摘要
      肠道微生物群涉及庞大而复杂的微生物群落，是传染病控制的重要组成部分。在中国，很少有关于野生土拨鼠肠道微生物群多样性的研究报告。为了获得野生土拨鼠肠道微生物群的全部细节，包括细菌、真菌、病毒和古菌，我们对中国内蒙古呼伦贝尔草原五个采样点粪便的宏基因组进行了测序。我们创建了一个细菌、真菌、病毒和古菌基因组的综合数据库，并将宏基因组序列（根据土拨鼠粪便样本确定）与数据库进行比对。我们描绘了土拨鼠详细而独特的肠道微生物群结构。共发现5891种细菌、233种病毒、236种真菌和217种古菌。优势细菌门为厚壁菌门、变形菌门、拟杆菌门和放线菌门。病毒科有Myoviride、Siphoviridae、Phycodnaviride、Herpesviridae和Podoviridae。优势真菌门为子囊菌门、担子菌门和芽孢霉门。占优势的古菌有生物细菌、大孔菌、纳米古菌和微细菌。此外，肠道微生物群受到宿主物种和环境的影响，环境是最重要的因素。微生物群中有36989个糖苷水解酶基因，其中365个基因与编码β-葡萄糖苷酶、纤维素酶和纤维素β-1,4-纤维糖苷酶的基因同源。此外，抗生素抗性基因如macB、bcrA和msbA也很丰富。综上所述，土拨鼠肠道微生物群具有种群多样性和功能多样性，这为进一步研究肠道微生物群对宿主的调节作用提供了基础。此外，宏基因组学显示，土拨鼠的肠道微生物群可以降解纤维素和半纤维素。
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10140447/