The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals

The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of individual members. Understanding the factors underlying variability in these communities may therefore provide critical insights on the biological links between the gut microbiome and human phenotypes. Here, we examined the effect of a range of host factors, including demographics, medical history, and dietary habits, on these communities in 938 healthy individuals using MANOCCA, a covariance-based approach developed to address existing limitations. Increased age and smoking were associated with a significant overall decrease in co-abundance, and conversely a higher body mass index was associated with increased co-abundance. At the taxon level, a core of 200 genera were systematically impacted in their co-abundance with other taxa, suggesting a central role in structuring the network. Finally, we demonstrate that our approach offers a powerful framework for prediction purposes, with taxa co-abundance being able to predict the age of participants with an accuracy three-fold higher than a model based on abundance only.

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Publication Details

Journal
Communications Biology
Published
2025-11-06
DOI
https://doi.org/10.1038/s42003-025-08895-y
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
0.00

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article

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals

Antoine Toubert, Antonio Rausell, Anavaj Sakuntabhai, Nadine Cerf–Bensussan et al.
Communications Biology
Gut microbiota and health
article

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals

Antoine Toubert, Antonio Rausell, Anavaj Sakuntabhai, Nadine Cerf–Bensussan, Gérard Eberl, Lluís Quintana‐Murci, Frédérique Michel, Darragh Duffy, Jost Enninga, Rose Anne Kenny, Gunilla Karlsson Hedestam, Pierre Bruhns, Milena Hasan, Frédéric Tangy, Ana Cumano, Sean Kennedy, Philippe Bousso, Ivo G. Boneca, Serge Herçberg, Lars Rogge, Sandra Pellegrini, Nollaig M. Bourke, Olivier Schwartz, Étienne Patin, Marius Bredon, Benno Schwikowski, Marie‐Noëlle Ungeheuer, Spencer Shorte, Hugo Mouquet, Léo Henches, Christophe Zimmer, Olivier Lantz, Molly A. Ingersoll, Arthur Frouin, Ludovic Deriano, Christophe d’Enfert, Petter Brodin, Matthew L. Albert, Marie‐Agnès Dillies, Andrés Alcover, Frédéric Rieux‐Laucat, Harry Sokol, Jacques Fellay, Laurent Abel, Cliona O’Farrelly, Antoine Auvergne, Christophe Boetto, James P. Di Santo, Mathilde Touvier, Violeta Basten Romero, Magnus Fontes, Mickaël Ménager
article en

Abstract

The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of individual members. Understanding the factors underlying variability in these communities may therefore provide critical insights on the biological links between the gut microbiome and human phenotypes. Here, we examined the effect of a range of host factors, including demographics, medical history, and dietary habits, on these communities in 938 healthy individuals using MANOCCA, a covariance-based approach developed to address existing limitations. Increased age and smoking were associated with a significant overall decrease in co-abundance, and conversely a higher body mass index was associated with increased co-abundance. At the taxon level, a core of 200 genera were systematically impacted in their co-abundance with other taxa, suggesting a central role in structuring the network. Finally, we demonstrate that our approach offers a powerful framework for prediction purposes, with taxa co-abundance being able to predict the age of participants with an accuracy three-fold higher than a model based on abundance only.

Communications BiologyVol. 8(1)
Hôpital Necker-Enfants Malades (FR), Centre National de la Recherche Scientifique (FR), Harvard University (US), Inserm (FR), Institut Pasteur (FR), Université Paris Cité (FR), Trinity College Dublin (IE), Université Paris-Saclay (FR), Karolinska Institutet (SE), Microbiologie de l’alimentation au service de la santé (FR), Sorbonne Université (FR), Université Sorbonne Paris Nord (FR), Assistance Publique – Hôpitaux de Paris (FR), Fédération Hospitalo-Universitaire, Paris Center for Microbiome Medicine (FR), Roche (France) (FR), Evolutionary Genomics (United States) (US), Centre de Recherche Saint-Antoine (FR), Hôpital Saint-Louis (FR), Institut des Maladies Génétiques Imagine (FR), École Polytechnique Fédérale de Lausanne (CH), University of San Francisco (US), Institut Curie (FR)
Agence Nationale de la Recherche
Openalex Percentile: Top 71%
Gut microbiota and health
DOIOpen Access PDFOpenAlex
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