The gut microbiome of bats in Minnesota

Microorganisms associated with the vertebrate gut can influence the behavior, immunity, and development of their hosts. The Chiropteran gut microbiome is poorly understood relative to other large mammalian orders; here we establish the baseline of taxonomic variation in the fecal microbiome of three North American bat species. We sequenced the 16S rRNA gene of the fecal pellet microbiome as a minimally invasive way of profiling the gut community of three bat species, Myotis lucifugus, M. septentrionalis, and Eptesicus fuscus. Pellets were collected from bats captured in mist-nets over three summers from 2015-2017 in the forested landscapes of Minnesota. In our analysis of 310 fecal samples, we investigated the influence of age class, species, sex, geographic location, and reproductive state on the diversity and taxonomic composition of the microbiome. Most identifiable bacteria present in all three bat species were members of the Proteobacteria, Actinobacteria, and Firmicutes phyla, though seven other phyla also contributed greater than 2% of the relative abundance in some samples. Gammaproteobacteria and Alphaproteobacteria together made up on average more than 60% of the Proteobacteria present in all samples. The microbiomes of M. lucifugus and M. septentrionalis showed similar levels of alpha diversity which was lower than the alpha diversity of E. fuscus. Pregnant and lactating female bats were host to more diverse fecal microbiomes than female bats that were not pregnant or lactating, perhaps in part due to the higher energetic demand of lactation and gestation, as well as changes in the immune system associated with pregnancy.