dietary fiber
The Role of Microbiota and Fecal Transplantation in Inflammatory Bowel Disease
21 April 2026
Lagos I, Pérez de Arce E, Faggiani I, D'Amico F, Zilli A, Furfaro F, Massironi S, Cicerone C, Solitano V, Parigi TL, Peyrin-Biroulet L, Danese S, Allocca M.
Summary
What the study found
This systematic review of 118 studies confirms that Inflammatory Bowel Disease (IBD) is consistently linked to a loss of bacterial variety in the gut. While fecal transplants show significant promise as a treatment for ulcerative colitis, the evidence for Crohn’s disease remains less certain and requires more intensive delivery methods.
Key findings
- The most consistent hallmark of IBD is a significant reduction in microbial diversity, which is typically more severe in patients with Crohn’s disease than in those with ulcerative colitis.
- Patients frequently show a depletion of Faecalibacterium prausnitzii, a "keystone" species that provides anti-inflammatory properties and protects the gut lining.
- There is a notable functional impairment in the production of short-chain fatty acids, which are vital metabolites used by the body to regulate the immune system and fuel colon cells.
- Clinical evidence supports the efficacy of fecal microbiota transplantation (FMT) for inducing remission in ulcerative colitis, particularly when patients receive multiple or intensive doses.
Practical takeaways
To support long-term gut health and longevity, emphasize a diet rich in diverse plant fibers to support "good" bacteria like Faecalibacterium prausnitzii. Maintaining high microbial richness is a key strategy for reducing chronic inflammation and protecting the intestinal barrier against disease triggers.
Limitations
Researchers still face challenges in determining if microbial imbalances are a causal factor or merely a consequence of gut inflammation. Furthermore, while short-term results for fecal transplants are encouraging, there is a lack of long-term safety data for these procedures.
Abstract
Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are consistently associated with alterations in gut microbial communities, although the extent and characteristics of these alterations vary across studies, supporting a potential role of the microbiota in disease pathogenesis and therapeutic modulation. We conducted a systematic review to synthesize current evidence on microbiota alterations in IBD and the clinical application of fecal microbiota transplantation (FMT). A total of 118 studies were included (76 focused on microbiota profiling and 42 evaluated FMT as therapy). Across heterogeneous study designs and microbial characterization methods, reduced microbial diversity was the most consistently reported alteration, generally more pronounced in CD than in UC. Depletion of <i>Faecalibacterium prausnitzii</i>-a key butyrate producer with anti-inflammatory properties-was commonly reported, often accompanied by functional impairment in short-chain fatty acid production. Microbial patterns were frequently associated with mucosal inflammation and varied across disease phenotypes; these patterns have been increasingly explored as predictors of treatment response and relapse, although mechanistic interpretation remains limited and causal relationships are difficult to establish. Evidence from randomized controlled trials suggests potential efficacy of FMT in UC, particularly with intensive or repeated protocols, whereas data in CD remain limited and heterogeneous, with signals of benefit often appearing transient. FMT was generally well tolerated, but long-term safety data remain scarce. Emerging multi-omic approaches are reshaping the field by integrating taxonomic and functional insights, with potential implications for risk stratification, diagnosis, prognosis, and therapeutic optimization. Further standardized, longitudinal, and mechanistically oriented studies are required to translate microbiome research into clinically actionable strategies in IBD.
Source study →