16S microbiomes of Belizean vampire bats

The gut microbiota of animals is increasingly appreciated for their direct influence over host nutrition, immunity, and fitness, but the impacts of landscape-scale disturbance on animal microbiomes is still poorly understood. Pathological changes in microbiome composition and function, known as dysbiosis, can arise due to changes in diet and other environmental attributes and may compromise immunity and fitness in wild hosts. Here, we analyzed long-term diet, gut microbiome composition, and innate immune function of free-ranging vampire bats in two sites, one highly fragmented and one continuous, in Belize. We found that vampire bats living in a forest fragment had more homogenous diets indicative of feeding on livestock and showed shifts in microbiome composition compared with vampires from a protected forest site. The gut microbiome alpha and beta diversity were reduced in the bats living in the fragment compared to the protected forest. The relative abundance of core microbiome members was associated with innate immune function, suggesting that future research should consider the impacts of shifts in microbiome structure on wildlife immunity. Because the presence of livestock rearing results in resource provisioning to vampire bats, we suggest that subsequent homogenization of diet and habitat loss may lead to further disruption to the microbiome that may have downstream impacts on host immunity and cross-species transmission.