Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana. Bacteria

Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here we use 16S rRNA sequencing to survey the gut bacteria of six previously uncharacterized non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region. We find that bacterial diversity per individual and phylogenetic dissimilarity within-population differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half the Bantu-speaking agropastoralists from Botswana have gut bacteria indistinguishable from the Philadelphian cohort. Based on imputed metagenomic content, U.S. samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Bacterial phylogenetic similarity between individuals increases with both geographic proximity and closer genetic relatedness. When weighted by bacterial abundance, phylogenetic similarity between individuals only has a significant dependence on geographic proximity.