Soil microbes drive gut fungal assembly and immunity in a wild rodent model

Environmental microbial communities, particularly in soil, play an increasingly recognized role in wildlife health, yet their influence on host-associated fungiremains largely overlooked.Host associated microbiota, in turn, are tightly linked to immune function and disease resistance, meaning that environmental impacts on the gut microbiome can directly affect host health. Using a wild-derived bank vole model, we experimentally tested how exposure to forest soils from national parks versus urban greenspaces affects gut microbiome assembly and host immune function. Soil exposure substantially altered the gut mycobiota, increasing fungal diversity and incorporating environmentally sourced taxa that formed larger and more complex co occurrence networks than those of animals kept on sterile bedding. In contrast, bacterial communities showed weaker shifts, though soil exposure still reorganized bacterial network structure. Strikingly, only urban soil triggered an innate immune response in the colon, including strong upregultion of IFN γ–inducible and epithelial defense genes. These results indicate that anthropogenic alterations to soil can stimulate host immunity independently of pathogen transfer to the gut. Our findings demonstrate that soil microbial diversity is a key ecological driver of gut fungal assembly, microbial network organization, and immune activation. These results highlight the value of integrating environmental microbiota, particularly soil fungi, into biodiversity monitoring, habitat management, and One Health–oriented conservation planning.