Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems

ABSTRACT

Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito‐ and bird‐associated communities. Ecological network analyses revealed substantial cross‐host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system‐wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host‐associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.