Abstract

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

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Data deposits

DNA sequences have been deposited in MG-RAST (http://metagenomics.anl.gov/) under accession numbers ‘qiime:850’ for Illumina V4 16S rRNA data sets, and ‘qiime:621’ for fecal microbiome shotgun sequencing data sets.

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Acknowledgements

We thank S. Wagoner and J. Manchester for superb technical assistance, plus B. Muegge, A. Grimm, A. Hsiao, N. Griffin and P. Tarr for suggestions, and M. Ndao, T. Tinnin and R. Mkakosya for patient recruitment and/or technical assistance. This work was supported in part by grants from the National Institutes of Health (DK078669, T32-HD049338), St. Louis Children’s Discovery Institute (MD112009-201), the Howard Hughes Medical Institute, the Crohn’s and Colitis Foundation of America, and the Bill and Melinda Gates Foundation. Parts of this work used the Janus supercomputer, which is supported by National Science Foundation grant CNS-0821794, the University of Colorado, Boulder, the University of Colorado, Denver, and the National Center for Atmospheric Research.

Author information

Affiliations

  1. Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, Missouri 63108, USA

    • Tanya Yatsunenko
    • , Federico E. Rey
    •  & Jeffrey I. Gordon
  2. Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri 63110, USA

    • Mark J. Manary
    • , Indi Trehan
    •  & Barbara Warner
  3. Department of Community Health, University of Malawi College of Medicine, Blantyre, Malawi

    • Mark J. Manary
  4. Department of Paediatrics and Child Health, University of Malawi College of Medicine, Blantyre, Malawi

    • Indi Trehan
  5. Department of Biology, University of Puerto Rico - Rio Piedras, Puerto Rico 00931-3360

    • Maria Gloria Dominguez-Bello
  6. Venezuelan Institute of Scientific Research (IVIC), Carretera Panamericana, Km 11, Altos de Pipe, Venezuela

    • Monica Contreras
  7. Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Amazonas, Venezuela

    • Magda Magris
    •  & Glida Hidalgo
  8. Division of Gastroenterology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA

    • Robert N. Baldassano
  9. Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri 63110, USA

    • Andrey P. Anokhin
    •  & Andrew C. Heath
  10. Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309, USA

    • Jens Reeder
    • , Justin Kuczynski
    • , Catherine A. Lozupone
    • , Christian Lauber
    • , Jose Carlos Clemente
    • , Dan Knights
    •  & Rob Knight
  11. Department of Computer Science, Northern Arizona University, Flagstaff, Arizona 86001, USA

    • J. Gregory Caporaso
  12. Howard Hughes Medical Institute, University of Colorado, Boulder 80309, USA

    • Rob Knight

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Contributions

T.Y., R.K. and J.I.G. designed the experiments, M.J.M., I.T., M.G.D.-B., M.C., M.M., G.H., A.C.H., A.P.A., R.K., R.N.B., C.A.L., C.L. and B.W. participated in patient recruitment, T.Y. generated the data, T.Y., F.E.R., J.R., J.K., J.G.C., J.C.C., D.K., R.K. and J.I.G. analysed the results, T.Y., R.K. and J.I.G. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jeffrey I. Gordon.

Supplementary information

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DOI

https://doi.org/10.1038/nature11053

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