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

Mobile genes, which can be transferred between bacterial species in the microbiome to impart properties such as antibiotic resistance, are reflective of human activity and local diets. Recent work has underscored the importance of the microbiome in human health, and has largely attributed difference...

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Bibliographic Details
Published in:Nature (London) Vol. 535; no. 7612; pp. 435 - 439
Main 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.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 21.07.2016
Nature Publishing Group
Subjects:
45
631/114/2785
631/326/2565/2134
631/326/2565/2142
631/326/325/1506
Antibiotics
Bacteria
Bacteriophages - genetics
Cohort Studies
Diet
DNA Transposable Elements - genetics
Drug resistance
Fiji
Gene Pool
Gene Transfer, Horizontal - genetics
Gene-Environment Interaction
Genes
Genetic research
Genetic Variation - genetics
Genomes
Genomics
Human population genetics
Human population structure
Human populations
Humanities and Social Sciences
Humans
letter
Metagenomics
Microbiota (Symbiotic organisms)
Microbiota - genetics
multidisciplinary
Multivariate analysis
North America
Plasmids - genetics
Population structure
Recombination, Genetic - genetics
Science
Selection, Genetic - genetics
Single-Cell Analysis
Studies
Transposons
North America
Fiji
ISSN:0028-0836, 1476-4687
Online Access:Get full text
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Summary:Mobile genes, which can be transferred between bacterial species in the microbiome to impart properties such as antibiotic resistance, are reflective of human activity and local diets. 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 1 , 2 , 3 , 4 , 5 . 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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ISSN:0028-0836
1476-4687
DOI:10.1038/nature18927