Elevated rates of horizontal gene transfer in the industrialized human microbiome

Mathieu Groussin, Mathilde Poyet, Ainara Sistiaga, Sean M. Kearney, Katya Moniz, Mary Noel, Jeff Hooker, Sean M. Gibbons, Laure Segurel, Alain Froment, Rihlat Said Mohamed, Alain Fezeu, Vanessa A. Juimo, Sophie Lafosse, Francis E. Tabe, Catherine Girard, Deborah Iqaluk, Le Thanh Tu Nguyen, B. Jesse Shapiro, Jenni LehtimäkiLasse Ruokolainen, Pinja P. Kettunen, Tommi Vatanen, Shani Sigwazi, Audax Mabulla, Manuel Domínguez-Rodrigo, Yvonne A. Nartey, Adwoa Agyei-Nkansah, Amoako Duah, Yaw A. Awuku, Kenneth A. Valles, Shadrack O. Asibey, Mary Y. Afihene, Lewis R. Roberts, Amelie Plymoth, Charles A. Onyekwere, Roger E. Summons, Ramnik J. Xavier, Eric J. Alm

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)2053-2067.e18
Issue number8
StatePublished - Apr 15 2021


  • antimicrobial resistance
  • bacterial genomics
  • culturomics
  • horizontal gene transfer
  • host-microbe interactions
  • human gut microbiome
  • industrialization
  • lifestyle
  • urbanization
  • virulence

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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