Metagenomics reveals biogeography and functional potential of phage communities in bee gut

Bacteriophages (phages) are pivotal regulators of microbiome ecology and function, yet their distribution, diversity and ecological roles within the bee gut remain largely unexplored, particularly across diverse bee species and geographic regions. Here, we used a large-scale metagenomic dataset to investigate phage communities associated with seven bee species across China. We recovered 121 viral operational taxonomic units (vOTUs) from 132 bee gut metagenomes, revealing that bee gut phages are dominated by the class Caudoviricetes and include numerous previously uncharacterized viral lineages. Biogeographic analyses revealed spatial structuring of phage communities such as latitudinal diversity gradient, distance–decay relationship. Variation partitioning analysis (VPA) indicated that bee host identity explained a substantially larger proportion of community variation than environmental factors. More, functional annotation further revealed that bee gut phages encode diverse carbohydrate-active enzymes (CAZymes) potentially involved in polysaccharide metabolism, as well as multiple anti-defense systems targeting bacterial antiviral mechanisms. Our study demonstrates that bee gut phages exhibit biogeographic structuring and host specificity. In addition, phages carry diverse functional genes that may influence bacterial metabolism and host–microbe interactions. These findings provide a comprehensive framework for understanding the ecological roles of phages in the bee gut and highlight their importance in shaping tripartite interactions among phages, bacteria, and bee hosts.