Multi-omics Dissection of Gut Microbiome Engraftment During FMT

Trial details

Who runs it

Catholic University of the Sacred Heart

Trial code

NCT06992453

Record updated

26 October 2026

Original description

The gut microbiota plays a key role in immunity and metabolism and contributes to diseases such as recurrent C. difficile infection (rCDI), ulcerative colitis (UC), and metabolic syndrome (MetS). Microbiota therapeutics, particularly fecal microbiota transplantation (FMT), show promise-achieving ~90% cure rates in rCDI-but demonstrate variable efficacy in chronic conditions. Microbiome engraftment appears critical for FMT success, yet consistent predictors remain lacking. A meta-analysis of 20 FMT studies by our group and the Segata Lab linked engraftment to clinical response across diseases, with taxon-specific patterns and ML-based predictability. While viral, fungal, host immune, genetic, and metabolic factors may affect engraftment, their roles are not well-defined. Key unresolved questions include the interplay among host factors, microbial strains, and metabolites, their influence on engraftment, and impact on clinical outcomes. This study aims to unravel microbiome engraftment dynamics and link them to therapeutic response.Read full original descriptionShow less

Disentangling Microbiome Engraftment by Multi-omics of the Gut Ecosystem During Fecal Transplant

The gut microbiota plays a key role in immunity and metabolism and contributes to diseases such as recurrent C. difficile infection (rCDI), ulcerative colitis (UC), and metabolic syndrome (MetS). Microbiota therapeutics, particularly fecal microbiota transplantation (FMT), show promise-achieving ~90% cure rates in rCDI-but demonstrate variable efficacy in chronic conditions. Microbiome engraftment appears critical for FMT success, yet consistent predictors remain lacking. A meta-analysis of 20 FMT studies by our group and the Segata Lab linked engraftment to clinical response across diseases, with taxon-specific patterns and ML-based predictability. While viral, fungal, host immune, genetic, and metabolic factors may affect engraftment, their roles are not well-defined. Key unresolved questions include the interplay among host factors, microbial strains, and metabolites, their influence on engraftment, and impact on clinical outcomes. This study aims to unravel microbiome engraftment dynamics and link them to therapeutic response.

Inclusion: Coorte: Patients affected by Ulcerative Colitis; Age ≥18 years; UC with mild-to-moderate activity (total Mayo score 3-10 + endoscopic subscore≥1) (23); UC during stable maintenance therapy (> 8 weeks with salicylates, immunosuppressants); Ability to give informed consent; Coorte: Patients affected by metabolic syndrome; Age ≥18 years; Patients with MetS (high glycaemia levels (> 100 mg/dL), hypertension (> 130/85 mmHg), raised triglyceride levels (> 150 mg/dL), low high-density lipoprotein cholesterol levels (< 40 mg/dL in men; <50 mg/dL in women), and abdominal obesity (waist circumference of > 102 cm in men; >88 cm in women); Stable treatment (> 8 weeks) of one of these disorders, included in MetS definition; Ability to give informed consent; Coorte: Patients affected by rCDI; Age ≥18 years; Mild recurrent Clostridioides difficile infection (26); Ability to give informed consent.

Exclusion: Antimicrobial treatment up to 4 weeks prior to screening visit (apart for patients with rCDI); Previous colorectal surgery or cutaneous stoma; Known active gastrointestinal disorders (e.g. infectious gastroenteritis except CDI, coeliac disease, irritable bowel syndrome, chronic pancreatitis, biliary salt diarrhoea) apart from UC, with clinical characteristics reports in inclusion criteria; Pregnancy, breastfeeding, and the refusal to follow an effective contraception method for all the study duration (for women); Critical and severe comorbidities; Inability to give informed consent.

ClinicalTrials.gov NCT06992453