Captivity Status and Climate Impact Gut Microbiome Composition and Function in Primates Through Diet

Abstract

Diet is a key determinant of gut microbiome diversity and composition in animals, yet predicting dietary patterns becomes challenging due to variable food sources. Captivity status largely determines food availability: captive animals are fed a controlled diet, whereas the wild animal diet is unpredictable and based on environmental availability. Climate, the long-term interaction between temperature and precipitation, can be a major determinant of food availability in the wild, and may serve as a useful proxy for dietary habits and variation. Thus, this study investigates the dynamics between climate and captivity in shaping the gut microbiome of Primates. Using McKenzie et al.'s 16S rRNA amplicon fecal sample dataset collected from mammals in zoos and sanctuaries globally, we compared gut microbial diversity, composition, and function across climate categories and captivity statuses. We found that wild Primate gut microbiomes differed significantly in both relative abundance and phylogenetic relatedness between climate groups, while captive Primates showed reduced climate-related differences. Climate and captivity also affected the number of phyla represented by indicator species, with tropical, temperate, and captive Primates showing indicator taxa from a narrower range of phyla. Functional predictions further revealed that wild Primates exhibited underrepresentation of digestion pathways in a climate-dependent manner. These findings suggest that both climate and captivity significantly shape gut microbial ecology in Primates, with implications for considering environmental factors in dietary management and health in captive care settings.