A metagenomic collection of 19,778 viruses reveals the diverse virome of the chicken gut

Viral communities, particularly phages, influence intestinal prokaryotic diversity and thus impact the host's metabolic processes, yet, the composition and function of the chicken gut virome is poorly understood. To address this knowledge gap, we collected 1,514 chicken gut metagenomic samples and mined them for viral sequences, assembling a comprehensive collection of viral genomes. We identified 19,778 species-level viral operational taxonomic units (vOTUs), with 97% representing dsDNA phages of the Caudoviricetes class, which predominantly infect gut-associated bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and could not be assigned to known biological functions. Furthermore, the distribution of vOTUs across samples revealed that the chicken virome is highly individualized and displays unique characteristics compared to other animal viromes. However, chickens of the same breed shared more vOTUs, and these viral communities between breeds differed in their predicted bacterial hosts, suggesting that host genetics and microbiota composition could shape the gut virome. This highlights the extensive novelty within the chicken gut virome and the largely unexplored functional potential of these viral communities to impact the chicken gut ecosystem.