{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T07:04:59Z","timestamp":1779433499887,"version":"3.53.1"},"reference-count":174,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD\u2014including aminosalicylates, biologics, and immunomodulators\u2014largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.<\/jats:p>","DOI":"10.3389\/fcimb.2026.1826972","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T06:08:35Z","timestamp":1779430115000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["From dysbiosis to precision medicine: targeting the microbial\u2013metabolic axis in IBD management"],"prefix":"10.3389","volume":"16","author":[{"given":"John K.","family":"Giju","sequence":"first","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Subin","family":"John","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amrutha","family":"Sivadas","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meera","family":"Prabhakar","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krishnakripa","family":"K.","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damu","family":"Sunilkumar","sequence":"additional","affiliation":[{"name":"The Ohio State University Wexner Medical Center and Comprehensive Cancer Center","place":["Columbus, OH, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bipin G.","family":"Nair","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay","family":"Pal","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidhya","family":"Prakash","sequence":"additional","affiliation":[{"name":"School of Biotechnology, Amrita Vishwa Vidyapeetham","place":["Kollam, Kerala, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,22]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.abn6660","article-title":"Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation","volume":"7","author":"Adiliaghdam","year":"2022","journal-title":"Sci. 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