Expanding the chicken gut virome: Uncovering viral diversity, host interactions, and regional variations across the intestinal tract

Abstract

Chicken gastrointestinal virome comprises a complex and diverse viral community with significant implications for host health and microbiome function. We analyzed 3,312 publicly available chicken gut metagenomic datasets to establish the chicken gastrointestinal virome collection (CGVD), which includes 39,380 non-redundant viral operational taxonomic units (vOTUs); notably, 84.90% (33,433/39,380) represent novel sequences absent from current databases. Over half of the CGVD vOTUs were classified as bacteriophages, predominantly from the order Caudovirales. The predicted hosts were mainly prokaryotes, particularly Bacillota and Bacteroidota, revealing a multifaceted landscape of virus-host interactions. Many vOTUs infected multiple bacterial phyla, indicating high adaptability and broad ecological impact. In addition, lifestyle prediction showed that 28.28% (11,137 /39,380) of the vOTUs in CGVD were identified as lytic phages. Functional annotation demonstrated that viral genes contribute to key metabolic processes, including nucleotide and amino acid metabolism, thereby facilitating viral replication and host adaptation. The detection of auxiliary metabolic genes and carbohydrate-active enzymes underscores the role of viruses in modulating the gut microbiome. Although antibiotic resistance genes and mobile genetic elements were present, their contribution to horizontal gene transfer appears limited. Additionally, marked regional differences in virome composition were observed between the small and large intestines, particularly in the abundance of families such as Siphoviridae and Myoviridae. CGVD not only highlights the key role of viruses in shaping the chicken gut microbiome and influencing microbial dynamics and metabolic pathways, but also provides new resources and insights for future research.