Faecal Microbiota Transplantation:
The Science, The Evidence, The Future

Recurrent C. difficile infection is the gold standard for FMT — the only indication with regulatory approval and strong guideline endorsement. The pivotal 2013 trial by van Nood et al. was stopped early because FMT was so clearly superior to vancomycin, achieving 81% resolution (94% after a second infusion) versus just 31% for the antibiotic alone.van Nood 2013

A 2017 meta-analysis pooling 37 studies confirmed an overall cure rate of 92%, with colonoscopic delivery achieving 95%.Quraishi 2017 The 2023 Cochrane review further validated these findings (NNT = 3). Two FDA-approved products now exist: Rebyota (rectal, Nov 2022) and Vowst (oral capsules, Apr 2023). In Australia, Biomictra received TGA approval in November 2022 and is now supplied to 33+ hospitals via BiomeBank.

Australian real-world data from Tucker et al. (2025) — 220 FMT cases from South Australia — confirms cure rates consistent with international trials: 81% after first FMT, 91% after second, with serious adverse events in only 3% of cases.Tucker 2025 The AGA 2024 guideline suggests fecal microbiota-based therapies for immunocompetent adults with recurrent CDI after standard antibiotics.AGA 2024

Ulcerative colitis is the most actively researched non-CDI indication for FMT, with Australian researchers contributing three of the five landmark RCTs. The FOCUS trial (Paramsothy et al., 2017) — the largest FMT-UC trial at publication — randomised 85 patients across three Sydney hospitals and achieved 27% steroid-free remission versus 8% placebo.Paramsothy 2017

The Adelaide-based Costello trial (2019) introduced anaerobic stool processing — preserving oxygen-sensitive bacteria — and achieved the highest remission rate among the original trials: 32% versus 9%.Costello 2019 Most striking was the Sydney LOTUS trial (Haifer et al., 2022), combining antibiotic preconditioning with oral capsules to achieve 53% remission versus 15% placebo — and demonstrating that 100% of patients who continued FMT maintained remission, while 100% who stopped relapsed.Haifer 2022

A 2025 meta-analysis of 14 RCTs (600 patients) confirmed a significant benefit with OR 2.25 for combined clinical and endoscopic remission.Gefen 2025 Current guidelines restrict FMT for UC to clinical trials, but the Australian contribution — through the FOCUS and LOTUS trials and BiomeBank infrastructure — positions local clinicians at the forefront of this research.

The IBS-FMT literature reveals a striking pattern: donor selection and delivery method are everything. The standout trial is El-Salhy et al. (2020), a Norwegian RCT of 165 patients using a single carefully selected "super-donor" — a healthy 36-year-old male with minimal antibiotic exposure and high microbial diversity. Response rates were 76.9% (30g dose) and 89.1% (60g) versus 23.6% placebo.El-Salhy 2020 Remarkably, 3-year follow-up showed sustained response in 65–72% of recipients.El-Salhy 2022

By contrast, trials using unselected donors or capsule delivery have consistently failed — some even performing worse than placebo. Meta-analyses show endoscopic delivery is significantly effective (RR 3.03) while capsules are not. The critical insight: FMT for IBS works when you get the donor, dose, and delivery right. All IBS subtypes (IBS-D, IBS-C, IBS-M) responded. Current guidelines recommend against routine use pending standardised protocols.

The direct evidence for FMT in SIBO is limited but mechanistically compelling. The only published placebo-controlled trial — Xu et al. (2021), a Chinese RCT of 55 SIBO patients — randomised participants to oral FMT capsules or placebo for 4 weeks. Symptom scores decreased significantly in the FMT group at 1, 3, and 6 months, breath test hydrogen normalised, and microbial diversity increased toward donor profiles.Xu 2021

A 2024 mBio study of 218 chronic constipation patients found those with coexisting SIBO responded significantly better to FMT than those without (P=0.003) — and small intestinal microbiota changed more than colonic microbiota, suggesting FMT can specifically modify small intestinal dysbiosis. The mechanistic rationale includes restoring colonisation resistance against overgrown organisms, normalising migrating motor complex function, and restoring bile acid metabolism.

