Convergent genomic evolution of human gut bacteria along an industrialization gradient
To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized human populations. We generated a broad collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that compared to MAGs, paired isolate genomes recover more functional elements and signals of horizontal gene transfers (HGTs). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent events of HGTs. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as stress response, cell envelope remodeling and central metabolism. Our results demonstrate that industrialization imprints evolutionary signatures on gut bacterial genomes, illuminating the effects of rapidly changing environments on human biology.
Authors
- Lénárd L. Szánthó (ORCID: https://orcid.org/0000-0003-3363-2488)
- Gergely J. Szöllősi (ORCID: https://orcid.org/0000-0002-8556-845X)
- Amoako Duah (ORCID: https://orcid.org/0000-0001-8104-7393)
- Silvio Waschina (ORCID: https://orcid.org/0000-0002-6290-3593)
- Yvonne Ayerki Nartey (ORCID: https://orcid.org/0000-0003-2891-3082)
- Yaw Asante Awuku (ORCID: https://orcid.org/0000-0001-8307-2242)
- Shadrack Osei Asibey (ORCID: https://orcid.org/0000-0002-4258-6885)
- Ramnik J. Xavier (ORCID: https://orcid.org/0000-0002-5630-5167)
- Alain Fezeu
- Mathieu Groussin (ORCID: https://orcid.org/0000-0002-0942-7217)
- Malte Christoph Rühlemann (ORCID: https://orcid.org/0000-0002-0685-0052)
- Ivan Emil Mwikarago
- Eric J. Alm (ORCID: https://orcid.org/0000-0001-8294-9364)
- Mathilde Poyet (ORCID: https://orcid.org/0000-0001-6905-9017)
- Hannah Jebens
- John Rusine
- Yvonne A L Lim
- Fatima Ibrahim
- John Baines
- Charles Onyekwere
- Maw Pin Tan
- Lucas Moitinho-Silva
- Andre Franke
- Mary Y. Afihene
- Vanessa Juimo
- Joan Faus-Camarena
- John Costa
- Yue Ma
- Laura C. Mews
- Adwoa Agyei
Institutions
- Broad Institute (US)
- Lagos State University (NG)
- University of Cape Coast (GH)
- Harvard University (US)
- University of Ghana (GH)
- Okinawa Institute of Science and Technology Graduate University (JP)
- Catholic University College of Ghana (GH)
- Korle Bu Teaching Hospital (GH)
- Kwame Nkrumah University of Science and Technology (GH)
- Karolinska Institutet (SE)
- Christian-Albrechts-Universität zu Kiel (DE)
- University of Malaya (MY)
- Medizinische Hochschule Hannover (DE)
- University of Rwanda (RW)
- Massachusetts General Hospital (US)
- Institut de Recherche pour le Développement (CG)
- University Hospital Schleswig-Holstein (DE)
- HUN-REN Centre for Ecological Research (HU)
- National Institute of Allergy and Infectious Diseases (US)
- Max Planck Institute for Evolutionary Biology (DE)
- Institut de Recherche pour le Développement (FR)
- Institute of Evolution (HU)
- University of Ghana Medical Centre (GH)
- Center for Computational and Integrative Biology, Massachusetts General Hospital (US)
- Massachusetts Institute of Technology (US)
Publication Details
- Journal
- Cell
- Published
- 2026-11-01
- DOI
- https://doi.org/10.1016/j.cell.2026.10.014
- Citations
- 2
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 4.06
Funders
- National Institute of Diabetes and Digestive and Kidney Diseases