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. Genetic variation between human populations is typically viewed as differences in the allele frequencies of shared Homo sapiens genes. Another source of genetic and metabolic diversity resides in differences in the representation of the millions of genes and myriad gene functions within our gut microbial communities 1-3 . Sampling a broad population of healthy humans representing different ages and cultural traditions offers an opportunity to discover how our gut microbiomes evolve within a lifespan, vary between populations, and respond to our changing lifestyles