The FMT-autism field exemplifies the tension between compelling open-label results and the challenge of placebo-controlled trials. The landmark Arizona State study (Kang et al., 2017) — designed with protocol input from Australia's Thomas Borody — treated 18 children with ASD and GI symptoms using a full MTT protocol (vancomycin, bowel cleanse, 7–8 weeks treatment). GI symptoms improved by approximately 80%, with significant behavioural improvements across CARS, SRS, and ABC measures.Kang 2017

The two-year follow-up was remarkable: professional assessments showed a 45% reduction in core ASD symptoms. At baseline, 83% were rated "severe" autism; at two years, only 17% remained "severe," 39% were "mild/moderate," and 44% fell below the ASD diagnostic cut-off.Kang 2019 However, the largest RCT (Wan et al., 2024; n=103) found no significant difference between FMT and placebo on primary behavioural outcomes — though it used a very different protocol (no antibiotics, no bowel cleanse, capsules only).Wan 2024

The FTACMT study — a multicentre, double-blind RCT enrolling 318 children across 15 Chinese hospitals — is currently the largest trial and may provide definitive data. An Australian RCT enrolling 100 adolescents and adults is also in progress. No clinical guidelines currently recommend FMT for ASD.

The first controlled trial of FMT specifically for depression was conducted in Australia — the Moving Moods study at Deakin University (Green et al., 2023), using BiomeBank's FMT product. Though small (n=15), it demonstrated safety, feasibility, and enormous patient demand — over 160 expressions of interest in just two months against a target of 15. The active FMT group showed significantly greater improvement in GI symptoms, with near-significant quality-of-life improvements.Green 2023

A 2025 meta-analysis pooling 12 RCTs with 681 participants found FMT significantly reduced depressive symptoms (SMD = −1.21, P = 0.0003). Both oral capsule and direct GI delivery were effective, with improvements most notable in the first few months. Emerging research suggests FMT may enhance the effects of conventional antidepressants — Jiang et al. (2025) demonstrated multi-omic mechanisms by which FMT boosts SSRI efficacy.

No clinical trials have yet tested FMT specifically for primary anxiety disorders, but the evidence connecting gut bacteria to anxiety is compelling. People with generalised anxiety disorder have been found to have significantly elevated levels of Escherichia-Shigella bacteria compared to healthy controls. Strikingly, Ritz et al. (2024) demonstrated that transplanting gut microbiota from individuals with social anxiety disorder into mice reliably produces anxiety-like behaviour in the recipients.Ritz 2024

Several clinical trials of FMT for other conditions — particularly IBS and depression — have reported improvements in anxiety as a secondary outcome. Notably, one study found these improvements occurred independently of any changes in gut symptoms, suggesting a direct microbiome-brain pathway. A 2024 systematic review of 14 studies confirmed FMT's potential to modify the bacterial markers associated with GAD. Dedicated clinical trials are expected as the field matures.

Parkinson's disease has one of the strongest established connections to the gut microbiome of any neurological condition. The "gut-first" hypothesis proposes that PD pathology may begin in the gut before spreading to the brain via the vagus nerve — supported by the fact that gut dysfunction, especially constipation, often precedes motor symptoms by years or even decades. Lewy body pathology has been found in the gut's own nervous system.

The most notable trial is the GUT-PARFECT study (Bruggeman et al., 2024) — a double-blind RCT of 46 early-stage PD patients. A single FMT treatment produced statistically significant and clinically meaningful motor improvement at 12 months (P = 0.0235), with the most pronounced improvement occurring between 6 and 12 months — suggesting a potentially disease-modifying effect.Bruggeman 2024 A Chinese RCT (Cheng et al., 2023; n=54) also showed significant improvement in movement and autonomic symptoms.Cheng 2023

However, a larger Finnish trial (Scheperjans et al., 2024; n=45) published in JAMA Neurology found no significant benefit on its primary outcome, underscoring that donor selection, delivery method, and protocol design are critical variables still being optimised.Scheperjans 2024

