Bat guano is a rich source of ecological data for bat biologists alike. In this study, we profiled the gut microbiomes of three species of bats on an individual level. While it has been hypothesized that bat's do not possess functional gut microbiomes, we found the composition to be consistent with that of an average mammalian small intestine. Reflecting the short and simple digestive tract, the gut community of all species were dominated by microbes that subsist on mucins and simple sugars. We used differential analysis and clustering algorithms to determine that lactic acid bacteria were proportionaly more abundant than most other groups, and that Little Brown Bats (Myotis lucifugus) tended to host more intracellular pathogens than Big Brown Bats (Eptesicus fuscus) and Northern Long-eared Bats (M. septentrionalis).