Meta-transcriptomics characterization of individual reveals a wide spectrum of viral and bacterial pathogens in Inner Mongolia of China.

Mongolian marmot is a reservoir for various zoonotic pathogens, including , , and hantaviruses. However, our understanding of the marmot's pathogen profile remains incomplete. Here, we used an unbiased metatranscriptomic approach to comprehensively characterize the virome and bacterial microbiome of 106 Mongolian marmot sampled from Chen Barag Banner, Inner Mongolian, China. A total of 12 mammalian-associated viruses from five families were identified, including novel species such as Chenqi marmot mastadenovirus 1 and Chenqi marmot enterovirus 1. Additionally, 62 species of picobirnaviruses were detected though they were not classified as mammalian viruses in this context. Co-infection was common, with an average of 1.35 mammalian viruses per marmot fecal sample, 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 sequences, indicating potential bacterial association. Based on meta-transcriptomics sequencing data, our study also revealed five potential bacterial pathogens though was not found. In summary, this study provides a more comprehensive view of pathogen diversity in Mongolian marmots and contributes important insights to support disease monitoring and prevention efforts in border areas of China.IMPORTANCEThe Mongolian marmot () is a critical mammalian species in Hulunbuir, playing a key role in harboring and transmitting , the causative agent of plague. However, research on the diversity, abundance, co-infection dynamics, and spillover potential of viruses and bacteria in these animals remains limited. This study characterizes pathogen diversity and ecology by examining the viral and bacterial microbiomes of Mongolian marmots in China's northeastern border regions. The findings offer unique insights into potential threats to both animal and human health and contribute valuable data to inform disease prevention and control efforts in these regions.