Parasites and diet as main drivers of the Malagasy gut microbiome richness and function

Stanislas Mondot (1) , Philippe Poirier (2, 3) , Ahmed Abou-Bacar (4) , Valentin Greigert (4) , Julie Brunet (4) , Céline Nourrisson (2, 3) , Milijaona Randrianarivelojosia (5, 6) , Jean-Louis Razafindrakoto (7) , Eugene Morel (8) , Rivo Rakotomalala (7) , Marion Leclerc (1) , Karine Le Roux (1) , Céline Monot (1) , Ermanno Candolfi (4) , Patricia Lepage (1)

1 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
2 M2iSH - Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte
3 Laboratoire de Parasitologie et Mycologie [CHU Clermont-Ferrand]
4 IPPTS - Institut de Parasitologie et de Pathologie Tropicale
5 Université de Toliara
6 Institut Pasteur de Madagascar
7 CHU PZaga [Mahajanga, Madagascar]
8 CHU Mahavoky Atsimo [Mahajanga, Madagascar]

Abstract Interactions between the prokaryotic microbiome and eukaryotic parasites in the vertebrate gut may affect overall host health and disease. While intertropical areas exhibit a high rate of parasites carriers, such interactions are understudied in these populations. Our objectives were to (1) describe the gut microbiome of individuals living in Madagascar, (2) identify potential associations between bacterial taxa and parasites colonizing the digestive tract and (3) highlight main determinants of the gut microbiota composition in this developing country. Metadata (socioeconomic, diet, clinical) and fecal samples were collected from 219 volunteers from North-West Madagascar (Mahajanga). Fecal microbiome was assessed through 16S rRNA gene sequencing and metabolomics, and related to dietary habits and parasites carriage. We highlight important Malagasy gut microbiome peculiarities. Out of three detected enterotypes, only one is similar to that observed in Westernized countries ( Ruminococcus -driven). Functions associated with the two others ( Clostridium sensu stricto-driven and Escherichia/Shigella -driven) are mostly directed toward amino acids biosynthesis and degradation, respectively. Diet and protozoan carriage were the main drivers of microbiota composition. High protozoan carriage was associated with higher diversity, richness and microbial functionalities. The gut microbiome of Malagasy strongly differs from that of Westernized countries. Asymptomatic protozoan carriage and dietary habits are the external factors with the deepest impact on gut microbiome. Further studies are needed to understand whether gut microbial richness constitute a predilection niche for protozoans colonization, due to their gazing features, or whether the parasites themselves induce a higher bacterial richness.

Domains: Food and Nutrition; Parasitology; Health

Stanislas Mondot, Philippe Poirier, Ahmed Abou-Bacar, Valentin Greigert, Julie Brunet, et al.. Parasites and diet as main drivers of the Malagasy gut microbiome richness and function. Scientific Reports, 2021, 11 (1), pp.1-11. ⟨10.1038/s41598-021-96967-4⟩. ⟨hal-03364386⟩