Microbial Co-occurrence Relationships in the Human Microbiome 英文参考文献.docVIP

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Microbial Co-occurrence Relationships in the Human Microbiome 英文参考文献.doc

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Microbial Co-occurrence Relationships in the Human Microbiome 英文参考文献

MicrobialCo-occurrenceRelationshipsintheHuman Microbiome KarolineFaust1,2.,J.FahSathirapongsasuti3.,JacquesIzard4,5,NicolaSegata3,DirkGevers6, JeroenRaes1,2.*,CurtisHuttenhower3,6. * 1DepartmentofStructuralBiology,VIB,Brussels,Belgium,2DepartmentofAppliedBiologicalSciences(DBIT),VrijeUniversiteitBrussel,Brussels,Belgium,3Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America, 4Department of Molecular Genetics, Forsyth Institute, Cambridge, Massachusetts, United States of America, 5Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, United StatesofAmerica,6MicrobialSystemsandCommunities,BroadInstituteofMITandHarvard,Cambridge,Massachusetts,UnitedStatesofAmerica Abstract The healthy microbiota show remarkable variability within and among individuals. In addition to external exposures, ecologicalrelationships(bothoppositionalandsymbiotic)betweenmicrobialinhabitantsareimportantcontributorstothis variation. It is thus of interest to assess what relationships might exist among microbes and determine their underlying reasons.TheinitialHumanMicrobiomeProject(HMP)cohort,comprising239individualsand18differentmicrobialhabitats, provides an unprecedented resource to detect, catalog, and analyze such relationships. Here, we applied an ensemble method based on multiple similarity measures in combination with generalized boosted linear models (GBLMs) to taxonomicmarker(16SrRNAgene)profilesofthiscohort,resultinginaglobalnetworkof3,005significantco-occurrence andco-exclusionrelationshipsbetween197cladesoccurringthroughoutthehumanmicrobiome.Thisnetworkrevealed strongnichespecialization,withmostmicrobialassociationsoccurringwithinbodysitesandanumberofaccompanying inter-body site relationships. Microbial communities within the oropharynx grouped into three distinct habitats, which themselvesshowednodirectinfluenceonthecompositionofthegutmicrobiota.Conversely,nichessuchast