Global Characterization of the Avian Gut Virome Reveals Extensive Viral Diversity and Functional Implications

Background The avian gut virome plays a crucial role in shaping the gastrointestinal microbial ecosystem of birds. However, its taxonomic and functional diversity remains poorly characterized due to the absence of a dedicated reference database. This limitation hampers our understanding of the complex interactions among viruses, their bacterial hosts, and the overarching avian host, as well as viral contributions to gut microbial ecology. Results To address this gap, we developed the Avian Virome Database (AvianViromeDB) by integrating 2,692 gut metagenomic samples from poultry and wild birds. This effort yielded 252,752 viral contigs, which are clustered into 61,608 high-quality, species-level viral operational taxonomic units (vOTUs). Taxonomic analysis revealed that 99.05% of these vOTUs belonged to the class Caudoviricetes , yet only 4.69% could be assigned to known viral families—suggesting over 95% likely represent novel viral lineages. Prediction of prokaryotic hosts indicated that these viruses primarily target core gut microbiota, particularly Bacillota and Bacteroidota , both central to carbohydrate metabolism. Functional annotation uncovered tens of thousands of auxiliary metabolic genes (AMGs), with enrichments in glycolysis, amino acid metabolism, and nucleotide biosynthesis pathways. Conclusion These findings demonstrate that avian gut viruses may modulate microbial communities both through direct lysis of their bacterial hosts (“top-down” control) and by altering host metabolism via AMGs (“bottom-up” modulation). The resulting high-quality genome catalog reveals the remarkable diversity and functional potential of the avian gut virome, offering a valuable resource for future research into avian microbial ecology and the intricate interplay between viruses, bacteria, and their avian hosts. The AvianViromeDB is publicly accessible at: https://phagebyte.github.io/avianviromedb.