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Central to this paradigm is the gut microbiota including non-bacterial components such as the virome, whose functional disruption marked by reduced short-chain fatty acids (SCFAs), increasingly implicated in pathogenic processes extending beyond intestinal mucosa. This review outlines how these alternations compromise the epithelial barrier and immune regulation, increasing the risk of recurrent Clostridioides difficile infections to anemia, neuropsychiatric comorbidities, and extraintestinal manifestations. We critically evaluate emerging microbiota-targeted strategies, including fecal microbiota transplantation (FMT), live biotherapeutic products (LBPs), and precision postbiotics, positioning them as potential adjuncts to conventional immunosuppression. Finally, we discuss the current barriers to clinical translation, such as safety and heterogeneity, and propose a future framework for personalized, functionally integrated IBD care aimed at restoring long-term microbiota homeostasis.<\/jats:p>","DOI":"10.3390\/ph19010118","type":"journal-article","created":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T09:25:02Z","timestamp":1767950702000},"page":"118","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Microbiota-Driven Strategies for Managing IBD-Associated Risks: From Infections to Mental Health"],"prefix":"10.3390","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4694-7334","authenticated-orcid":false,"given":"Patrycja","family":"Krynicka","sequence":"first","affiliation":[{"name":"Department of Gastroenterology and Nutrition Disorders, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Bydgoszcz, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8793-5890","authenticated-orcid":false,"given":"Pablo","family":"Cortegoso Valdivia","sequence":"additional","affiliation":[{"name":"Gastroenterology and Endoscopy Unit, University Hospital of Parma, 43126 Parma, Italy"},{"name":"Department of Clinical Research, University of Southern Denmark, 5230 Odense, Denmark"},{"name":"Surgical Research Unit, Odense University Hospital og Svendborg Sygehus, 5700 Svendborg, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maciej","family":"Morawski","sequence":"additional","affiliation":[{"name":"Clinical Department of Ophthalmology, 10th Military Clinical Hospital with Polyclinic, 85-681 Bydgoszcz, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2649-5967","authenticated-orcid":false,"given":"Wojciech","family":"Marlicz","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Pomeranian Medical University, 70-204 Szczecin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3430-9079","authenticated-orcid":false,"given":"Karolina","family":"Skonieczna-\u017bydecka","sequence":"additional","affiliation":[{"name":"Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2248-489X","authenticated-orcid":false,"given":"Anastasios","family":"Koulaouzidis","sequence":"additional","affiliation":[{"name":"Department of Clinical Research, University of Southern Denmark, 5230 Odense, Denmark"},{"name":"Surgical Research Unit, Odense University Hospital og Svendborg Sygehus, 5700 Svendborg, Denmark"},{"name":"Department of Gastroenterology, Pomeranian Medical University, 70-204 Szczecin, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Yadegar, A., Salahi-Niri, A., Dai, C., and Shen, J. 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