Authors
Malte Rühlemann, Yue Ma, Lénárd L Szánthó, Silvio Waschina, Lucas Moitinho-Silva, Laura C Mews, Joan Faus-Camarena, Hannah Jebens, John Costa, Vanessa Juimo, Alain Fezeu, Adwoa Agyei, Mary Y Afihene, Shadrack O Asibey, Yaw A Awuku, Amoako Duah, Yvonne A Nartey, Fatimah Ibrahim, Yvonne A L Lim, Maw Pin Tan, Charles Onyekwere, John Rusine, Ivan E Mwikarago, John Baines, Andre Franke, Gergely J Szöllősi, Ramnik J Xavier, Eric J Alm, Mathieu Groussin, Mathilde Poyet
Published in
Cell. Nov 02, 2026. Epub Nov 02, 2026.
Abstract
Whether human-associated environments drive adaptive genome evolution in gut commensal bacteria remains largely unknown. Here, we investigate how genomic adaptation in gut bacteria differs between industrialized and non-industrialized human populations. We generated a collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that, compared with metagenome-assembled genomes (MAGs), paired isolate genomes recover more functional elements and signals of horizontal gene transfer (HGT). 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 HGT events. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as the stress response, cell-envelope remodeling, and central metabolism. Our results demonstrate that industrialization drives convergent genome evolution in gut bacteria, providing a framework for understanding the mechanisms of microbial adaptation to rapidly changing human environments.
PMID:
42971204
Bibliographic data and abstract were imported from PubMed on 03 Nov 2026.
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