{
  "abstract": "Fecal microbiota transplantation (FMT) from healthy donors with a normally functioning colon has limited clinical effect in the treatment of chronic pouchitis. However, a normally functioning ileal pouch-anal anastomosis (IPAA) physiology differs from individuals with a healthy intact colon. We aimed to investigate the microbial characteristics of patients with a normally functioning IPAA (HealthyPouch) compared with chronic pouchitis (SickPouch), ulcerative colitis (UC), and a healthy intact colon microbiome (NormalGut). Furthermore, we investigated how repeated antibiotic use influences antimicrobial resistance on a bacterial genome level. Fecal samples from 190 participants were collected; HealthyPouch (n = 38), SickPouch (n = 37), UC (n = 23), and NormalGut (n = 92) and sequenced with Illumina and taxonomically profiled. Samples from HealthyPouch, SickPouch, and NormalGut were also long-read sequenced using Oxford Nanopore Technologies for reconstruction of 12 282 metagenome-assembled genomes (MAGs). DNA methylation motifs were used for plasmid-host association. The HealthyPouch microbiome is distinct from both the UC, NormalGut, and SickPouch microbiome. Escherichia coli MAGs in the SickPouch (n = 21) microbiome had significantly higher co-occurring ciprofloxacin resistance mutations in the gyrA and parC genes, compared to both HealthyPouch (n = 26; BH adjusted P < .05) and NormalGut (n = 40; BH adjusted P < .05). Based on DNA methylation pattern, three plasmids were associated with E. coli carrying extended-spectrum beta lactamase genes. HealthyPouch microbiota differs from NormalGut microbiota, and could therefore be more appropriate for FMT treatment of chronic pouchitis. The association between E. coli and resistance gene-carrying plasmids underscores the importance of integrating plasmid analysis into metagenome-based approaches for personalized antibiotic treatment and resistance monitoring.",
  "abstract_shown": true,
  "affiliations": [
    "Center for Microbial Communities, Department of Chemistry & Bioscience, Aalborg University, Aalborg, Denmark.",
    "Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark.",
    "Department of Gastroenterology and Hepatology, Aalborg University Hospital, Aalborg, Denmark.",
    "Center for Molecular Prediction of Inflammatory Bowel Disease, PREDICT, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Sebastian Mølvang Dall",
      "orcid": "0000-0003-0108-152X"
    },
    {
      "affs": [
        0
      ],
      "name": "Alberte Holm Møllekær",
      "orcid": "0009-0000-4948-8068"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Sabrina Just Kousgaard",
      "orcid": "0000-0002-2394-7104"
    },
    {
      "affs": [
        1
      ],
      "name": "Sarah Søgaard Jakobsen",
      "orcid": "0000-0002-0450-8317"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Lone Larsen",
      "orcid": "0000-0003-4067-2381"
    },
    {
      "affs": [
        0
      ],
      "name": "Bertil Sørensen",
      "orcid": "0009-0005-4516-330X"
    },
    {
      "affs": [
        1
      ],
      "name": "Ole Thorlacius-Ussing",
      "orcid": "0000-0003-4963-1551"
    },
    {
      "affs": [
        0
      ],
      "name": "Mads Albertsen",
      "orcid": "0000-0002-6151-190X"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/1z3yp7778pw0d.bib",
  "cited_by": 1,
  "doi": "10.1093/ecco-jcc/jjag150",
  "fulltext_url": "https://europepmc.org/articles/PMC13744404",
  "id": "1z3yp7778pw0d",
  "issns": [
    "1873-9946",
    "1876-4479"
  ],
  "landing_url": "https://europepmc.org/article/MED/42998368",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7127064966",
  "pdf_url": "https://europepmc.org/articles/PMC13744404?pdf=render",
  "pmcid": "PMC13744404",
  "pmid": "42998368",
  "published": "2026-11-01",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/1z3yp7778pw0d.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T15:20:34Z",
      "native_id": "MED:42998368",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42998368"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Microbial and antimicrobial resistance signatures differentiate healthy and inflamed ileal pouches in patients with ulcerative colitis.",
  "title_text": "Microbial and antimicrobial resistance signatures differentiate healthy and inflamed ileal pouches in patients with ulcerative colitis.",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T15:20:34Z",
  "url": "https://research.draconitic.com/paper/1z3yp7778pw0d",
  "venue": "Journal of Crohn's & colitis",
  "versions": []
}