Composition of the Common Noctule (Nyctalus noctula) Gut Microbiota Determined by Bacteriological Analysis and High-Throughput 16S rRNA Gene Sequencing

Since bats are the second most diverse order of mammals after rodents, they play a key role in the functioning of ecosystems. The microbiota of bats, especially the bacterial one, is poorly studied, which hinders accurate assessment of the role of bats in microbial ecology. In this study, we determined the composition and diversity of the intestinal microbiota of the common noctule (Nyctalus noctula) in Rostov-on-Don using bacteriological analysis and metagenomic sequencing of the 16S rRNA gene V3–V4 region. Microbial diversity determined using metagenomic sequencing was found to be statistically significantly higher (p < 0.001) compared to that determined by the bacteriological method. However, mass spectral identification of bacterial isolates at the species level was possible, while the sensitivity of the metagenomic sequencing protocol used was limited to reliable identification at the genus level. Bacteria of the genera Enterococcus, Citrobacter, Enterobacter, Lactococcus, and Latilactobacillus were predominant in the intestinal microbiota of the common noctule. Our study provides the first data on the composition of the cultured and uncultured microbiota of the common noctule, which is a fundamental step in the study of the microbiota of synanthropic bats.