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dc.contributor.authorZhao, Shijie
dc.contributor.authorLieberman, Tami
dc.contributor.authorPoyet, Mathilde
dc.contributor.authorKauffman, Kathryn
dc.contributor.authorGibbons, Sean M.
dc.contributor.authorGroussin, Mathieu
dc.contributor.authorXavier, Ramnik J.
dc.contributor.authorAlm, Eric J
dc.date.accessioned2020-05-11T19:50:52Z
dc.date.available2020-05-11T19:50:52Z
dc.date.issued2019-05
dc.date.submitted2019-01
dc.identifier.issn1931-3128
dc.identifier.urihttps://hdl.handle.net/1721.1/125160
dc.description.abstractNatural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization. Bacteria acquire adaptive mutations during infections, but the role of mutations in the gut microbiome is unknown. Zhao and Lieberman et al. report that Bacteroides fragilis adapts via mutation within healthy people. They discover genes important to survival in humans and detail dynamics within individuals and across populations. Keywords: adaptive evolution; human microbiome; Bacteroides; microbial evolution; microbial genomics; de novo mutation; horizontal gene transfer; metagenomics; whole-genome sequencingen_US
dc.language.isoen
dc.publisherElsevier BVen_US
dc.relation.isversionofhttp://dx.doi.org/10.1016/j.chom.2019.03.007en_US
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivs Licenseen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en_US
dc.sourcePMCen_US
dc.titleAdaptive Evolution within Gut Microbiomes of Healthy Peopleen_US
dc.typeArticleen_US
dc.identifier.citationZhao, Shijie, et al. "Adaptive Evolution within Gut Microbiomes of Healthy People." Cell Host & Micorbe, 25, 5 (may 2019) 656-667. © 2019 Elsevier Inc.en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biological Engineeringen_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Biologyen_US
dc.contributor.departmentMassachusetts Institute of Technology. Center for Microbiome Informatics and Therapeuticsen_US
dc.contributor.departmentBroad Institute of MIT and Harvarden_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Civil and Environmental Engineeringen_US
dc.contributor.departmentMassachusetts Institute of Technology. Institute for Medical Engineering & Scienceen_US
dc.relation.journalCell Host & Microbeen_US
dc.eprint.versionAuthor's final manuscripten_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2020-05-11T16:03:06Z
dspace.date.submission2020-05-11T16:03:08Z
mit.journal.volume25en_US
mit.journal.issue5en_US
mit.licensePUBLISHER_CC


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