{
  "abstract": "IntroductionSalmonella enterica phages are important drivers of bacterial evolution and potential tools for phage-based applications. However, differences in genome architecture, codon usage, and predicted translational adaptation between Salmonella temperate and virulent phages remain uncertain and need to be determined.MethodsThis study elucidates genome-wide and functional-module-specific molecular signatures across Salmonella phage lifestyles. We analyzed 41 temperate and 41 virulent Salmonella phage genomes comprising 7,759 protein-coding genes. Because lifestyle is a genome-level attribute, statistical inference employed equal-genome-weight comparisons, whole-genome permutations, genome-cluster bootstrapping, and sensitivity analyses.ResultsThe virulent phages exhibited greater broad-scale genomic disconnectedness (81.7% versus 74.0% of within-group genome pairs lacking significant BLAST similarity) and larger mean genomes (80,784 versus 44,433 bp). The temperate phages showed higher genome-average overall GC and GC3 content, with “virulent”-minus-“temperate” differences of −4.484 and −7.706 percentage points, respectively (both q = 0.00013). Conversely, the virulent phages exhibited higher genome-average Codon Adaptation Index (CAI-2; difference = +0.0131) and Index of Translation Elongation (ITE; +0.0321), with associations persisting after adjustment for the nucleotide composition and coding-sequence length. The genome-equal effective number of codons (Nc) difference was not significant (q = 0.383). Genome-equal PERMANOVA detected significant differentiation across the complete molecular dataset (R2 = 0.1518; q = 0.0001) and all five gene functional categories, with the greatest effects in the DNA repair/recombination, lysis-associated, and structural genes. Only regulatory genes showed significantly different genome-level multivariate dispersion. Genome-average PCA scores differed significantly along GC-associated PC1 and a second axis associated with CAI-2, ITE, and sequence size. GC-adjusted CAI-2 -ITE correlations remained positive across both phage lifestyles (ρ = 0.771 and 0.776), with genome-cluster bootstrap confidence intervals excluding zero. Genome-level relative synonymous codon usage analyses identified 23 of 59 codons with FDR-significant, large-effect differences. Principal findings persisted in functional-annotation and genome-relatedness sensitivity analyses.DiscussionCollectively, these results identify complementary compositional and predicted codon-adaptation signatures in the selected phage lifestyle groups, while taxonomic imbalance and the absence of direct translational measurements limit further interpretation.",
  "abstract_shown": true,
  "affiliations": [
    "ne Health Institute, School of Science and Technology, University of Georgia, Tbilisi, Georgia"
  ],
  "article_type": "Original Research",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Ketevan Taktakishvili"
    },
    {
      "affs": [
        0
      ],
      "name": "Davit Janelidze"
    },
    {
      "affs": [
        0
      ],
      "name": "Ana Gamkrelidze"
    },
    {
      "affs": [
        0
      ],
      "name": "Saba Kobakhidze"
    },
    {
      "affs": [
        0
      ],
      "name": "Tinatin Elbakidze"
    },
    {
      "affs": [
        0
      ],
      "name": "Mamuka Kotetishvili"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6br305stwjezj.bib",
  "cited_by": 0,
  "doi": "10.3389/fmicb.2026.1927342",
  "fulltext_url": "https://www.frontiersin.org/articles/10.3389/fmicb.2026.1927342/full",
  "id": "6br305stwjezj",
  "issns": [
    "1664-302X"
  ],
  "landing_url": "https://doi.org/10.3389/fmicb.2026.1927342",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "feed-journal",
      "biology/microbiology"
    ],
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      "lcc",
      "QR1-502"
    ]
  ],
  "openalex": null,
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-05",
  "publisher": "Frontiers Media S.A.",
  "ris": "https://research.draconitic.com/paper/6br305stwjezj.ris",
  "sources": [
    {
      "first_seen": "2026-11-05T14:21:25Z",
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  "subjects": [
    {
      "field": "biology",
      "origin": "feed-journal:biology/microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Genome architecture, GC3 content, codon usage, and predicted translational adaptation of Salmonella temperate and virulent phages",
  "title_text": "Genome architecture, GC3 content, codon usage, and predicted translational adaptation of Salmonella temperate and virulent phages",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T00:21:16Z",
  "url": "https://research.draconitic.com/paper/6br305stwjezj",
  "venue": "Frontiers in Microbiology",
  "versions": []
}