METAGENOMIC INVESTIGATION OF INSECTIVOROUS SYNANTHROPIC BATS INTESTINAL MICROBIOTA

Bats serve as important ecological reservoirs for diverse microbial communities, including viruses with zoonotic potential and antibiotic-resistance genes. This study presents a metagenomic analysis of the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, collected from the Rostov Bat Rehabilitation Center in Southern Russia. Using whole metagenome shotgun sequencing, we investigated the taxonomic composition, functional profiles, and resistome features of the bat gut microbiota. Taxonomic profiling revealed an unexpectedly high abundance of densoviruses, particularly sequences closely related to Parus major densovirus, across multiple samples. Metagenome-assembled densovirus genomes exhibited high genomic similarity but also structural variations, including gene inversions and duplications. Phylogenomic analysis showed these sequences formed a distinct clade with densoviruses previously found in mealworms, suggesting a dietary origin, and with strains isolated from birds and shown to infect vertebrate cells, raising the possibility of bats serving as potential hosts. Functional annotation revealed microbial pathways involved in cell wall biosynthesis, energy metabolism, and biofilm formation. Antibiotic resistance screening identified numerous resistance genes, including efflux pumps and beta-lactamases, while virulence factor analysis revealed conserved iron acquisition and stress response genes across samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes, suggesting that synanthropic bats may contribute not only to the circulation but also to the emergence of insect-targeting viruses, antimicrobial resistance, and potentially novel viral interactions within urban environments that warrant further investigation.