Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.

Abstract

Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.