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Enterosignatures define common bacterial guilds in the human gut microbiome

hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
dc.contributor.authorFRIOUX, Clémence
hal.structure.identifierQuadram Institute
dc.contributor.authorANSORGE, Rebecca
hal.structure.identifierQuadram Institute
dc.contributor.authorÖZKURT, Ezgi
hal.structure.identifierPleiade, from patterns to models in computational biodiversity and biotechnology [PLEIADE]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorGHASSEMI NEDJAD, Chabname
hal.structure.identifierQuadram Institute
dc.contributor.authorFRITSCHER, Joachim
hal.structure.identifierEarlham Institute [Norwich]
dc.contributor.authorQUINCE, Christopher
hal.structure.identifierCentre for Molecular Medicine Norway [NCMM]
dc.contributor.authorWASZAK, Sebastian
hal.structure.identifierQuadram Institute
dc.contributor.authorHILDEBRAND, Falk
dc.date.issued2023-06
dc.identifier.issn1931-3128
dc.description.abstractEnThe human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures.Temporal analysis implies that the Bacteroides-associated ES is “core” in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
dc.language.isoen
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enmetagenomics
dc.subject.enhuman gut microbiome
dc.subject.ennon-negative matrix factorization
dc.subject.endysbiosis
dc.subject.enenterosignatures
dc.subject.enenterotypes
dc.title.enEnterosignatures define common bacterial guilds in the human gut microbiome
dc.typeArticle de revue
dc.identifier.doi10.1016/j.chom.2023.05.024
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halStatistiques [stat]/Machine Learning [stat.ML]
dc.description.sponsorshipEuropeerc-stg-948219
bordeaux.journalCell Host & Microbe
bordeaux.page1111
bordeaux.volume31
bordeaux.issue7
bordeaux.peerReviewedoui
hal.identifierhal-04141300
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04141300v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Cell%20Host%20&%20Microbe&rft.date=2023-06&rft.volume=31&rft.issue=7&rft.spage=1111&rft.epage=1111&rft.eissn=1931-3128&rft.issn=1931-3128&rft.au=FRIOUX,%20Cl%C3%A9mence&ANSORGE,%20Rebecca&%C3%96ZKURT,%20Ezgi&GHASSEMI%20NEDJAD,%20Chabname&FRITSCHER,%20Joachim&rft.genre=article


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