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

## TL;DR

This study explores how antibiotics and plant-based supplements affect the virus communities in chickens' guts, revealing different impacts on viral diversity and function.

## Contribution

The study identifies a novel antibiotic-phage synergy and shows how phytogenics support gut virome diversity.

## Key findings

- Phage communities show structured assembly with distinct successional patterns across age and gut regions.
- Antibiotics enhance phage infectivity via phage-encoded genes aiding bacterial immune evasion.
- Phytogenic supplements promote richer and more diverse phage communities, supporting gut homeostasis.

## Abstract

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.