Bipolar disorder has been associated with distinct gut microbiota profiles, and preclinical research has demonstrated that FMT from individuals with BD into mice produces behavioural changes and metabolic shifts consistent with BD pathology. The most compelling clinical evidence comes from an Australian case report (Parker et al., 2022, UNSW Sydney): a young male with treatment-resistant bipolar disorder experienced distinct improvement in mood oscillations following FMT, was able to cease all psychiatric medications, and maintained improved mood stability for over 470 consecutive days of daily tracking.Parker 2022

A formal pilot RCT is underway in Canada (NCT03279224), and preclinical research from Austria (2023) has demonstrated that microbiome-related metabolic and behavioural traits of BD are partially transferable via FMT — establishing the biological plausibility for therapeutic intervention.

The gut-brain axis rationale for FMT in ME/CFS is scientifically compelling — ME/CFS patients consistently show reduced bacterial diversity and elevated markers of microbial translocation. The earliest clinical data came from Australia's Thomas Borody, whose retrospective review of 60 CFS patients reported 70% response to treatment, with long-term follow-up (15–20 years) finding 58% maintained complete symptom resolution.Borody 2012

However, the only completed RCT — Salonen et al. (2023), a Finnish double-blind trial of 11 patients — found no benefit of FMT over sham on any measure. While severely underpowered, this represents the highest-quality evidence currently available. The Norwegian Comeback Study (n=80) has completed recruitment but results suggest it may also be negative. The proposed mechanism — dysbiosis leading to reduced SCFA production, increased gut permeability, bacterial translocation, and ultimately neuroinflammation — remains biologically plausible even as clinical evidence falls short.

PANS and PANDAS are conditions where children suddenly develop severe OCD, tics, anxiety, and behavioural changes — typically after an infection. In PANDAS, streptococcal infections trigger an autoimmune response where antibodies mistakenly attack parts of the brain. Research has revealed that children with PANS/PANDAS have distinct differences in their gut bacteria, including reduced diversity and an imbalance that promotes inflammation.Quagliariello 2018

Gut microbiome disruption has been linked to altered dopamine metabolism — connecting directly to the brain pathology seen in these patients. A 2025 narrative review of approximately 250 studies confirmed that alterations in gut and oral microbial communities modulate neuroinflammation through increased intestinal and blood-brain barrier permeability, immune dysregulation, and altered neuroactive metabolite production. While no FMT trials have been published specifically for PANS/PANDAS, the condition involves immune dysregulation, gut barrier dysfunction, and microbiome disruption — all of which FMT has addressed in other conditions. Many patients have undergone multiple courses of antibiotics, further damaging their gut microbiome.

People with RA — particularly those newly diagnosed — harbour a distinct gut microbiome, with higher levels of Prevotella copri and lower levels of anti-inflammatory species. Remarkably, Alpizar-Rodriguez et al. (2019) showed these changes appear before joint symptoms begin, suggesting the gut may be involved in triggering the disease. Pianta et al. (2017) identified specific P. copri peptides that triggered Th1 immune responses in 42% of new-onset RA patients.Pianta 2017

One published case report describes a young woman with treatment-resistant RA who improved after FMT (Zeng et al., 2021). A randomised controlled trial in Canada (NCT05790356) is now testing FMT capsules against placebo in 30 ACPA-positive RA patients, with results anticipated. Preclinical work by Zheng et al. (2023) confirmed the causal direction — FMT from pre-RA individuals into mice worsened arthritis.

AS has one of the strongest known connections between gut health and joint disease. Up to 60% of AS patients have silent gut inflammation, and the disease overwhelmingly affects people carrying the HLA-B27 gene. Decades of research have shown that Klebsiella species may trigger the immune system to mistakenly attack joint tissues through molecular mimicry with HLA-B27.

Critically, HLA-B27-positive animals raised in completely germ-free conditions do not develop the disease — only when normal gut bacteria are present does inflammation develop (Taurog et al., 1994). This is among the most powerful demonstrations in any autoimmune condition that the microbiome is essential, not incidental. While no completed FMT trials exist, AS is included in an ongoing Danish clinical trial (NCT04924270) testing FMT in newly diagnosed inflammatory conditions.

