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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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.