microbiome characterization of individual Marmota sibirica reveals a wide spectrum of viral and bacterial pathogens in Inner Mongolia of China

The Mongolian marmot is a reservoir for various zoonotic pathogens, including Yersinia pestis, Bartonella, and hantaviruses. However, our understanding of the marmot's pathogen profile remains incomplete. Here we used an unbiased metatranscriptomic approach to comprehensively characterize the microbiome of Mongolian marmots in Inner Mongolia. 106 marmots were sampled from Chen Barag Banner, Hulunbuir, and the microbiome , including mammalian-associated viral communities and bacterial pathogens, was characterized. A total of 74 viruses from five families were identified, including 13 mammalian-associated viruses and 61 picobirnaviruses, along with new species such as Chenqi marmot mastadenovirus 1 and Chenqi marmot enterovirus 1. Co-infection was common, with an average of 1.33 mammalian viruses per marmot (excluding picobirnaviruses). Phylogenetic analysis showed high homology between these viruses and those found in Himalayan marmots, although some showing close relationship with rodent and pig viruses. Ribosomal binding site analysis suggested that 32 Picobirnaviruses contained Shine-Dalgarno (SD) sequences, indicating potential bacterial association. Based on meta-transcriptomics sequencing data, our study also revealed potential five bacterial pathogens, though Yersinia pestis was not found. In summary, this study enhances the understanding of pathogen diversity in marmots and provides crucial insights for disease monitoring and control in border areas.