Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes

Host-associated microbiomes are influenced by evolutionary history and proximate factors such as diet and environment. Zoos house animals in relatively standardized and manipulatable environments, making zoo populations valuable for studying microbiomes. Using five closely related primate species housed under nearly identical environmental conditions, we investigated gut microbiome variation regarding (a) congruence between host evolutionary history and gut bacterial composition (i.e., phylosymbiosis), (b) a longitudinal reduction in dietary sugar intake, and (c) ingestion of bacteria from dietary sources. We found that the primate gut microbiomes were species-specific and showed phylosymbiosis. When animals were fed a more wild-type diet, which reduced sugar and increased fiber intake, we found host-specific changes in the relative abundance of taxonomically distinct microbes (Phascolarctobacterium, Megasphaera, and Sharpea). Yet, these bacterial genera share similar functional potential (fiber degradation), indicating that species-specific bacterial communities may fulfill similar functions. Although all individuals received the same diet, the diet-associated bacteria in primate gut microbiomes were distinct among species, suggesting a species-specific mechanism that selects for unique dietary microbes to persist in animal guts. Our findings show that host evolutionary history and diet shape primate microbiomes in captivity and demonstrate the potential of microbiome research to inform holistic animal care and conservation.