{
  "abstract": "Renewed interest in phage therapy has highlighted a need to understand how bacteria subvert phage infection through antiphage defense systems. Traditionally, strategies to identify antiphage defense systems lack throughput or have limitations for bacterial species where antiphage defense systems are understudied. Herein, we developed a bioinformatic pipeline that uses a small serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that small serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our bioinformatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage domains and reinforce prokaryotic Schlafen proteins as a new class of antiphage defense. Our work shows that small serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.\n\nIdentifying antiphage defense systems is challenging for bacterial species where such systems are understudied. This study describes a bioinformatic pipeline that uses a small serine recombinase as a genetic marker to identify novel antiphage defense systems across diverse bacterial phyla.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America",
    "Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada",
    "Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada",
    "Department of Biochemistry and Molecular Genetics, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, Colorado, United States of America"
  ],
  "article_type": "Methods and Resources",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Shelby E. Andersen"
    },
    {
      "affs": [
        1
      ],
      "name": "Joshua M. Kirsch"
    },
    {
      "affs": [
        2
      ],
      "name": "Navtej Singh"
    },
    {
      "affs": [
        3
      ],
      "name": "Stephen R. Garrett"
    },
    {
      "name": "John C. Whitney"
    },
    {
      "name": "Jay R. Hesselberth"
    },
    {
      "name": "Breck A. Duerkop"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/35fzx87582gpc.bib",
  "cited_by": 1,
  "doi": "10.1371/journal.pbio.3003991",
  "fulltext_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003991",
  "id": "35fzx87582gpc",
  "issns": [
    "1545-7885"
  ],
  "landing_url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003991",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2303|Bacteriophages and microbial interactions"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Enzymology/Enzymes/Recombinases"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Amino acids/Hydroxyl amino acids/Serine"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Enzymes/Recombinases"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Proteins/Protein domains"
    ],
    [
      "plos",
      "/Biology and life sciences/Computational biology/Genome analysis/Gene prediction"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Genome analysis/Gene prediction"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Metagenomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Bacterial pathogens/Enterococcus/Enterococcus faecalis"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Bacteria/Enterococcus/Enterococcus faecalis"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Bacteriophages"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Bacterial pathogens/Enterococcus/Enterococcus faecalis"
    ],
    [
      "plos",
      "/Physical sciences/Chemistry/Chemical compounds/Organic compounds/Amino acids/Hydroxyl amino acids/Serine"
    ],
    [
      "plos",
      "/Physical sciences/Chemistry/Organic chemistry/Organic compounds/Amino acids/Hydroxyl amino acids/Serine"
    ]
  ],
  "openalex": "W7204804990",
  "pdf_url": "https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3003991&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-31",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/35fzx87582gpc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:02Z",
      "native_id": "10.1371/journal.pbio.3003991",
      "source": "plos",
      "url": "https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003991"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Small serine recombinases are markers for antiphage defense system discovery",
  "title_text": "Small serine recombinases are markers for antiphage defense system discovery",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:02Z",
  "url": "https://research.draconitic.com/paper/35fzx87582gpc",
  "venue": "PLOS Biology",
  "versions": []
}