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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn\u2019s disease (CD), arises from complex interactions among genetic susceptibility, immune dysregulation, environmental factors, and the gut microbiome. Bacterial dysbiosis has been extensively studied, whereas the gut virome\u2014comprising eukaryotic viruses and bacteriophages\u2014remains less understood. Viruses can affect the intestinal barrier directly by infecting epithelial and immune cells, or indirectly by reshaping bacterial communities and host immunity. However, current evidence is dominated by cross-sectional associations and animal models, and whether virome alterations drive or result from intestinal inflammation remains unresolved. In this review, we provide a focused overview of intestinal barrier components relevant to IBD, synthesize human and animal evidence on IBD-associated viruses, and distinguish direct viral effects, microbiota-mediated effects, and bidirectional virus\u2013microbiota interactions. We highlight bacteriophage\u2013bacteria interactions as a central and potentially causal axis, discuss UC- and CD-specific differences, and outline causality gaps, search methodology, and emerging therapeutic strategies. Finally, we propose key unresolved questions and future research directions.<\/jats:p>","DOI":"10.3390\/ijms27198711","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T12:09:25Z","timestamp":1790683765000},"page":"8711","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Viral\u2013Gut Microbiota Interactions: Implications for the Gut Mucosa in Inflammatory Bowel Disease"],"prefix":"10.3390","volume":"27","author":[{"given":"Yonghong","family":"Wu","sequence":"first","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8821-642X","authenticated-orcid":false,"given":"Lei","family":"Hou","sequence":"additional","affiliation":[{"name":"Yuelushan Laboratory, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiao","family":"Li","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Hua","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"He","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0017-680X","authenticated-orcid":false,"given":"Sujuan","family":"Ding","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Fang","sequence":"additional","affiliation":[{"name":"College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"91","DOI":"10.3748\/wjg.v20.i1.91","article-title":"Inflammatory bowel disease: Pathogenesis","volume":"20","author":"Zhang","year":"2014","journal-title":"World J. 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