Host diet may shape bat RNA viromes within geographic and phylogenetic constraints at a global-scale

Bats are key models for studying the ecological mechanisms driving viral community structure, yet the role of diet remains unclear. By integrating 1627 RNA virome libraries from 78 bat species across 13 countries, we recovered 309,546 vOTUs spanning 66 recognized RNA virus families, whereas 82.74% remained unclassified, suggesting extensive viral “dark matter”. Classified viruses were associated with vertebrates, invertebrates, plants and plant-associated fungi, with invertebrate-associated viruses contributing prominently to overall diversity. Viral community composition differed significantly among feeding guilds, with sanguivorous bats exhibiting a specialized viral community structure. However, sampling site and host phylogeny explained substantially more variation than feeding guild, indicating that broad-scale bat virome structure is primarily shaped by geography and host evolutionary history. Analyses restricted to vertebrate-associated viruses further showed that feeding guild was associated with community composition but not viral species diversity. Viral sharing was more strongly structured by sampling site and host phylogenetic distance than by shared diet. Together, these findings indicate that geography and host phylogeny dominate broad-scale viral community structure, whereas diet plays a secondary role by modulating exposure to viruses through predation. This improves our understanding of bat viral assemblages and informs assessments of host–virus associations and spillover risk. By analyzing 1,627 bat RNA viromes from 78 species worldwide, the study shows that geography and host evolution shape bat viral communities more strongly than diet, while feeding ecology plays a secondary role in viral exposure.