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

cbnd
Thumbnail Image
Files
Date
2026-04-23
Authors
Goswami, Sourav
Ansari, Alisha
Sharaf, Chetan
O’Toole, Paul W.
Shanahan, Fergus
Ahuja, Vineet
Ghosh, Tarini Shankar
Journal Title
Journal ISSN
Volume Title
Publisher
Nature Research
Published Version
10.1038/s41467-026-72289-9
Research Projects
Organizational Units
Journal Issue
Abstract
Bifidobacteria 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.
Description
Keywords
Non-Bifidobacterial taxa , Firmicutes , Collinsella , Bacteroidota taxa , Receptive-Scores , [APCMicrobiome] , [Microbiology] , [Medicine]
Citation
Goswami, 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
Link to publisher’s version
URI
https://hdl.handle.net/10468/19234
Collections
School of Medicine
APC Microbiome Ireland
School of Microbiology
Copyright
© 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/.