Effects of naturalistic housing conditions on amphibian growth and microbiome in captivity

Animals in captivity are inherently separated from their natural environments, which both exposes them to new heterospecific organisms as well as reduces contact with naturally occurring predators, prey or microbiota. The microbes that live on and in animals are increasingly recognized as having important impacts on animal health, development and behavior. We raised post-metamorphic treefrogs in 1) naturalistic containers in groups, 2) regularly sterilized containers in groups, or 3) regularly sterilized containers but solitary. Froglets were raised for over eight months; in addition to monitoring growth and development, we collected fecal samples on three occasions, gut samples on two occasions, and skin swab samples once. We compared the diversity of microbial communities across sample types and over time. Froglets raised in group housing, either naturalistic or regularly cleaned, had the fastest growth and sexual differentiation, but naturalistic housing also improved survival. Alpha diversity of bacteria on the skin or in the gut did not vary with rearing conditions, whereas diversity in the gut increased over time. Alpha diversity of feces did vary with rearing treatment and changed over time. Bacterial community composition (beta diversity) varied most strongly with sample type, but also with rearing conditions and over time. In addition, bacterial communities of feces were highly correlated with those of guts, indicating that feces can serve as an accurate and non-invasive biomarker of the gut microbiome. Lastly, transferring frogs from regularly sterilized environments to naturalistic vivaria improved bacterial community diversity. Our study suggests that naturalistic housing improves the overall health and development of captive amphibians and that these improvements may occur by facilitating a more stable and diverse microbiome.