Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation

This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.