Documenting the natural diversity of eukaryotic organisms in the nonhuman primate (NHP) gut is important for understanding the evolution of the mammalian gut microbiome, its role in digestion, health and disease, and the consequences of anthropogenic change on primate biology and conservation. 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 fragment metabarcoding approach to assess the eukaryotic assemblage of 62 individuals representing 16 NHP species. We find that cercopithecoids, and especially the cercopithecines, have substantially higher alpha diversity than other NHP groups. Gut-associated protists and nematodes are widespread among NHPs, consistent with their ancient association with NHP hosts. However, we do not find a consistent signal of phylosymbiosis or host-species specificity. Rather, gut eukaryotes are only weakly structured by primate phylogeny with minimal signal from diet, in contrast to previous reports of NHP gut bacteria. The results of this study indicate that gut-associated eukaryotes offer different information than gut-associated bacteria and add to our understanding of the structure of the gut microbiome.
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Acknowledgements The authors would like to thank Klára Pet-rželková (Czech Academy of Sciences), the Ethiopian Wildlife Conservation Authority, Steven R. Leigh, Fidy Rasambainarivo, and Alexandre (Madagascar National Parks), Professor Lydia Rabetafika (University of Antananarivo), and MICET for facilitating this research and access to samples. Collection of data presented herein were supported by funds awarded by US NSF BCS-0922465, NSF BCS-0935349, and NIH grant TW009237 as part of the joint NIH-NSF Ecology of Infectious Disease program and the UK Economic Social Research Council (ES/J011266/1), Primate Conservation Inc., the University of Texas at Austin, the American Association of Physical Anthropologists, Hunter College of City University of New York, Rowe-Wright Primate Fund, the Leaky Foundation, the University of Arizona, the University of Colorado-Boulder, International Primatological Society, the Margot Marsh Biodiversity Foundation, and St. Louis Zoological Park FRC 06-1. A Banting Postdoctoral Fellowship supported FM in this work. The Malagasy government and CAFF/CORE authorized RL’s research in country. The authors would also like to acknowledge Madagascar National Parks, who gave permission for a portion of the research (Permit 056/13/MEF/ SG/DGF/DCB.SAP/SCB), and the University of Arizona IACUC approved protocol 13-470. A Human Frontier in Science Program grant to LWP (RGY0078/2015) supported generation of sequence data, analysis, and interpretation.
© 2019, The Author(s).