Gut microbiomes of the little free-tailed bat ( Mops pumilus ) show high prevalence of potential bacterial pathogens but limited responses to land cover

Land cover change is a threat to wildlife globally. It may also impact the gut microbiome harbored by wildlife, with implications for their health, conservation, and One Health more broadly. Bats are a diverse group of mammals that can be found in a range of habitats, with differing degrees of anthropogenic disturbance. Here, we analyzed the V3–V4 region of 16S rRNA from fecal samples from 109 individual little free-tail bats ( Mops pumilus ) in northeastern Eswatini. We aimed to describe the species composition, richness, and community structure of the gut microbiome and identify and potentially pathogenic bacteria that M. pumilus might harbor. We then measured the effects of host characteristics, land cover composition and configuration on the species richness, phylogenetic diversity, prevalence of potentially pathogenic genera, and community composition of the gut microbiome. We found high levels of individual variability and no significant differences in species richness, phylogenetic diversity, or community composition based on sex, age, or reproductive condition. We detected five potentially pathogenic bacterial genera, four at high prevalence: Mycoplasma (88 %), Rickettsia (36 %), Salmonella (34 %), Bartonella (23 %), and Campylobacter (4 %). The co-occurrence of two to five of these genera within an individual was common. Using a subsample of 83 individuals captured at 17 distinct roosts, we found a small influence of fine-scale land cover on the community composition but none on the richness or phylogenetic diversity of the gut microbiome. We did not find associations between land cover composition, configuration, or host characteristics with the prevalence of potentially pathogenic genera. Our results demonstrate the complex influences on bat gut microbiome, while the high prevalence of potential pathogens shows the importance of continued research and surveillance.