Popov Ilia V, Manakhov Andrey D, Gorobets Vladislav E, Diakova Kristina B, Lukbanova Ekaterina A, Malinovkin Aleksey V, Venema Koen, Ermakov Alexey M, Popov Igor V
Faculty "Bioengineering and Veterinary Medicine", Don State Technical University, 344000 Rostov-on-Don, Russia.
Division of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius, Russia.
Int J Mol Sci. 2025 Jun 20;26(13):5941. doi: 10.3390/ijms26135941.
Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, and , at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to , were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.
蝙蝠是多种微生物群落的关键生态宿主，这些群落包括新出现的病毒和抗生素抗性基因。本研究利用全宏基因组鸟枪法测序，对俄罗斯南部罗斯托夫蝙蝠康复中心的两种食虫蝙蝠物种—— 和 的肠道微生物群进行了调查。我们分析了分类组成、功能途径、抗生素抗性基因和毒力因子。浓核病毒，尤其是那些与 密切相关的浓核病毒，是鉴定出的最主要病毒序列。宏基因组组装的浓核病毒基因组显示出与结构变异的高度序列相似性，并在系统发育上与来自黄粉虫和鸟类的病毒聚类，这既反映了饮食来源，也反映了脊椎动物感染潜力。功能分析揭示了与细胞壁生物合成、能量代谢和生物膜形成相关的微生物途径。共鉴定出510个抗生素抗性基因，代表142种独特类型，主要是外排泵和β-内酰胺酶。此外，还检测到870个毒力因子基因，所有样本中都有一组保守的铁获取系统和应激反应调节因子。这些发现突出了与蝙蝠相关的微生物群和病毒群落的生态复杂性，并表明与人类共生的蝙蝠可能在城市环境中促进昆虫相关病毒的传播和抗菌抗性。
