@article{1692556a2acc48e7b4b1b8f047ea029f,
title = "Elevated rates of horizontal gene transfer in the industrialized human microbiome",
abstract = "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.",
keywords = "antimicrobial resistance, bacterial genomics, culturomics, horizontal gene transfer, host-microbe interactions, human gut microbiome, industrialization, lifestyle, urbanization, virulence",
author = "Mathieu Groussin and Mathilde Poyet and Ainara Sistiaga and Kearney, {Sean M.} and Katya Moniz and Mary Noel and Jeff Hooker and Gibbons, {Sean M.} and Laure Segurel and Alain Froment and Mohamed, {Rihlat Said} and Alain Fezeu and Juimo, {Vanessa A.} and Sophie Lafosse and Tabe, {Francis E.} and Catherine Girard and Deborah Iqaluk and Nguyen, {Le Thanh Tu} and Shapiro, {B. Jesse} and Jenni Lehtim{\"a}ki and Lasse Ruokolainen and Kettunen, {Pinja P.} and Tommi Vatanen and Shani Sigwazi and Audax Mabulla and Manuel Dom{\'i}nguez-Rodrigo and Nartey, {Yvonne A.} and Adwoa Agyei-Nkansah and Amoako Duah and Awuku, {Yaw A.} and Valles, {Kenneth A.} and Asibey, {Shadrack O.} and Afihene, {Mary Y.} and Roberts, {Lewis R.} and Amelie Plymoth and Onyekwere, {Charles A.} and Summons, {Roger E.} and Xavier, {Ramnik J.} and Alm, {Eric J.}",
note = "Funding Information: We are grateful to our field collaborators in Montana (US), Canada, Finland, Cameroon, Tanzania, Nigeria, and Ghana. We thank all human participants that agreed to provide samples to the GMbC project. We are also thankful to Christopher Corzett for his support and for documenting our field work in Tanzania through photography. We are grateful to the Pattern team at the Broad Institute for designing the graphical abstract. This work was supported by grants from the Center for Microbiome Informatics and Therapeutics at MIT and the Rasmussen Family Foundation , as well as by a BroadNext10 award from the Broad Institute . A.S. was supported by a Marie Sk{\l}odowska-Curie fellowship ( H2020-MSCA-IF-2016-780860 ). S.M.G. was supported by a Washington Research Foundation Distinguished Investigator Award . L.S. was supported by an ANR grant (MICROREGAL, ANR-15-CE02-0003 ). K.A.V. and L.R.R. were supported by the Mayo Clinic Center for Clinical and Translational Science ( TL1 TR002380 and UL1 TR002377 , respectively). We thank Tamara Mason and the team at the Walkup Sequencing platform at the Broad Institute for support on sequencing efforts. Funding Information: We are grateful to our field collaborators in Montana (US), Canada, Finland, Cameroon, Tanzania, Nigeria, and Ghana. We thank all human participants that agreed to provide samples to the GMbC project. We are also thankful to Christopher Corzett for his support and for documenting our field work in Tanzania through photography. We are grateful to the Pattern team at the Broad Institute for designing the graphical abstract. This work was supported by grants from the Center for Microbiome Informatics and Therapeutics at MIT and the Rasmussen Family Foundation, as well as by a BroadNext10 award from the Broad Institute. A.S. was supported by a Marie Sk?odowska-Curie fellowship (H2020-MSCA-IF-2016-780860). S.M.G. was supported by a Washington Research Foundation Distinguished Investigator Award. L.S. was supported by an ANR grant (MICROREGAL, ANR-15-CE02-0003). K.A.V. and L.R.R. were supported by the Mayo Clinic Center for Clinical and Translational Science (TL1 TR002380 and UL1 TR002377, respectively). We thank Tamara Mason and the team at the Walkup Sequencing platform at the Broad Institute for support on sequencing efforts. M.G. M.P. and E.J.A. designed this study. M.G. M.P. A.S. K.M. R.E.S. R.J.X. and E.J.A. founded the GMbC project under which field collections occurred. M.G. and M.P. managed field administrative work and performed the collection of data and samples. A.S. M.N. J.H. S.M.G. L.S. A. Froment, R.S.M. A. Fezeu, V.A.J. S.L. F.E.T. C.G. L.T.T.N. D.I. B.J.S. J.L. L.R. P.P.K. T.V. S.S. A.M. M.D.-R. Y.A.N. A.A.-N, A.D. Y.A.A. K.A.V. S.O.A. M.Y.A. L.R.R. A.P. and C.A.O. provided local support, and contributed to the field administrative work and the collection of data and samples. M.P. performed bacteria culturing, DNA extraction from isolates, and library preparation for whole-genome sequencing. M.P. performed DNA extraction from stool samples and library preparation for metagenomics sequencing. M.G. performed computational work and data analyses. M.G. and S.M.K. performed functional annotations on transferred genes. M.G. M.P. and E.J.A. analyzed the results. M.G. M.P. and E.J.A. wrote the manuscript, which was improved by K.M. and all other authors. R.J.X. is a consultant to Novartis and Nestle. E.J.A. is a co-founder and shareholder of Finch Therapeutics, a company that specializes in microbiome-targeted therapeutics. We worked to ensure gender balance in the recruitment of human subjects. We worked to ensure ethnic or other types of diversity in the recruitment of human subjects. We worked to ensure that the study questionnaires were prepared in an inclusive way. One or more of the authors of this paper self-identifies as an underrepresented ethnic minority in science. One or more of the authors of this paper self-identifies as a member of the LGBTQ+ community. The author list of this paper includes contributors from the location where the research was conducted who participated in the data collection, design, analysis, and/or interpretation of the work. Publisher Copyright: {\textcopyright} 2021 The Authors",
year = "2021",
month = apr,
day = "15",
doi = "10.1016/j.cell.2021.02.052",
language = "English (US)",
volume = "184",
pages = "2053--2067.e18",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "8",
}