Determination of the gut microbiota composition of common noctule by bacteriological analysis and high-throughput sequencing of 16S rRNA

Bats (Chiroptera) are the second most diverse order of mammals after rodents, which ensures their key role in the functioning of ecosystems. The microbiota of bats, especially the bacterial one, is poorly studied, which does not allow an accurate assessment of the role of bats in global 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 V3-V4 16S rRNA gene. As a result, we found that microbial diversity determined using metagenomic sequencing was statistically significantly higher (p 0.001) compared to the bacteriological method. However, mass spectrometric identification of bacterial isolates made it possible to determine their species, while the sensitivity of the metagenomic sequencing protocol used is limited to reliable identification of bacteria to genus rank. Also, bacteria of the genera Enterococcus, Citrobacter, Enterobacter, Lactococcus, and Latilactobacillus were the most prevalent in the intestinal microbiota of the common noctule. Our study provides the first data on the composition of the cultivated and uncultivated microbiota of the rufous noctule, which is a fundamental step in the study of the microbiota of synanthropic bats.