Psoriasis is increasingly recognised as a systemic condition with deep connections to the gut. People with psoriasis consistently show gut microbiome patterns that mirror those seen in inflammatory bowel disease — including reduced Faecalibacterium prausnitzii (anti-inflammatory) and elevated pro-inflammatory species.

The Danish FLORA trial (Kragsnaes et al., 2021) was the first-ever RCT of FMT in any immune-mediated arthritis, testing a single gastroscopic FMT in 31 adults with active PsA. FMT was safe and well-tolerated, but did not improve disease activity compared to sham. The researchers concluded that higher doses, repeated administration, and careful donor selection — factors proven important in FMT for IBD — may be necessary, and modified protocols are now underway.

MS patients consistently harbour distinct gut microbiome profiles, and elevated intestinal permeability ("leaky gut") has been documented, providing a pathway for bacterial products to influence CNS inflammation. A pilot RCT (Al et al., 2022) of monthly FMTs in 9 RRMS patients confirmed safety and found that two patients with elevated baseline permeability saw their gut barrier function return to normal after treatment, with beneficial donor-specific microbiome shifts.

Case reports spanning over a decade describe MS symptom improvement following FMT — including one remarkable case where a patient with progressive MS appeared to remain stable for over 10 years after FMT originally administered for a gut infection (Makkawi et al., 2018). A Phase 1b trial at UCSF (NCT03594487) is formally investigating FMT in relapsing-remitting MS with immunological endpoints.

Metabolic syndrome has the strongest and most replicated metabolic evidence for FMT. The foundational Vrieze et al. (2012) trial demonstrated a ~73% improvement in peripheral insulin sensitivity at 6 weeks after lean-donor FMT in men with metabolic syndrome — an effect size exceeding many pharmacological interventions.Vrieze 2012 Kootte et al. (2017) confirmed the improvement but showed it reverted to baseline by 18 weeks, and that patients with the lowest baseline microbial diversity benefited most.Kootte 2017

A meta-analysis of 9 RCTs (303 participants) confirmed significant reductions in fasting glucose, HbA1c, and insulin. Mocanu et al. (2021) in Nature Medicine showed that combining FMT with fibre supplementation produced the best metabolic outcomes. The central challenge remains durability — effects peak at 6 weeks and diminish without ongoing intervention, suggesting repeated dosing or adjunctive therapies may be needed.Mocanu 2021

FMT for obesity consistently demonstrates successful microbiome engraftment and safety, with some metabolic improvements — but consistently fails to produce clinically meaningful weight loss. The Gut Bugs Trial (Leong et al., 2020), the largest adolescent FMT trial (n=87), showed no BMI change but significantly reduced android-to-gynoid fat ratio and, remarkably, resolved metabolic syndrome in many recipients (adjusted OR 0.06, P=0.007).Leong 2020

The most striking data came from the 4-year follow-up (Wilson et al., 2025): FMT recipients showed smaller waist circumference (−10cm), lower total body fat (−4.8%), lower metabolic syndrome severity, and lower inflammation markers — with donor-derived strains still persisting at 4 years. These are the longest-term FMT outcome data in metabolic disease, though the follow-up was unblinded.Wilson 2025

The most directly relevant T2DM trial (Wu et al., 2022) enrolled 31 newly diagnosed patients in three arms: metformin alone, FMT alone, and FMT plus metformin. FMT alone improved insulin resistance and BMI, while FMT plus metformin improved insulin resistance, BMI, fasting glucose, postprandial glucose, and HbA1c — demonstrating that FMT can enhance metformin's effectiveness.Wu 2022

This synergy is biologically grounded: metformin itself partly works through the gut microbiome, increasing Akkermansia muciniphila and modulating bile acid metabolism. Repeated monthly FMTs achieved 100% engraftment at 24 weeks when combined with lifestyle intervention (Ng et al., 2022). A 2024 meta-analysis confirmed pooled reductions in fasting glucose, triglycerides, and HOMA-IR. Pre-treatment microbiome profiling may identify which patients will respond best.Ng 2022

The liver receives approximately 75% of its blood supply from the portal vein, making it the first-pass organ for all gut-derived products. NAFLD patients show 5-fold greater intestinal permeability than controls. The mechanistic case is compelling — bacterial endotoxins, endogenous alcohol production by gut bacteria, choline depletion, and bile acid dysregulation all drive hepatic fat accumulation and inflammation.

