FDA-recognised
- Recurrent C. difficile — 85–95% cure after multiply-recurrent CDI. Standard of care after the second recurrence.
Strong / emerging evidence
- Ulcerative colitis — Multiple RCTs show induction of remission in a subset of patients.
Active research
- Autism spectrum disorder — Open-label trials show sustained GI and behavioural improvements two years on.
- Depression — Small pilots suggest improvements in depressive and anxiety symptoms via the gut–brain axis.
Also under study
- MDRO decolonisation, NAFLD, Parkinson's, melanoma immunotherapy response, GVHD. Smaller search interest, more limited evidence — covered briefly across the site.
Conditions covered in brief
Conditions with smaller search interest or more preliminary evidence — summarised here rather than given a dedicated page.
Irritable bowel syndrome (IBS)
IBS was an early target for FMT on the logic that altered gut microbial communities contribute to symptoms. The trial record is genuinely split. Johnsen and colleagues (2018, Norway) found single-dose colonoscopic FMT improved symptoms at three months versus placebo, while Halkjær and colleagues (2018, Denmark) found capsule FMT performed worse than placebo. El-Salhy's group in Bergen has since reported dose-dependent benefit from a well-characterised "super-donor", with response rates around 65–75% at 30g and higher doses.
Net read: FMT may help a subset of IBS patients, but donor selection, dose, and route appear to matter more than for CDI. It is not standard care, and meta-analyses across mixed protocols are inconclusive.
Crohn's disease
Evidence for FMT in Crohn's is far thinner than for ulcerative colitis. Small open-label series and pilot RCTs (Sokol 2020; Vaughn 2016) show that FMT can be delivered safely in Crohn's and that some patients achieve clinical response, but durable remission rates are modest and inconsistent. A recurring concern is that the inflamed Crohn's mucosa may resist long-term donor microbiota engraftment.
FMT for Crohn's remains investigational. Most active research is exploring it as maintenance after surgically induced remission rather than as primary induction therapy.
Hepatic encephalopathy
Hepatic encephalopathy (HE) — the neurocognitive complication of cirrhosis driven in large part by gut-derived ammonia and inflammation — is one of the more mechanistically coherent FMT indications. Bajaj and colleagues have run a series of small randomised and open-label trials showing that FMT (by enema or capsule) reduces recurrent HE episodes, improves cognition, and shifts the microbiome away from ammonia-producing taxa.
Sample sizes are small and follow-up is limited, but the signal is consistent. Larger phase 2/3 trials are ongoing, and the FDA has granted orphan-drug designation to FMT products targeting recurrent HE.
Metabolic health (obesity, insulin resistance, NAFLD)
The proof-of-concept came from Vrieze et al. (2012), who showed that FMT from lean donors transiently improved insulin sensitivity in men with metabolic syndrome. Subsequent trials — Kootte 2017, Allegretti 2020, Yu 2020 — broadly replicated short-term metabolic improvements but found that effects waned by 12–18 weeks as the recipient microbiome reverted.
FMT does not produce meaningful or sustained weight loss in humans, despite striking mouse data. Current interest centres on combining FMT with dietary or pharmacological maintenance, and on identifying the specific microbial consortia (rather than whole stool) that drive the metabolic signal.