Variation in rural African gut microbiomes is strongly shaped by parasitism and diet 1 2

17 The human gut microbiome is influenced by its host's nutrition and health status, and represents 18 an interesting adaptive phenotype under the influence of metabolic and immune constraints. 19 Previous studies contrasting rural populations in developing countries to urban industrialized 20 ones have shown that geography is an important factor associated with the gut microbiome; 21 however, studies have yet to disentangle the effects of factors such as climate, diet, host 22 genetics, hygiene and parasitism. Here, we focus on fine-scale comparisons of African rural 23 populations in order to (i) contrast the gut microbiomes of populations that inhabit similar 24 environments but have different traditional subsistence modes and (ii) evaluate the effect of 25 parasitism on microbiome composition and structure. We sampled rural Pygmy hunter-gatherers 26. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not. 2 as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon 27 and found that the presence of Entamoeba is strongly correlated with microbial composition and 28 diversity. Using a random forest classifier model, we showed that an individual's infection status 29 can be predicted with 79% accuracy based on his/her gut microbiome composition. We 30 identified multiple taxa that differ significantly in frequency between infected and uninfected 31 individuals, and found that alpha diversity is significantly higher in infected individuals, while 32 beta-diversity is reduced. Another factor associated with microbial composition in our data is 33 subsistence mode, notably with some taxa previously shown to differ between Hadza Eastern 34 African hunter-gatherers and Italians also discriminating Pygmy hunter-gatherers from 35 Cameroon from neighboring farming or fishing populations. In conclusion, our results stress the 36 importance of taking into account an individual's parasitism status in studies of the microbiome, 37 and highlight how sensitive the microbial ecosystem is to subtle changes in host nutrition. Our 38 fine-scale analysis allowed us to identify microbial features that are specific to hunter-gatherers 39 versus ones shared by all rural African populations, increasing our understanding of the 40 influence of subsistence mode and lifestyle on gut microbiome composition.