Fecal Microbiota Transplantation in Gastrointestinal Disorders

Fecal microbiota transplantation (FMT) has emerged as a transformative therapy for conditions linked to microbial imbalance, most notably recurrent Clostridioides difficile infection. By introducing a diverse community of healthy donor microbes into the recipient gut, FMT restores colonisation resistance, rebalances metabolic activities and modulates immune responses. Beyond C. difficile, FMT is under investigation for inflammatory bowel diseases, irritable bowel syndrome and metabolic syndrome, where dysbiosis contributes to pathogenesis. Delivery methods range from colonoscopic infusion to oral capsules, and newer approaches employ defined bacterial consortia or isolated viromes to improve safety and reproducibility. As antibiotic resistance and chronic inflammatory disorders become more prevalent worldwide, FMT offers a globally significant, microbiome-based strategy to re-establish gut homeostasis and enhance patient outcomes.

Research from Nature Portfolio

Recent integrated metagenomic analyses across multiple clinical cohorts have delineated the trajectories of donor microbial strains in recipients and their association with therapeutic success. A systematic meta-analysis of over 200 donor–pre-FMT–post-FMT triads covering diverse disease indications revealed that higher levels of engraftment—particularly of Bacteroidetes and Actinobacteria species—correlate with clinical remission. Combined delivery routes and prior antibiotic conditioning were shown to enhance strain transfer. Importantly, machine-learning models trained on cross-study data achieved robust prediction of post-FMT species presence, paving the way for personalised donor selection and protocol optimisation in targeted FMT applications.

Fecal Microbiota Transplantation in Gastrointestinal Disorders publication trend

The graph below shows the total number of articles in fecal microbiota transplantation in gastrointestinal disorders across all publications each year (not limited to Nature Index journals).

Technical terms

Fecal Microbiota Transplantation (FMT): the process of transferring processed stool from a healthy donor into the gastrointestinal tract of a recipient to restore microbial diversity and function.

Dysbiosis: an imbalance or maladaptation in the composition or activity of the gut microbiota linked to disease development.

Engraftment: the establishment, growth and persistence of donor-derived microbial strains within the recipient’s intestinal ecosystem.

Metagenomics: the culture-independent analysis of collective microbial genomes from environmental or host-associated samples to characterise community structure and function.

Colonisation Resistance: the native microbiota’s capacity to inhibit colonisation and overgrowth of pathogenic organisms through competition and metabolic interactions.

References

1. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans. Microbiome (2023).
2. The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome. Advanced Science (2023).
3. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome (2013).
4. Fecal microbiota transplantation in metabolic syndrome: History, present and future. Gut Microbes (2017).
5. Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases. Nature Medicine (2022).