African populations have adapted to a range of environments and foods as they spread through the continent, and their gut microbiomes (GMs) may have co-evolved with them. The GMs from sixty ethnically diverse Tanzanians practicing different subsistence strategies (Hadza hunter-gatherers, Burunge agriculturalists, Maasai pastoralists, recently-settled Sandawe hunter-gatherers) with urban American individuals were sequenced using the V1/V2 regions of 16s rRNA from fecal samples to interrogate potential covariates shaping GM composition including traditional diet, quantification of gut parasites, geography, nutritional and ethnographic surveys, and genetic data from an Illumina 5M Omni SNP Array.
IBS relatedness for 1,066 Africans, including microbiome-sequenced individuals, was calculated from SNP array data and visualized using Multi-Dimensional Scaling plots of genetic similarity, and showed that Hadza are genetically differentiated from other Tanzanian ethnic groups. Bacterial compositional analysis showing that Hadza have lower within-group diversity than other populations indicates that they have a strong within-group bacterial composition. The Sandawe had higher-within group diversity and similar bacterial composition in heatmap analyses to Burunge, which may relate to their recent settlement and adoption of agriculture. Principal-coordinate analysis of bacterial families revealed that Tanzanians have two predominant bacterial gradients associated with broad global gut enterotypes: A strong Prevotellaceae-Ruminococcaceae gradient and a weak Bacteroidales-Ruminococcaceae gradient. Bacteroidales is associated with diets high in protein and fats, whereas Prevotellaceae and Ruminococcaceae are associated with plant and fiber rich diets, which affirms expectations for populations eating rural, nonwestern foods. The Hadza are enriched in Treponema, which may assist with nutrient extraction from fibrous plants. Maasai show variation in Prevotella relative abundance and an enrichment of Bacteroidales, which may assist with digestion of dairy and meat. This represents one of the largest GM studies to date of Africans, including the first pastoralist GM results, and provides novel microbiome data from sparsely characterized African groups.