Metagenomics research on the gut microbiota of the Marmota himalayana of the Sanjiangyuan National Nature Reserve in Qinghai Province, China.

With the improvement of transportation and the rise of tourism on the Qinghai-Xizang Plateau, the scope of human activities has continuously expanded, increasing opportunities for contact with wildlife, also exacerbating the outbreak rate of zoonotic emerging infectious diseases. Currently, research on the gut microbiota of wildlife, especially Marmota himalayana (M. himalayana), which are reservoir hosts for plague, is scarce. In this study, we investigated the composition, function, and regional variations of the gut microbiota in M. himalayana based on the metagenomic sequencing of 45 fecal samples from the Sanjiangyuan National Nature Reserve in Qinghai Province. The results indicated that at the phylum level, the dominant bacterial phyla in the gut microbiota of the M. himalayana were Firmicutes, Bacteroidota, and Proteobacteria, collectively accounting for 74.16 % of the community. At the genus level, the top three most abundant genera were Alistipes (11.86 % ± 1.56 %), Bacteroides (6.68 % ± 0.95 %), and Clostridium (4.92 % ± 1.04 %). Kyoto encyclopedia of genes and genomes (KEGG) database annotation results showed that the most enriched functional categories of the marmot gut microbiota were metabolism, genetic information processing (GIP), and environmental information processing (EIP). These active functions played a crucial role in food digestion, nutrient absorption, metabolic balance maintenance, and pathogen defense, aiding the marmot in better adapting to the extreme environment of the Qinghai-Xizang Plateau. The study provided critical insights into host-microbe interactions, highlighting the role of microbiota in the survival and conservation of endangered species in unique habitats.