{
  "abstract": "Host–microbe interactions are essential for maintaining intestinal homeostasis, yet most in vitro models lack physiological oxygen gradients, mucosal architecture, and reproducibility. We developed the Mucosal Mimetic 3D–Host Aerobic Microbiota Anaerobic Co-culture (Mm 3D-HaeMan) system, a colon-mimetic, oxygen-stratified platform enabling stable co-culture of colonic epithelial cells, human peripheral blood mononuclear cells (hPBMCs), and obligate anaerobes. Oxygen profiling confirmed a stable gradient consistent with human colonic stratification. Using a canonical short-chain fatty acid (SCFA) cross-feeding pair (Anaerostipes caccae and Bifidobacterium bifidum, AcBb consortium), we performed integrated, multilayered analyzes of the host-microbe interface. Co-culture with the SCFA-producing AcBb consortium was associated with enhanced epithelial-mitochondrial respiration, maintenance of transepithelial resistance, tight junction protein expression without barrier disruption, and rebalanced cytokine profiles. Host transcriptomics identified 41 differentially expressed genes (15 upregulated, 26 downregulated) associated with homeostatic-relevant epithelial responses. Simultaneously, bacterial metatranscriptomics revealed 29 differentially expressed gene families; notably, glaK was enriched in bacteria-only cultures; SORD, nuoG, and nuoE were specifically induced during co-culture, indicating host-associated bacterial transcriptional changes. The compartmentalized design permits independent sampling for layer-resolved multi-omics and functional readouts. These findings establish Mm 3D-HaeMan as a physiologically grounded platform for dissecting bidirectional host–microbe responses and immune-associated interactions. This model offers broad applicability for mechanistic research and translational screening of probiotics and microbiome-based therapeutics.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea.",
    "Department of Life Science, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.",
    "Department of Biomedical Sciences, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.",
    "Department of Biotechnology, Yonsei University, Seoul, Republic of Korea.",
    "Department of Nutritional Science and Food Management, Ewha Womans University, Seoul, Republic of Korea.",
    "Global Food and Nutrition Research Institute, Ewha Womans University, Seoul, Republic of Korea.",
    "Graduate Program in System Health Science and Engineering, Ewha Womans University, Seoul, Republic of Korea."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 10,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Taewon Kim",
      "orcid": "0009-0008-0825-428X"
    },
    {
      "affs": [
        1
      ],
      "name": "Joon-Young Park",
      "orcid": "0000-0002-7077-0807"
    },
    {
      "affs": [
        0
      ],
      "name": "Minae Kim"
    },
    {
      "affs": [
        0
      ],
      "name": "Na Young Kim",
      "orcid": "0009-0001-3189-7485"
    },
    {
      "affs": [
        1
      ],
      "name": "Seol-A Jang"
    },
    {
      "affs": [
        2
      ],
      "name": "Han-Gyeol Park",
      "orcid": "0009-0005-9490-0978"
    },
    {
      "affs": [
        3
      ],
      "name": "Dong-Woo Lee",
      "orcid": "0000-0002-2272-8321"
    },
    {
      "affs": [
        2
      ],
      "name": "Keunwook Lee",
      "orcid": "0000-0002-4713-8547"
    },
    {
      "affs": [
        4,
        5,
        6
      ],
      "name": "Bong-Soo Kim",
      "orcid": "0000-0003-1243-8280"
    },
    {
      "affs": [
        0
      ],
      "name": "Nam Joo Kang",
      "orcid": "0000-0003-1500-2845"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ctk890mw0vyhx.bib",
  "cited_by": 0,
  "doi": "10.1080/19490976.2026.2749954",
  "fulltext_url": "https://www.tandfonline.com/doi/10.1080/19490976.2026.2749954",
  "id": "ctk890mw0vyhx",
  "issns": [
    "1949-0984",
    "1949-0976"
  ],
  "landing_url": "https://doi.org/10.1080/19490976.2026.2749954",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Research Article"
    ],
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      "lcc",
      "RC799-869"
    ],
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      "openalex",
      "1312|Gut microbiota and health"
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  "openalex": "W7223391660",
  "pdf_url": "https://europepmc.org/articles/PMC13699875?pdf=render",
  "pmcid": "PMC13699875",
  "pmid": "42912418",
  "published": "2026-10-23",
  "publisher": "Taylor & Francis Group",
  "ris": "https://research.draconitic.com/paper/ctk890mw0vyhx.ris",
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    {
      "first_seen": "2026-10-30T12:17:19Z",
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Gut microbiota and health",
      "subfield": "molecular-biology"
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  ],
  "title": "A stratified human colon model reveals SCFA cross-feeding-driven host–microbe dynamics associated with epithelial and immune responses",
  "title_text": "A stratified human colon model reveals SCFA cross-feeding-driven host–microbe dynamics associated with epithelial and immune responses",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T13:44:12Z",
  "url": "https://research.draconitic.com/paper/ctk890mw0vyhx",
  "venue": "Gut Microbes",
  "versions": []
}