Variation in rural African gut microbiomes is strongly shaped by parasitism and diet

Elise R Morton , Joshua Lynch , Alain Froment , Sophie Lafosse , Evelyne Heyer , Molly Przeworski , Ran Blekhman , Laure Segurel
doi: http://dx.doi.org/10.1101/016949

The human gut microbiome is influenced by its host’s nutrition and health status, and represents an interesting adaptive phenotype under the influence of metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that geography is an important factor associated with the gut microbiome; however, studies have yet to disentangle the effects of factors such as climate, diet, host genetics, hygiene and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiomes of populations that inhabit similar environments but have different traditional subsistence modes and (ii) evaluate the effect of parasitism on microbiome composition and structure. We sampled rural Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon and found that the presence of Entamoeba is strongly correlated with microbial composition and diversity. Using a random forest classifier model, we show that an individual’s infection status can be predicted with 79% accuracy based on his/her gut microbiome composition. We identified multiple taxa that differ significantly in frequency between infected and uninfected individuals, and found that alpha diversity is significantly higher in infected individuals, while beta-diversity is reduced. Subsistence mode was another factor significantly associated with microbial composition, notably with some taxa previously shown to differ between Hadza East African hunter-gatherers and Italians also discriminating Pygmy hunter-gatherers from neighboring farming or fishing populations in Cameroon. In conclusion, these results provide evidence for a strong relationship between human gut parasites and the microbiome, and highlight how sensitive this microbial ecosystem is to subtle changes in host nutrition.