Exploring diversity and distribution patterns of chicken gut bacteriophage community

Abstract Chickens harbor a diverse gut virome, with bacteriophages playing a central role in shaping microbial communities, modulating gut microbiota composition, and influencing metabolic pathways. Despite significant recent advances in gut virome studies, comprehensive analyses of the bacteriophage component within the chicken gut viral genomes remain limited. A comprehensive chicken virome database (CVD) was developed by integrating diverse datasets from various continents, containing 32,792 viral contig sequences with an estimated completeness of over 50% and representing 17,268 species-level medium-quality operational taxonomic units (vOTUs) genomes inhabiting the chicken gut. Comparative analyses revealed minimal overlap between CVD and other virome databases, underscoring its distinctiveness and highlighting the need for high-quality, host-specific viral catalogs in studying chicken gut microbiota. Metagenomic analyses revealed the functional attributes of these prokaryotic viruses, including their potential roles in modulating gut microbiota composition, metabolic pathways, and antibiotic resistance. Classification results showed that the majority of known virus vOTUs (80.2%) were identified as Caudoviricetes (74.8%) and Malgrandaviricetes (3.5%) at the class level. Caudoviricetes, the most dominant phage class in all samples, varied in the relative abundance. At the genus level, Lactobacillus was considered the most common host, aligning with the bacterial composition of the chicken gut. Correlation analysis between the composition of gut bacteriome and the phage component of the virome indicated a significant relationship. Additionally, these bacteriophages carry a variety of potential auxiliary metabolic genes (AMGs) and a few potential antibiotic resistance genes (ARGs), but the relationship between potential ARGs and viral communities was not significant. This study provides a foundational resource for understanding the chicken gut bacteriophage community across regions, while recognizing current geographic limitations. Our findings contribute to the growing knowledge of host- bacteriophage interactions and offer a basis for exploring how bacteriophage communities may influence poultry health and management.