment","volume":"21","author":"Jiang","year":"2020","journal-title":"BMC Genomics"},{"key":"2022010507421167500_B33","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41591-019-0406-6","article-title":"Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer","volume":"25","author":"Wirbel","year":"2019","journal-title":"Nat. Med."},{"key":"2022010507421167500_B34","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1158\/2326-6066.CIR-13-0101","article-title":"Microbes and inflammation in colorectal cancer","volume":"1","author":"Kostic","year":"2013","journal-title":"Cancer Immunol. Res."},{"key":"2022010507421167500_B35","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1053\/j.gastro.2018.04.028","article-title":"Association between bacteremia from specific microbes and subsequent diagnosis of colorectal cancer","volume":"155","author":"Kwong","year":"2018","journal-title":"Gastroenterology"},{"key":"2022010507421167500_B36","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1038\/ncomms5724","article-title":"Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer","volume":"5","author":"Arthur","year":"2014","journal-title":"Nat. Commun."},{"key":"2022010507421167500_B37","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1016\/j.micpath.2017.08.038","article-title":"Comparison of gut microbiota in adult patients with type 2 diabetes and healthy individuals","volume":"111","author":"Sedighi","year":"2017","journal-title":"Microb. Pathog."},{"key":"2022010507421167500_B38","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"Qin","year":"2012","journal-title":"Nature"},{"key":"2022010507421167500_B39","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1093\/bib\/bbw005","article-title":"An analysis of human microbe-disease associations","volume":"18","author":"Ma","year":"2017","journal-title":"Brief. Bioinform."},{"key":"2022010507421167500_B40","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1016\/j.gpb.2020.11.001","article-title":"MicroPhenoDB associates metagenomic data with pathogenic microbes, microbial core genes, and human disease phenotypes","volume":"18","author":"Yao","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2022010507421167500_B41","doi-asserted-by":"crossref","first-page":"D84","DOI":"10.1093\/nar\/gky1078","article-title":"The European Nucleotide Archive","volume":"47","author":"Harrison","year":"2019","journal-title":"Nucleic. Acids. Res."},{"key":"2022010507421167500_B42","doi-asserted-by":"crossref","first-page":"D54","DOI":"10.1093\/nar\/gkr854","article-title":"The Sequence Read Archive: explosive growth of sequencing data","volume":"40","author":"Kodama","year":"2012","journal-title":"Nucleic. Acids. Res."},{"key":"2022010507421167500_B43","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"Suppl. 9","key":"2022010507421167500_B44","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2105-15-S9-S10","article-title":"CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing","volume":"15","author":"Kwon","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2022010507421167500_B45","doi-asserted-by":"crossref","first-page":"3808","DOI":"10.1093\/bioinformatics\/btx517","article-title":"MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis","volume":"33","author":"Rodrigues","year":"2017","journal-title":"Bioinformatics"},{"key":"2022010507421167500_B46","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"2012","journal-title":"Nat. Methods"},{"key":"2022010507421167500_B47","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gkz764","article-title":"GMrepo: a database of curated and consistently annotated human gut metagenomes","volume":"48","author":"Wu","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2022010507421167500_B48","doi-asserted-by":"crossref","first-page":"baaa062","DOI":"10.1093\/database\/baaa062","article-title":"NCBI Taxonomy: a comprehensive update on curation, resources and tools","volume":"2020","author":"Schoch","year":"2020","journal-title":"Database (Oxford)"},{"key":"2022010507421167500_B49","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkx1124","article-title":"MVP: a microbe\u2013phage interaction database","volume":"46","author":"Gao","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022010507421167500_B50","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D808\/42058695\/gkab973.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/D1\/D808\/42058695\/gkab973.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,5]],"date-time":"2022-01-05T08:25:14Z","timestamp":1641371114000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/D1\/D808\/6413603"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,28]]},"references-count":50,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2021,10,28]]},"published-print":{"date-parts":[[2022,1,7]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkab973","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,7]]},"published":{"date-parts":[[2021,10,28]]}}}