Abstract
BackgroundGut 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 seven 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.ResultsWe find that bacterial diversity per individual and within-population phylogenetic dissimilarity 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 of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals.ConclusionsAcross the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.
Highlights
Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies
Gut bacteria compositions of individuals from the US are more similar to Botswanans than to Tanzanians Using principal coordinate analysis (PCoA), we find that the similarities in overall bacterial operational taxonomic units (OTUs) composition among individuals are strongly correlated with the abundances of three common bacterial families, Prevotellaceae, Bacteroidaceae, and Ruminococcaceae (Spearman’s rho correlation with PCo1 p values are 1.0 × 10−40, 1.0 × 10−18, and 3.3 × 10−12, respectively, and Spearman’s rho correlation with PCo2 p values are 5.0 × 10−7, 6.0 × 10−2, and 1.1 × 10−20, respectively) (Fig. 5, Additional file 1: Figure S12)
Bacterial compositional similarity increases with geographic proximity and inter-individual relatedness We investigated the differences in gut bacteria based on geographic distance and the degree of host genetic relatedness
Summary
Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. We use 16S rRNA sequencing to survey the gut bacteria of seven 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. The gut bacteria of urban-industrialized populations often have high abundances of Bacteroides, while the gut bacteria from traditional hunter-gatherer or agropastoral societies have higher abundances of Prevotella [22,23,24,25,26,27,28] Whether these trends are due to the types or quantities of foods consumed, cultural or social practices, geographic, genetic, or other factors is unclear. There have been several studies of microbiome diversity within African populations [22,23,24, 27, 29,30,31], the range of gut microbiome compositions among African populations with diverse subsistence practices remains largely unknown
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