Local community shapes gut microbiome composition of the African primates

抄録

Gut microbiome is actively involved in multiple physiological processes of the animals, including accessing nutrients and maintaining health. Although knowledge on functional impact of gut microbiome has increased greatly in the past decades, our understanding of the mechanisms governing the ecology and evolution of gut microbiome remains obscure. The gut microbiome is potentially affected by factors relating to the hosts (e.g. digestive system, phylogeny) and the environment (e.g. season, habitat type, interactions with sympatric animals of the same and different species). Many previous studies have revealed that mammalian microbiome strongly correlates with host phylogenetic relationship and digestive system, indicating co-divergence of gut microbiome with the host specific characteristics. However, there has been debate about the influence of host phylogeny on gut microbiome comparing to the environmental factors. Since mammals must acquire gut microbes from the outside environment, differences in diet, local habitat and other environmental factors could substantially alter gut microbiome. One way to disentangle the effects of environmental factors on gut microbiome from the host-related factors is to compare gut microbiome of closely related species living sympatrically and allopatrically. Using 16S rRNA Illumina sequencing, we investigated the gut microbiome of 15 primate species living in Moukalaba-Doudou National Park, Gabon and Kibale National Park, Uganda. Utilizing matrix and topological comparisons, we assessed the relative role of host phylogeny, digestive system (colobus/non-colobus), substrate use (arboreal/ terrestrial) and sharing of habitats (geographic distance) in influencing microbiome composition of the nonhuman primates. In particular, weighted UniFrac was found correlated with host phylogeny, digestive system and geographic distance, whereas unweighted UniFrac was found unrelated with any of the factors tested. Overall, our result revealed that in addition to the host-related factors, habitat sharing also played a nonnegligible role in determining gut microbiome composition. This study contributes to a deeper understanding the underlying mechanism governing the ecology and evolution of gut microbiome.