# Comprehensive genome analysis uncovers the diversity of jumbo phages in the pig gut microbiome

## TL;DR

This study explores jumbo phages in pig gut microbiomes, revealing their diversity, host interactions, and functional roles in metabolism and defense.

## Contribution

The study identifies 14 novel jumbo phage families and their functional and ecological roles in the pig gut.

## Key findings

- 1,545 jumbo phage genomes were identified from 450 pig gut metagenomes.
- 10 novel jumbo phage families encode auxiliary metabolic genes and anti-defense systems.
- Co-abundance and CRISPR analyses revealed ecological interactions among jumbo phages.

## Abstract

Gut microbiome research has historically focused on bacterial communities. In contrast, the roles of viruses, especially jumbo phages, remain poorly understood. Jumbo phages are of major interest because their large genomes encode unique functions that can influence host metabolism and ecosystem dynamics. This study bridges this gap by identifying 1,545 jumbo phage genomes from 450 pig gut metagenomes. Using CRISPR spacer analysis, we predicted archaeal or bacterial hosts and reconstructed competitive phage networks within this ecosystem. Phylogenetic divergence combined with orthologous protein comparisons supported establishing 14 novel jumbo phage families. Functionally, 10 of these novel families encode auxiliary metabolic genes (AMGs) that enhance host metabolism alongside anti-defense systems including DNA methyltransferases, HNH endonucleases, and glycosyltransferases. Ecological interactions were further elucidated through co-abundance networks (n = 857 pairs) and CRISPR spacer matching (n = 425 pairs), revealing relationships between novel jumbo phages and other jumbo phages. Collectively, this work expands genomic resources for pig gut viromes and delivers new insights into jumbo phages’ functional capabilities, host associations, and global prevalence.