Abstract: Myodes rufocanus, Apodemus peninsulae and Apodemus agrarius are the three main rodent pests in the Northeast region of China. The gut microbiota of animals, along with their gastrointestinal tract, form a complex microbial ecosystem and play an important role in the host’s intestine. To investigate the composition and phylogenetic relationships of gut viruses in these three rodent species and the impact of their habitats, this study conducted metagenomic sequencing on 17 samples of Korean field mice, 17 samples of brown-backed voles from the same habitat, and 9 samples of striped field mice from a different habitat. After screening for viral information, the gut viral composition and differences among the three rodent species were compared and analyzed. The results showed that Artverviricota and Uroviricota were dominant viral phyla shared by the three rodent species, while Betaretrovirus and Gammaretrovirus were dominant viral genera shared by the three rodent species. Furthermore, significant differences were observed among the gut viral communities of the three rodent species, with nine phyla and 18 genera of viruses enriched in different samples. Among the top ten viruses in terms of relative abundance in the gut, Korean field mice and striped field mice exhibited significant differences in five phyla and five genera, while brown-backed voles and Korean field mice exhibited significant differences in three phylum and six genera. At the phylum level, the gut viral composition of brown-backed voles was more similar to that of Korean field mice, whereas at the genus level, the gut viral composition of striped field mice was more similar to that of Korean field mice. Based on these findings, it can be inferred that habitat had a greater influence on gut viral composition at the phylum level, while factors such as diet, phylogenetic relationship had a greater impact.

Key words: rodent, enterovirus, metagenome, northeast of China