I Like the Way You Eat It: the possible environmental drivers of Lemur (Indri indri) Gut Microbiome and Mycobiome

Research on gut microbiome may help with increasing our understanding of primate health with species’ ecology, evolution, and behavior. Microbiome-related information has the potential to clarify ecology issues, providing knowledge in support of wild primates’ conservation and their associated habitats. Indri (Indri indri) is the largest extant living lemur of Madagascar able to survive only in wild conditions. This species is classified as “critically endangered” by the IUCN Red List of Threatened Species, representing one of the world’s 25 most endangered primates. Indris diet is mainly folivorous, but these primates frequently and voluntarily engage in geophagy. Here, we investigated the possible linkages among geophagy, soil characteristics, and gut microbiome and mycobiome of indri (Indri indri). In these works, we explored the chemical composition of soil eaten by indri, which resulted rich in secondary oxide-hydroxides and clays, together with a high concentration of specific essential micronutrients. This could partially explain the role of the soil in detoxification and as a nutrient supply. Then, we explored the gut microbiome composition of 18 indris belonging to 5 different family groups. The most represented phyla were Proteobacteria 40.1 ± 9.5%, Bacteroidetes 28.7 ± 2.8%, and Synergistetes 16.7 ± 4.5%. Besides, we found that soil subject to geophagy and indris’ faeces shared about 8.9% of the fungal OTUs. Also, several genera (e.g. Fusarium, Aspergillus and Penicillium) were found in both geophagic soil and indri samples. In conclusion, the intimate connection between gut mycobiome and soil, demonstrated that fungal species may be involved in the digestion processes of leaves and could have a beneficial role in their health. Altogether, the data presented in our works, provide a baseline for outlining some possible drivers responsible for the gut microbiome and mycobiome diversity in indris, thus laying the foundations for developing further strategies involved in indris’ conservation.