Mobile genes in the human microbiome are structured from global to individual scales
Open accessAbstract
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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The lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be partly explained by higher microbiome richness, possibly due to increased acquisition from other environmental or family sources.
“suggesting the lower fraction of microbes shared in non-westernized microbiomes is not due to technical artifacts and may be in part explained by a much higher microbiome richness, possibly due to increased acquisition of microbiome members from other environmental or family sources.42,43”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [43]
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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
- Venue
- Nature
- Published
- 2016-07-13
- Volume
- 535
- Issue
- 7612
- Pages
- 435-439
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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 · 2012: 1
- FWCI
- 13.34
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-03-22)
- Open access
- green
- www.ncbi.nlm.nih.gov
- 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
- Physical Sciences › Environmental Science › Ecology › 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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