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Elevated rates of horizontal gene transfer in the industrialized human microbiome

Groussin, M.
Poyet, M.
Sistiaga, A.
Kearney, S.M.
Moniz, K.
Noel, M.
Hooker, J.
Gibbons, S.M.
Segurel, L.
Froment, A.
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Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.
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Antimicrobial resistance,Bacterial genomics,Culturomics,Horizontal gene transfer,Host-microbe interactions,Human gut microbiome,Industrialization,Urbanization,Lifestyle,Virulence,SDG-03 Good health and well-being
Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021 Apr 15;184(8):2053-2067.e18. doi: 10.1016/j.cell.2021.02.052.
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