Speaker
Description
The gastrointestinal tract of chickens harbors complex microbial communities that play vital roles in host nutrition, physiological development, and immune regulation [1]. While bacterial microbiomes in poultry have been extensively characterized, the viral communities, or virome, remain poorly understood. However, the virome has significant potential to alter bacterial communities through predatory behavior or horizontal gene transfer. For example, phages can influence the abundance of key metabolic bacteria, thereby affecting the host's bacterial functional profile [2]. Therefore, studying virome dynamics is vital for a better understanding of the factors that contribute to poultry health and productivity and for potentially minimizing the amount of traditional antimicrobial additives used in poultry.
In this study, we conducted a large-scale global metagenomic exploration of the chicken gut virome. We combined our internal datasets with those available in public repositories and compiled a large dataset comprising 1,514 metagenomic samples (1,458 chicken gut metagenomes and 56 viral-enriched samples), originating from 15 countries. This dataset accounted for approximately 6 TB of raw data, with more than 50 TB of intermediate files created during processing. Bioinformatic analyses were initially performed on the BinAC cluster (University of Tübingen), followed by migration to BinAC2, which was crucial due to its larger storage capacities and faster performance. The analyses were performed as follows: raw samples were quality-controlled and filtered to exclude host DNA, then assembled into metagenomic contigs, which were used to recover viral operational taxonomic units (vOTUs). After dereplication and taxonomic annotation, vOTUs were used to build a comprehensive species-level viral catalog. We also performed additional downstream analyses to investigate virus-host interactions and to evaluate spatial diversity of phages across distinct geographical locations.
As a result, we first assembled 47,092 medium- to high-quality viral genomes and then successfully reconstructed a massive, non-redundant catalog containing 19,778 distinct species-level vOTUs. Taxonomic profiling revealed that most of them (97%) are double-stranded DNA (dsDNA) phages belonging to the Caudoviricetes class. Host-prediction analyses demonstrated that these phages primarily target bacteria from the gastrointestinal tract (GIT), including Lactobacillus, Limosilactobacillus, and Escherichia. We encountered difficulties during functional annotation, which was relatively inefficient, as most of the detected protein-coding genes remained uncharacterized and lacked known biological functions. The viral communities exhibited high specificity to the host, and, at the same time, a highly structured spatial stratification along the GIT. More precisely, the virome composition changed drastically between proximal and distal regions, with differences primarily driven by phages belonging to the Lactobacillaceae family.
Our findings demonstrated that the chicken gut virome is highly diverse, largely uncharacterized, and strongly localized along the GIT. It suggests that relying exclusively on fecal samples substantially misrepresents viral diversity. In addition, our findings contribute to our understanding of GIT microbial ecology and provide a basis for developing phage-based strategies to improve poultry health and productivity as an alternative to antibiotics.