Distinct Microbiotas Are Present in Urban and Rural Native South Africans, and in African Americans

Recent advances in our ability to define the composition and diversity of the human microbiome has led to an increasing appreciation of its importance in the maintenance of health and suppression of disease. A variety of 16S ribosomal RNA based studies demonstrated that each individual has a unique microbiota composition, with higher similarity within monozygotic twin pairs than random individuals. Moreover, it is apparent that the microbiota composition can be drastically different between human populations that are living at different continents. However, it is not clear whether this is due to genetic differences or diet, lifestyle and environment. Therefore, the aim of the current study was to compare and contrast the microbiota between African Americans (AA), native Africans who live in a more Western semi-urban environment (NA), and rural Africans who consume a more traditional African diet (RA). Energy distribution and dietary composition was estimated to be 49% carbohydrate (CHO), 34% fat and 15% protein among AA; 72% CHO, 16% fat and 12% protein among NA; and 65% CHO, 21% fat and 12% protein among RA. Fecal samples were collected from 12 healthy middle-aged volunteers from each of these groups and frozen immediately until analysis. DNA was isolated from these samples and subsequently used for microbiota profiling using the Human Intestinal Tract Chip (HITChip), a 16S rRNA-based phylogenetic microarray covering over 1000 of the currently known bacterial species from the intestine. Microbiota profiling demonstrated that the microbiota composition is significantly different between all three groups. Although AA and NA have high Bacteroidetes populations (.40%), this phylum is dominated by Prevotella in NA (22%) and Bacteroides in AA (28%). The genus Prevotella has been associated to people consuming high carbohydrate diets, while Bacteroides has been associated to diets rich in animal fat. Remarkably, the Bacteroidetes phylum was significantly lower in RA (~14%) compared to NA and AA. In contrast, Oscillospira and related bacteria were dominantly present in RA (16%) compared to AA (2%) and NA (7%). The function of the genus Oscillospira has not been described in humans, but is in ruminants it has been associated to fresh grass diets. Functional genes for acetate and butyrate production were significantly higher in RA compared to NA and NA compared to AA. Similar findings were observed for hydrogen consumers (methanogens and sulfatereducing bacteria), except that methanogens were more abundant in NA. Our findings clearly describe that microbiota composition differs drastically between genetically similar human populations with different lifestyles, even when they live on the same continent