Parasitism and diet as main drivers of the Malagasy gut microbiome specificity and richness

Considering the higher rate of parasitic carriers in intertropical area, we focused our research study on volunteers from Madagascar Island and previously described a wide panel of intestinal parasites Our objectives were to i) describe the gut microbiota composition of individuals living in Madagascar Island, ii) identify potential associations between gut bacterial taxa and parasites colonizing the digestive tract and iii) highlight main determinants of the gut microbiota composition in this developing country. Our study included 219 individuals issued from Mahajanga (North-West Madagascar) and its rural neighborhood. Fecal samples were collected from either healthy volunteers or patients hospitalized in the gastroenterology department of the university hospital PZaGa of Mahajanga. FecalFaecal microbiota composition was assessed through 16S rRNA rDNA gene sequencing and compared to dietary habits and parasites carriage. The Malagasy gut microbiomes are distributed across three enterotypes. The ruminococcus driven enterotype 1 (Ent1) harboured common features with the one identified of individuals issued from westernized countries. The two remaining were mainly driven by Clostridium sensu stricto (Ent2) and Escherichia/Shigella (Ent3) genera. While Ent1 and Ent2 were mostly enriched in functions related to amino acids biosynthesis, Ent3 was mostly dedicated to their degradation. Diet and protozoan carriage were the main drivers of microbiota composition. High protozoan carriage was associated with higher diversity, richness and microbial functionalities. People living on Madagascar Island harbours three different enterotypes characterized with marked range of diversity, richness and microbial functionalities. Asymptomatic protozoan carriage and dietary habits are the two main external factors that have the deepest impact on their gut microbiota composition. Further studies are needed to understand whether gut microbial richness constitute a predilection niche for protozoans colonization, probably due to their gazing features, or whether the parasites themselves induce a higher bacterial richness.