Data from: The excreted microbiota of bats: evidence of niche specialization based on multiple body habitats

Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira, Rickettsia, Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.与动物共生的微生物群构成复杂群落，对宿主发挥关键功能，其中包括调控宿主对病原体感染的易感性。尽管学界对蝙蝠作为人畜共患病病原体储存宿主的关注度日益提升，但目前对其微生物群的研究记载仍较为匮乏，尤其是尿液、唾液这类可能参与病原体传播的样本类型。本研究采用低生物量个体样本，对食虫蝙蝠排泄的细菌群落组成与结构进行了分析，重点关注唾液、尿液和粪便三类身体生境。研究发现，细菌群落在不同身体生境间存在显著组成差异，多数系统型（phylotype）均具有生境特异性，表明存在生态位特化现象。本研究结果显示，尿液定植的细菌群落多样性高于唾液与粪便；同时在所有三类身体生境中均检测到潜在人畜共患病细菌，包括钩端螺旋体属（Leptospira）、立克次体属（Rickettsia）、巴尔通体属（Bartonella）以及考克斯体属（Coxiella）。本研究强调，除粪便这类传统研究常用的肠道相关样本外，尿液与唾液也因自身多样的微生物群以及携带致病菌传播的潜在风险而具有研究价值。本研究结果为未来探究蝙蝠微生物群与感染动态之间的相互作用提供了重要的基准参考。