{
  "abstract": "Background: Enterobacteria harboring the polyketide synthase (pks) island (clbA–clbS), which encodes colibactin (pks⁺ enterobacteria), is a putative risk factor for colorectal cancer. Polymerase chain reaction (PCR) is the current standard for detection. Primer-independent shotgun metagenomic sequencing (SMS) is increasingly used; however, thresholds and analysis parameters for identifying pks⁺ enterobacteria remain unstandardized. This study aimed to evaluate how accurately SMS can reproduce PCR-defined pks⁺ status and identify practical cutoffs by analyzing fecal samples from 223 healthy adults in a Japanese cohort.\n\nResults: PCR identified 60/223 (26.9%) participants as pks⁺. SMS detected at least one clb gene in 85/223 (38.1%) at ≥ 90% identity; 49 of these agreed with PCR positives. Among the single-gene rules, clbB yielded the best discrimination (area under the curve (AUC) = 0.826) across 70–90% identity. The total-read rule across 19 clb genes performed best overall (AUC = 0.838), with higher AUCs above the 60% threshold (all p ≤ 0.045). The rule requiring detection of at least eight clb genes was inferior (AUC = 0.734–0.773). Detection performance depended on gene length; longer clb genes (> 1,500 amino acids) achieved higher accuracy (AUC ≥ 0.800).\n\nConclusions: Optimized SMS can reproduce PCR-based detection of pks⁺ enterobacteria in feces with high accuracy. clbB and a cluster-level rule aggregating reads across clbA–clbS are effective, although tightening the sequence-identity threshold did not consistently improve performance. The standardized criteria proposed here enable cross-study comparability and may accelerate epidemiologic assessment of pks⁺ enterobacteria and its clinical translation for colorectal cancer prevention.\n\nSupplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12866-026-05460-3.",
  "abstract_shown": true,
  "affiliations": [
    "Graduate School of Sport Sciences, Waseda University, Tokorozawa, 359-1192 Japan",
    "Center for Clinical Nutrition, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, 566-0002 Japan",
    "Microbial Research Center for Health and Medicine, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, 567-0085 Japan",
    "Faculty of Sport Sciences, Waseda University, 2-579-15 Mikajima, Tokorozawa, 359-1192 Japan",
    "Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526 Japan",
    "Graduate School of Medicine, The University of Osaka, Suita, 565-0871 Japan",
    "Graduate School of Pharmaceutical Sciences, The University of Osaka, Suita, 565-0871 Japan",
    "Graduate School of Dentistry, The University of Osaka, Suita, 565-0871 Japan",
    "Graduate School of Science, The University of Osaka, Toyonaka, 560-0043 Japan",
    "International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan",
    "Department of Microbiology and Immunology, Kobe University Graduate School of Medicine, Kobe, 650-0017 Japan",
    "Research Organization for Nano and Life Innovation, Waseda University, Tokyo, 162-8480 Japan",
    "Department of Physical Activity Research, National Institutes of Biomedical Innovation, Health and Nutrition, Settsu, 566-0002 Japan"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Yusei Tataka"
    },
    {
      "affs": [
        2
      ],
      "name": "Hitoshi Kawashima"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Hinako Nanri"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Daiki Watanabe"
    },
    {
      "affs": [
        4
      ],
      "name": "Kenji Watanabe"
    },
    {
      "affs": [
        2,
        5,
        6,
        7
      ],
      "name": "Masaya Yamaguchi"
    },
    {
      "affs": [
        2,
        5,
        6,
        7,
        8,
        9,
        10,
        11
      ],
      "name": "Jun Kunisawa"
    },
    {
      "affs": [
        3,
        12
      ],
      "name": "Motohiko Miyachi",
      "orcid": "0000-0002-1146-0905"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/av8j441xy1fb3.bib",
  "cited_by": 0,
  "doi": "10.1186/s12866-026-05460-3",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13715221/",
  "id": "av8j441xy1fb3",
  "issns": [
    "1471-2180"
  ],
  "landing_url": "https://doi.org/10.1186/s12866-026-05460-3",
  "language": "en",
  "licence": "CC-BY-NC-ND-4.0",
  "licence_label": "CC BY-NC-ND 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Research"
    ],
    [
      "openalex",
      "1310|Escherichia coli research studies"
    ]
  ],
  "openalex": "W7171974912",
  "pdf_url": null,
  "pmcid": "PMC13715221",
  "pmid": "42946988",
  "published": "2026-08-01",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/av8j441xy1fb3.ris",
  "sources": [
    {
      "first_seen": "2026-11-01T12:22:34Z",
      "native_id": "PMC13715221",
      "source": "pmc",
      "url": "https://doi.org/10.1186/s12866-026-05460-3"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:1310|Escherichia coli research studies",
      "subfield": "endocrinology-metabolism"
    }
  ],
  "title": "Standardization of shotgun metagenomics parameters for pks-positive enterobacteria detection in human fecal samples: Receiver operating characteristic analysis using polymerase chain reaction as reference standard",
  "title_text": "Standardization of shotgun metagenomics parameters for pks-positive enterobacteria detection in human fecal samples: Receiver operating characteristic analysis using polymerase chain reaction as reference standard",
  "type": "peer-reviewed",
  "updated_at": "2026-11-01T12:22:34Z",
  "url": "https://research.draconitic.com/paper/av8j441xy1fb3",
  "venue": "BMC Microbiology",
  "versions": []
}