Precision microbiota therapy for IBD: premise and promise

Gut Microbes. 2025 Dec;17(1):2489067. doi: 10.1080/19490976.2025.2489067. Epub 2025 Apr 7.

Abstract

Inflammatory Bowel Disease (IBD) is a spectrum of chronic inflammatory diseases of the intestine that includes subtypes of ulcerative colitis (UC) and Crohn's Disease (CD) and currently has no cure. While IBD results from a complex interplay between genetic, environmental, and immunological factors, sequencing advances over the last 10-15 years revealed signature changes in gut microbiota that contribute to the pathogenesis of IBD. These findings highlight IBD as a disease target for microbiome-based therapies, with the potential to treat the underlying microbial pathogenesis and provide adjuvant therapy to the emerging spectrum of advanced therapies for IBD. Building on the success of fecal microbiota transplantation (FMT) for Clostridioides difficile infection, therapies targeting gut microbiota have emerged as promising approaches for treating IBD; however, unique aspects of IBD pathogenesis highlight the need for more precision in the approach to microbiome therapeutics that leverage aspects of recipient and donor selection, diet and xenobiotics, and strain-specific interactions to enhance the efficacy and safety of IBD therapy. This review focuses on both pre-clinical and clinical studies that support the premise for microbial therapeutics for IBD and aims to provide a framework for the development of precision microbiome therapeutics to optimize clinical outcomes for patients with IBD.

Keywords: Crohn’s disease; Inflammatory bowel disease; precision microbiome therapeutics; ulcerative colitis.

Publication types

  • Review

MeSH terms

  • Animals
  • Fecal Microbiota Transplantation* / methods
  • Gastrointestinal Microbiome*
  • Humans
  • Inflammatory Bowel Diseases* / microbiology
  • Inflammatory Bowel Diseases* / therapy
  • Precision Medicine* / methods