A novel widely distributed marine Staphylococcus phage representing a new virus genus

Bacteriophages play critical roles in marine microbial ecology and evolution, partly through their carriage of auxiliary metabolic genes (AMGs). Staphylococcus is widely distributed across seawater, sediments, and marine organisms, contributing to biogeochemical cycling. The presence and ecological roles of Staphylococcus equorum in marine environments remain largely unexplored, and the characteristics of marine phages infecting S. equorum and their interactions remain poorly understood. This study aimed to provide deeper insights into the genomics, evolution, and environmental adaptation of S. equorum temperate phages. In this study, a temperate phage infecting S. equorum , identified as Lyfv1, was isolated from seawater of western Pacific Ocean using mitomycin C induction. Transmission electron microscopy revealed that Lyfv1 had an icosahedral head (56 ± 0.62 nm in diameter) and a long tail (300 ± 1.23 nm in length). Genomic analysis showed that Lyfv1 had a double-stranded DNA genome (41,602 bp) encoding 62 genes, including the lysogeny/lysis control genes, confirming that it was a temperate phage. Additionally, the phage genome contained a putative AMG encoding MazG-like family protein. The phage tail contained both polysaccharide deacetylase and tail spike proteins. Protein-sharing network and phylogenetic analyses indicated that Lyfv1 represents a distinct lineage among known Staphylococcus phages. Notably, intergenomic similarity, average amino acid identity (AAI), orthologous fraction (OF), and whole-genome comparisons supported its low genomic similarity (< 26%) with other phages, suggesting that Lyfv1 may represent a novel virus genus within the class Caudoviricetes . Interestingly, Lyfv1 has a wider ecological distribution than other Staphylococcus phages, particularly in polar zones. The phage Lyfv1 is a temperate siphovirus isolated from S. equorum . It may represent a novel virus genus within the Caudoviricetes class. Lyfv1 encoded a putative MazG-like AMG, which may involved in reprogramming host metabolism during infection. Structural predictions generated using AlphaFold and genomic-context analyses predicted that gp19 may function as a receptor-binding protein, while gp18 may act as a polysaccharide-modifying tail-associated protein, suggesting their potential involvement in host recognition and phage–host interactions. Lyfv1 was found to be widely distributed across multiple oceanic zones. These findings highlight Lyfv1 as a unique phage with evolutionary and ecological significance.