The gut microbiome of primates is known to be influenced by both host genetic background and subsistence strategy. However, these inferences have been made mainly based on adaptations in bacterial composition - the bacteriome and have commonly overlooked the fungal fraction - the mycobiome. To further understand the factors that shape the gut mycobiome of primates and mycobiome-bacteriome interactions, we sequenced 16 S rRNA and ITS2 markers in fecal samples of four different nonhuman primate species and three human groups under different subsistence patterns (n = 149). The results show that gut mycobiome composition in primates is still largely unknown but highly plastic and weakly structured by primate phylogeny, compared with the bacteriome. We find significant gut mycobiome overlap between captive apes and human populations living under industrialized subsistence contexts; this is in contrast with contemporary hunter-gatherers and agriculturalists, who share more mycobiome traits with diverse wild-ranging nonhuman primates. In addition, mycobiome-bacteriome interactions were specific to each population, revealing that individual, lifestyle and intrinsic ecological factors affect structural correspondence, number, and kind of interactions between gut bacteria and fungi in primates. Our findings indicate a dominant effect of ecological niche, environmental factors, and diet over the phylogenetic background of the host, in shaping gut mycobiome composition and mycobiome-bacteriome interactions in primates.

Anicoon Vétérinaires Ploemeur France

Bulindi Chimpanzee and Community Project Hoima Uganda

Callitrichid Research Center at the University of Nebraska at Omaha Omaha NE USA

Department of Animal Science University of Minnesota St Paul MN USA

Department of Anthropology Hunter College of the City University of New York 695 Park Avenue New York NY USA

Department of Anthropology Purdue University West Lafayette IN USA

Department of Biology University of Nebraska at Omaha Omaha NE USA

Department of Food Science and Nutrition University of Minnesota St Paul MN USA

Department of Food Science and Technology University of Nebraska Lincoln Lincoln NE USA

Department of Gastroenterology Inflammatory Bowel and Immunology Research Institute Cedars Sinai Medical Center Los Angeles CA USA

Department of Social Sciences Faculty of Humanities and Social Sciences Oxford Brookes University Oxford UK

Institute of Parasitology Biology Centre Czech Academy of Sciences Ceske Budejovice Brno Czech Republic

Institute of Vertebrate Biology Czech Academy of Sciences Brno Czech Republic

New York Consortium in Evolutionary Primatology New York NY USA

Prague Zoo Prague Czech Republic

Primate Microbiome Project University of Nebraska Lincoln Lincoln NE USA

WWF Central African Republic Bayanga Central African Republic

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