Elucidating the gut microbiomes of healthy South African individuals from rural and urban localities

Abstract

The diversity and functional potential of the gut bacterial community of healthy South African individuals are not well understood. This study investigated the gut microbiomes of two populations: individuals living in rural (n = 45) and urban (n = 50) areas using high-throughput 16S rRNA gene sequencing. The bacterial diversity (alpha diversity) was not significantly different between rural and urban populations (Welch test: p = 0.3; Shannon) and that the composition differed significantly between urban and rural cohorts (PERMANOVA: R2 = 0.03, p < 0.001, higher β-diversity). At the phylum level, both populations were dominated by Firmicutes, while Spirochete was uniquely associated with the rural population. Although 24 core bacterial genera were detected across the two distinct populations, the gut bacterial composition revealed signatures that was specific to the geographical location and dietary intake of the individuals. Analysis of the predicted metabolic pathways showed that urban population had carbohydrates, amino acids, lipids, and xenobiotics metabolism. The rural cohort was characterized by species richness and more interindividual homogeneity. In conclusion, the variability of gut bacterial communities within and between populations differed dietary habits based on lifestyle and geographic location.