biostudies-literatureMa RNational Natural Science Foundation of ChinaScience and Technology Development Fund of MacauChina Postdoctoral Science FoundationInnovation Team Project of Universities in Guangdong ProvinceGuangdong Major Project of Basic and Applied Basic Researche0022825https://www.ebi.ac.uk/biostudies/studies/S-EPMC12482185biostudies-literatureUnknown10(9)<i>Vibrio harveyi</i>, a pathogenic bacterium, contains prophages that significantly influence its pathogenesis and evolutionary traits. Investigating the prevalence, evolution, and ecological roles of these prophages is of great importance as <i>V. harveyi</i> is responsible for luminous bacteriosis in aquatic organisms. In this study, 13 tailed prophages were identified from 55 globally sourced <i>V. harveyi</i> genomes, with prophage-bacterium junctions precisely annotated. These prophages exhibited distinct parasitic mechanisms, including Mu-type transposition, site-specific recombination, and a plasmid-like non-integrated state, reflecting their adaptive plasticity. Proteome-based phylogenetic analysis classified these prophages into eight subfamilies and nine genera, with half represmSpherePrevalence, diversity, and parasitism of tailed prophages in &lt;i&gt;Vibrio harveyi&lt;/i&gt;.PMC124821852023KCXTD02832400014FDCT-0055/2023/RIB22023B03030000172023M742393Ma RZhong HZhang RfalsePrevalence, diversity, and parasitism of tailed prophages in &lt;i&gt;Vibrio harveyi&lt;/i&gt;.<i>Vibrio harveyi</i>, a pathogenic bacterium, contains prophages that significantly influence its pathogenesis and evolutionary traits. Investigating the prevalence, evolution, and ecological roles of these prophages is of great importance as <i>V. harveyi</i> is responsible for luminous bacteriosis in aquatic organisms. In this study, 13 tailed prophages were identified from 55 globally sourced <i>V. harveyi</i> genomes, with prophage-bacterium junctions precisely annotated. These prophages exhibited distinct parasitic mechanisms, including Mu-type transposition, site-specific recombination, and a plasmid-like non-integrated state, reflecting their adaptive plasticity. Proteome-based phylogenetic analysis classified these prophages into eight subfamilies and nine genera, with half repres2025-01-01T00:00:00Z2025 Sep2026-06-03T23:37:14.696Z2026-05-03T03:12:25.933ZS-EPMC124821854085300110.1128/msphere.00228-25