基于宏基因组测序揭示青海地区田鼠肠道微生物多样性

Metagenomic sequencing reveals the diversity of intestinal microbiota in Neodon fuscus

摘要:

背景 青海田鼠仓鼠科田鼠属是中国青藏高原地区特有的物种，其作为病原微生物传播媒介的风险受到广泛关注。然而，目前针对青海地区野生田鼠研究较少。目的 解析不同海拔甘德(GD)地区和玉树(YS)地区青海田鼠微生物群落及其携带病原微生物组成。方法 通过宏基因组测序分析及基因组组装，揭示青海地区野生田鼠肠道微生物组成及其携带病原微生物特征。结果 通过对GD地区和YS地区野生田鼠宏基因组分析表明，在门水平上，不同海拔青海田鼠肠道中优势菌门均为芽孢杆菌门(Bacillota)、拟杆菌门(Bacteroidota)、放线菌门(Actinomycetota)、热脱硫杆菌门(Thermodesulfobacteriota)、螺旋体门(Spirochaetota)和假单胞菌门(Pseudomonadota)等；说明青海田鼠肠道微生物在门水平上具有高度保守性。在物种水平上，GD和YS地区青海田鼠肠道微生物优势物种及其微生物群落结构均存在显著差异，并且GD地区田鼠微生物多样性显著高于YS地区，表明青海田鼠肠道微生物组成受地域和环境因素的显著影响。通过宏基因组组装基因组(metagenome-assembled genomes, MAGs)，我们在田鼠肠道微生物中检测到大量未知微生物类群，其中包括克雷伯氏菌属(Klebsiella)、链球菌属(Streptococcus)、假单胞菌属(Pseudomonas)、葡萄球菌属(Staphylococcus)和巴斯德氏菌属(Pasteurella)等多种病原微生物。此外，通过进一步对田鼠上携带的潜在病毒和寄生虫分析发现，GD和YS地区青海田鼠均携带有鼠痘病毒(Ectromelia virus)及弓形虫(Toxoplasma gondii)、兔脑胞内原虫(Encephalitozoon cuniculi)、赫氏脑胞内原虫(Encephalitozoon hellem)、肠道脑胞内原虫(Encephalitozoon intestinalis)、罗姆勒脑胞内原虫(Encephalitozoon romaleae)等。通过KEGG代谢分析表明，青海田鼠肠道微生物代谢通路基因数量最多，其中“碳水化合物代谢”子类别占主导，反映了肠道微生物在田鼠代谢过程中的关键作用。结论 本研究揭示了青海地区不同海拔田鼠肠道微生物群落结构差异显著，并且均携带潜在病原菌。本研究为全面了解高寒地区青海田鼠微生物多样性及其携带病原菌的情况提供了基础数据，也为防控相关人畜共患病提供了科学依据。

Abstract:

Background Neodon fuscus, an endemic vole species of the Qinghai-Xizang Plateau in China, garners considerable interest due to its potential role as a vector for pathogens, while the research on wild vole populations in Qinghai remains limited.Objective To characterize the microbial community composition and identify potential pathogens carried by N. fuscus in Gandé (GD) and Yushu (YS) with different altitudes.Methods We employed metagenomic sequencing and genome assembly techniques to comprehensively analyze the intestinal microbiota and identify the pathogens present in wild N. fuscus.Results Metagenomic analysis of voles collected from GD and YS revealed that Bacillota, Bacteroidota, Actinomycetota, Thermodesulfobacteriota, Spirochaetota, and Pseudomonadota were dominant in the intestinal microbiota in both sampling regions, indicating the intestinal microbiota was highly conserved at the phylum level. However, significant differences in dominant species and overall community structure were observed between voles from GD and YS. Notably, the microbial diversity of GD voles was significantly higher than that of YS voles, suggesting that geographical and environmental factors exerted considerable influences on the intestinal microbiota composition of N. fuscus. Through metagenome-assembled genomes (MAGs), several potential pathogenic bacteria were identified in the intestinal microbiota, including Klebsiella spp., Streptococcus spp., Pseudomonas spp., Staphylococcus spp., and Pasteurella spp. Furthermore, Ectromelia virus, Toxoplasma gondii, Encephalitozoon cuniculi, Encephalitozoon hellem, Encephalitozoon intestinalis, and Encephalitozoon romaleae were detected in N. fuscus from both regions. KEGG analysis indicated that the intestinal microbiota of N. fuscus exhibited abundant metabolic pathway genes, with carbohydrate metabolism being the most prominent subcategory, highlighting the crucial role of the intestinal microbiota in vole metabolism.Conclusion This study demonstrates significant variations in the intestinal microbiota structure of N. fuscus at different altitudes and confirms the presence of potential pathogenic bacteria in all sampled individuals. These findings provide baseline data for comprehensively understanding the microbial diversity and carried pathogens in N. fuscus, thereby contributing valuable scientific evidence for the prevention and control of related zoonotic diseases.