SRA

Documenting the natural diversity of eukaryotic organisms in the non-human primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in health and disease, and the consequences of anthropogenic change and increasing human encroachment into NHP habitats. Despite the ecological significance of gut-associated eukaryotes, little is known about the factors that influence their assembly and diversity in mammals. In this study, we used an 18S rRNA gene amplicon approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher diversity than other NHPs. Common gut eukaryotes such as nematodes and Entamoeba are widespread among NHPs and consistent with their association with NHP hosts over long evolutionary time scales. However, we did not detect a consistent signal of co-diversification or host-species specificity. Instead, gut eukaryotes are weakly structured by primate phylogeny and no detectable patterns by diet are observed, in contrast to previous reports of NHP gut bacteria. The results of this study affirm the importance of gut-associated eukaryotes in understanding mechanisms that structure the gut microbiome.