What is it about?
This review explains how therapies that target the gut microbiome—such as probiotics, prebiotics, fecal microbiota transplantation (FMT), engineered bacteria, bacteriophages, and microbial metabolites—are reshaping modern gastroenterology. Drawing on clinical trials, systematic reviews, and regulatory developments, the paper summarises: - Established treatments such as probiotics and FMT - New FDA-approved microbiome therapeutics, including Rebyota and Vowst - Emerging innovations like engineered probiotics, phage therapy, and metabolite-based drugs - Evidence across major gut conditions, including C. difficile infection, IBS, IBD, NAFLD, and H. pylori - Future directions, including AI-enabled precision medicine, biomarkers, and personalised microbial interventions The review highlights effectiveness, safety, limitations, and where evidence remains uncertain.
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Photo by National Institute of Allergy and Infectious Diseases on Unsplash
Why is it important?
1. Microbiome therapies are moving from experimental to mainstream care The approvals of Rebyota and Vowst represent the first regulatory recognition of microbiome-based treatments, paving the way for a new class of therapeutics. 2. Strong evidence exists for specific conditions For recurrent C. difficile infection, cure rates of 67–94% make FMT and microbiome therapeutics the most effective options available. Table 1 clearly shows high-certainty evidence for CDI, but far lower certainty for other conditions. 3. Other gastrointestinal diseases show promise—but mixed evidence IBS, ulcerative colitis, Crohn’s disease, and fatty liver disease show strain-specific or protocol-dependent benefits, but results are variable and often low-certainty. 4. The pipeline is expanding rapidly More than 200 active clinical trials and growing biotech investment indicate major growth in microbiome therapeutics. Figure 1 visually maps the trajectory of innovations such as engineered probiotics and bacteriophage therapy. 5. Precision medicine is the future Microbiome profiling, multi-omics, and AI-driven analytics may soon guide personalised digestive disease treatment.
Perspectives
Clinical Perspective Clinicians now have validated microbiome therapies for recurrent C. difficile and emerging options across IBS, IBD, metabolic liver disease, and H. pylori. The field requires careful patient selection, attention to strain-specific evidence, and awareness that benefits vary widely across conditions. Scientific Perspective Rapid advances in synthetic biology, bacteriophage design, and metabolite-targeted strategies (pages 8–9) are creating new therapeutic possibilities. However, mechanistic understanding, biomarker validation, and long-term safety data remain incomplete. Regulatory & Policy Perspective The establishment of FDA pathways for microbiome products is a major milestone. Yet challenges remain: - high costs, - cold-chain logistics, - donor-screening protocols, and - global inequities in access. International harmonisation will be essential for safe, scalable adoption. Patient Perspective Microbiome therapies align with natural biological processes and offer alternatives when traditional treatments fail—particularly for C. difficile, a condition with high recurrence and significant quality-of-life impact. Future Outlook The field is moving rapidly toward precision, personalised care. With expanding trials, AI-assisted profiling, and commercial investment, microbiome-targeted treatments are expected to become an integral part of gastroenterology.
Professor Chi Eung Danforn Lim
University of Technology Sydney
Read the Original
This page is a summary of: Microbiome-Targeted Therapies in Gastrointestinal Diseases: Clinical Evidence and Emerging Innovations, Acta Microbiologica Hellenica, September 2025, MDPI AG,
DOI: 10.3390/amh70030036.
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