Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns

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dc.contributor.authorGoswami, Sourav
dc.contributor.authorAnsari, Alisha
dc.contributor.authorSharaf, Chetan
dc.contributor.authorO’Toole, Paul W.
dc.contributor.authorShanahan, Fergus
dc.contributor.authorAhuja, Vineet
dc.contributor.authorGhosh, Tarini Shankar
dc.contributor.funderMinistry of Science and Technology, India
dc.contributor.funderIIIT-Delhi
dc.date.accessioned2026-09-10T10:51:01Z
dc.date.available2026-09-10T10:51:01Z
dc.date.issued2026-04-23
dc.description© 2026, the Author(s). This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived fromthis article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
dc.description.abstractBifidobacteria are key health-associated members of the human gut microbiome and are widely used as probiotics, but their colonization success varies substantially between individuals, partly due to baseline microbiome composition. We analyzed 51,244 gut microbiomes from 149 cohorts (45 countries) to identify non-Bifidobacterial taxa associated with the Bifidobacterial features. We observed several consistent and age-/life-style-specific association patterns of different non-Bifidobacterial taxa with the different Bifidobacteria. Multiple Bifidobacteria showed positive associations with butyrate-producing Firmicutes and Collinsella; negative associations involved pathobiont-Firmicutes and specific Bacteroidota taxa. B. adolescentis and B. breve showed the strongest positive and negative associations, respectively, with health-associated adult gut microbiome members. We quantified these relationships as Association-Scores, stratified by age/life-style/sequencing-strategy/disease, which were significantly reproducible after adjusting for multiple microbiome-linked, host life-style/clinical covariates, and predictable using species-specific genomic functions. We used these Association-Scores to derive microbiome-level Receptive-Scores that quantify how permissive a baseline microbiome is to increases or persistence of a given Bifidobacterium. In an external dataset of eight Bifidobacterium interventions (n = 1633 gut microbiomes), Receptive-Scores combined with baseline abundance of the administered Bifidobacteria significantly predicted post-treatment persistence/increase in 69.23% of trial-probiotic pairs. Together, this work identifies microbiome features governing Bifidobacterial colonization and provides tools to predict personalized probiotic responses.en
dc.description.sponsorshipMinistry of Science and Technology, India|BT/HRD/35/02/2006
dc.format.extent21
dc.format.extent7546774
dc.identifier.articleid5678
dc.identifier.authororcidGoswami, Sourav
dc.identifier.authororcidAnsari, Alisha
dc.identifier.authororcidSharaf, Chetan
dc.identifier.authororcidO’Toole, Paul W.
dc.identifier.authororcidShanahan, Fergus
dc.identifier.authororcidAhuja, Vineet
dc.identifier.authororcidGhosh, Tarini Shankar
dc.identifier.citationGoswami, S, Ansari, A, Sharaf, C, O’Toole, P W, Shanahan, F, Ahuja, V & Ghosh, T S 2026, 'Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns', Nature Communications, vol. 17, no. 1, 5678, pp. 1-21. https://doi.org/10.1038/s41467-026-72289-9
dc.identifier.doi10.1038/s41467-026-72289-9
dc.identifier.endpage21
dc.identifier.issn2041-1723
dc.identifier.issued1
dc.identifier.journaltitleNature Communications
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/19234
dc.identifier.urlhttps://www.scopus.com/pages/publications/105043514720
dc.identifier.volume17
dc.language.isoeng
dc.rightscc_by_nc_nd
dc.subjectNon-Bifidobacterial taxa
dc.subjectFirmicutes
dc.subjectCollinsella
dc.subjectBacteroidota taxa
dc.subjectReceptive-Scores
dc.subject[APCMicrobiome]
dc.subject[Microbiology]
dc.subject[Medicine]
dc.subjectGeneral Chemistry
dc.subjectGeneral Biochemistry,Genetics and Molecular Biology
dc.subjectMultidisciplinary
dc.subjectGeneral Physics and Astronomy
dc.titleGut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patternsen
dc.typeArticle (Peer reviewed)
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