Cultivable Gut Microbiota in Synanthropic Bats: Shifts of Its Composition and Diversity Associated with Hibernation

Simple Summary Bats play a significant role in public health and animal welfare as these animals are hosts for emerging pathogens. Urbanization has resulted in the acquisition of these animals' synanthropic behavior. Urban infrastructure suits bats as their hibernacula more than their natural sites due to the absence of predators, relatively high temperatures, and the close location of potential roost sites. However, the microbiota of hibernating bats is little studied, leaving some degree of uncertainty on how the abundance and diversity of gut bacteria are affected by low body temperature and food deprivation. In this study, we investigated the composition of cultivable gut microbiota before, during, and after hibernation of bats in the rehabilitation center. As a result, we observed a high abundance of opportunistic pathogens in the gut microbiota of active bats that had just arrived at the rehabilitation center that they had probably received from the environment. During the hibernation of bats, the abundance of these bacteria was significantly decreased, while the abundance of some other commensals was increased with an overall decrease in microbial diversity. This study shows how hibernation affects bat gut microbiota, pointing to the necessity of investigation of the bat-microbiota relationship during hibernation to prevent emerging diseases.Abstract The role of bats in the global microbial ecology no doubt is significant due to their unique immune responses, ability to fly, and long lifespan, all contributing to pathogen spread. Some of these animals hibernate during winter, which results in the altering of their physiology. However, gut microbiota shifts during hibernation is little studied. In this research, we studied cultivable gut microbiota composition and diversity of Nyctalus noctula before, during, and after hibernation in a bat rehabilitation center. Gut microorganisms were isolated on a broad spectrum of culture media, counted, and identified with mass spectrometry. Linear modeling was used to investigate associations between microorganism abundance and N. noctula physiological status, and alpha- and beta-diversity indexes were used to explore diversity changes. As a result, most notable changes were observed in Serratia liquefaciens, Hafnia alvei, Staphylococcus sciuri, and Staphylococcus xylosus, which were significantly more highly abundant in hibernating bats, while Citrobacter freundii, Klebsiella oxytoca, Providencia rettgeri, Citrobacter braakii, and Pedicoccus pentosaceus were more abundant in active bats before hibernation. The alpha-diversity was the lowest in hibernating bats, while the beta-diversity differed significantly among all studied periods. Overall, this study shows that hibernation contributes to changes in bat cultivable gut microbiota composition and diversity.