Insights from healthy mares reveal that mammalian uteri harbor a diverse virome

The Earth's estimated 10³¹ virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.