Cited by 295Gut microbiota and healthBacteriophages and microbial interactionsGenomics and Phylogenetic Studies

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Mobile genes in the human microbiome are structured from global to individual scales

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Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., Birren, B. W., Xavier, R. J., Blainey, P. C., Singh, A. K., Gevers, D., Alm, E. J.·2016·Nature

DOI 10.1038/nature18927PMC PMC4983458

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Abstract

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

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Authors: Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili, W., Tamminen, M., Smillie, C. S., Wortman, J. R., Birren, B. W., Xavier, R. J., Blainey, P. C., Singh, A. K., Gevers, D., & Alm, E. J.
Affiliations: Broad Institute (US)
Sandia National Laboratories California (US)
Wildlife Conservation Society Fiji (FJ)
Edith Cowan University (AU)
University of Helsinki (FI)
Massachusetts Institute of Technology (US)
Corresponding author: Alm, E. J.
ORCID: Brito, I. L.
Yilmaz, S.
Huang, K.
Jupiter, S. D.
Jenkins, A. P.
Tamminen, M.
Smillie, C. S.
Wortman, J. R.
Birren, B. W.
Xavier, R. J.
Blainey, P. C.
Singh, A. K.
Gevers, D.
Alm, E. J.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-07-13
Volume: 535
Issue: 7612
Pages: 435-439
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature18927
PMC: PMC4983458
OpenAlex: W2464096417
Cited by: 288
References: 56
Citations by year: 2026: 15 · 2025: 28 · 2024: 33 · 2023: 32 · 2022: 29 · 2021: 38 · 2020: 35 · 2019: 31 · 2018: 22 · 2017: 21 · 2016: 3
FWCI: 13.34
Type: journal article
Language: en
Update notices: erratum (2017-03-22)
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
DORA Eawag (Swiss Federal Institute of Aquatic Science and Technology (Eawag)) (submittedVersion, other-oa)
Edith Cowan University Research Online (Edith Cowan University) (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
PMC
Funders: U.S. Department of Energy
Wildlife Conservation Society
Broad Institute (U54HG003067)
Fiji National University
Earth Institute, Columbia University
Office of Science
National Human Genome Research Institute (U54HG003067)
National Institute of General Medical Sciences (T32GM087237)
National Institute of Diabetes and Digestive and Kidney Diseases (P30DK043351)
National Institute of Dental and Craniofacial Research (R01DE020891)
Biological and Environmental Research
Sandia National Laboratories
Lawrence Berkeley National Laboratory
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: human microbiome, horizontal gene transfer, mobile genetic elements, population structure, North American populations, dietary differences, recombination, single-cell genomics, metagenomics, environmental selection
MeSH terms: Bacteriophages, Diet, DNA Transposable Elements, Fiji, Gene Pool, Humans, North America, Plasmids, Recombination, Genetic, Selection, Genetic, Genetic Variation, Cohort Studies, Gene Transfer, Horizontal, Metagenomics, Single-Cell Analysis, Gene-Environment Interaction, Microbiota

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