Bioinformatic approaches to pig gut phagobiome (phageome) analysis: tools, applications, and current state of research

Abstract The pig intestine contains a diverse bacteriophage community that helps regulate the gut microbiome and host health. Growing interest in phage therapy reflects its potential as a cost-effective, targeted approach to modulating microbial communities and treating diseases, particularly those involving antibiotic-resistant bacteria. This review proposes an alternative operational definition of the phagobiome that integrates the phageome with host responses and summarises current knowledge of swine gut phages. It includes well-studied Caudoviricetes as well as less abundant groups such as crAss-like phages and jumbo phages carrying clustered, regularly interspaced short palindromic repeat spacers. Differences across pig breeds and age groups are outlined, highlighting data gaps. Current knowledge of gut phages and their interactions with the host remains limited, prompting the development of new bioinformatic tools. The paper also critically compares bioinformatic tools for phageome analysis, supporting method selection and future research on core phages shared within pig populations and their potential applications.