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However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes.\u00a0Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples.\u00a0About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence,\u00a0both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access\/queries to all its contents easily. mMGE is freely available for academic use at: https:\/\/mgedb.comp-sysbio.org.<\/jats:p>","DOI":"10.1093\/nar\/gkaa869","type":"journal-article","created":{"date-parts":[[2020,9,24]],"date-time":"2020-09-24T11:56:37Z","timestamp":1600948597000},"page":"D783-D791","source":"Crossref","is-referenced-by-count":40,"title":["mMGE: a database for human metagenomic extrachromosomal mobile genetic elements"],"prefix":"10.1093","volume":"49","author":[{"given":"Senying","family":"Lai","sequence":"first","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longhao","family":"Jia","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Balakrishnan","family":"Subramanian","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, Hubei\u00a0430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaojun","family":"Pan","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinglong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yanqi","family":"Dong","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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, Hubei\u00a0430074, China"},{"name":"College of Life Science, Henan Normal University, Xinxiang, Henan\u00a0453007, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"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\u00a0200433, China"},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433,\u00a0China"},{"name":"Research Institute of Intelligent Complex System, Fudan University, Shanghai\u00a0200433, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,10,19]]},"reference":[{"key":"2021010313121401200_B1","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/nrmicro1235","article-title":"Mobile genetic elements: the agents of open source evolution","volume":"3","author":"Frost","year":"2005","journal-title":"Nat. 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Microbiol."},{"key":"2021010313121401200_B3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/s40168-018-0551-z","article-title":"Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities","volume":"6","author":"Sitaraman","year":"2018","journal-title":"Microbiome"},{"key":"2021010313121401200_B4","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/s40168-019-0737-z","article-title":"Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut","volume":"7","author":"Suzuki","year":"2019","journal-title":"Microbiome"},{"key":"2021010313121401200_B5","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.tim.2019.02.008","article-title":"Bacteriophages as environmental reservoirs of antibiotic resistance","volume":"27","author":"Calero-Caceres","year":"2019","journal-title":"Trends Microbiol."},{"key":"2021010313121401200_B6","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1038\/s41467-019-10600-7","article-title":"Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance","volume":"10","author":"Wein","year":"2019","journal-title":"Nat. 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