The effects of captivity on the mammalian gut microbiome

Recent studies are increasingly noting the effect of captivity or the built environment on the microbiome of humans and other animals. As symbiotic microbes are essential to many aspects of biological functions (e.g., digestive and immune functions), it is important to understand how lifestyle differences can impact the microbiome, and consequently the health of hosts. Animals living in captivity experience a range of changes that may influence the gut microbiome, such as diet changes, treatments, and reduced contact with other individuals, species and variable environmental substrates that act as sources of bacterial diversity. Thus far, initial results from previous studies point to a pattern of decreased bacterial diversity in captive animals, however, these studies are relatively limited in the scope of species that have been examined. We present a novel dataset that includes paired wild and captive samples from 41 mammal species to investigate generalizable patterns of the effects captivity has on the microbiome. In comparing the wild to the captive condition, our results indicate that alpha diversity of the gut bacteria remains consistent in some mammalian hosts (bovids, giraffes, anteaters, and aardvarks), declines in the captive condition in some hosts (canids, primates, and equids), and increases in the captive condition in one host taxon (rhinoceros). Differences in gut bacterial beta diversity between the captive and wild state were observed for most of the mammal taxa, except the even-toed ungulates (bovids and giraffes). Additionally, beta diversity variation was also strongly influenced by host taxonomic group, diet type, and gut fermentation physiology. Bacterial taxa that responded most strongly to captivity included members of the Firmicutes and Bacteroidetes. Overall, the patterns that we observe will inform a range of disciplines from veterinary practice to captive breeding efforts for biological conservation. Furthermore, bacterial taxa that persist in the captive state provide unique insight into symbiotic relationships with the host.