However, clinical evidence remains at proof-of-concept with approximately 137 total patients across 4 completed RCTs. No trial has demonstrated robust improvement in primary endpoints of hepatic fat or metabolic parameters. The only trial with paired liver biopsies (Witjes et al., 2020) showed a trend toward improved inflammation but no significant change. A key insight from Groenewegen et al. (2025): responders correlated with donor-specific engraftment patterns, highlighting that donor selection may be the critical variable.Groenewegen 2025

Hepatic encephalopathy — brain fog caused by liver disease — often recurs despite standard medications. Cirrhosis-associated dysbiosis leads to overgrowth of ammonia-producing bacteria with depletion of beneficial SCFA-producing taxa. In the landmark THEMATIC trial (Bajaj et al., 2025), a Phase II double-blind RCT of 60 patients, FMT produced zero treatment-related serious adverse events, with HE recurrence of 0–13% in FMT groups versus 40% placebo, and hospitalisations reduced from 47% to 7–20%.

Earlier Phase I trials by the same group showed sustained cognitive improvement, zero HE episodes versus 1.5 in controls (P<0.05), and zero hospitalisations versus 3 (P<0.02) over 12+ months of follow-up. Multi-omic analysis revealed that donor engraftment of SCFA-producing taxa correlated directly with lower recurrence. Quality of life improved significantly (P=0.003).

Specific gut bacteria promote anti-tumour immunity by enhancing CD8⁺ T-cell infiltration into tumours. In the MIMic trial (Routy et al., 2023), FMT from healthy donors combined with immunotherapy in treatment-naïve melanoma achieved an overall response rate of 65% (4 complete + 9 partial responses in 20 patients). At nearly 5 years of follow-up, median progression-free survival was 29.6 months and median overall survival was 52.8 months.Routy 2023

The Phase II FMT-LUMINate trial (2024) reported a 70% response rate for FMT combined with dual checkpoint blockade. A 2025 pooled analysis of 10 studies (164 patients) found an overall response rate of 43%, with dual immunotherapy yielding 60% vs 37% for monotherapy (P=0.01). The first large randomised trial (ME.17, pan-Canadian) is now recruiting.

After a bone marrow transplant, the donor's immune cells can attack the patient's intestine, causing severe diarrhoea that often resists steroids. A meta-analysis of 242 patients reported a pooled remission rate of 64% (95% CI 51–77%), including many patients who had failed all other treatments. Van Lier et al. (2020) achieved 67% complete remission within one month, with immunosuppressants successfully tapered in 6 of 10 responders.

A Phase III trial of MaaT013 (pooled donor FMT product) for steroid- and JAK-inhibitor-refractory GI-aGVHD is ongoing (NCT04769895). Safety note: one fatal drug-resistant E. coli bacteraemia transmitted by FMT was reported in an immunocompromised patient (DeFilipp et al., 2019, NEJM), prompting enhanced donor screening protocols.

Antibiotic-resistant "superbugs" can colonise the gut and cause dangerous infections, especially in hospitalised patients. A systematic review (Macareño-Castro et al., 2019) of 121 patients reported an overall FMT eradication rate of 70.3% (VRE 63%, CRE 67%, ESBL 73%). The PREMIX Phase I RCT (Woodworth et al., 2023) found 89% of FMT recipients became MDRO-negative, identifying a novel "conspecific strain competition" mechanism where susceptible strains replace resistant ones.

Important context: spontaneous decolonisation rates are substantial (CRE ~50% at 6 months), making adequately powered RCTs essential. The UK FERARO feasibility RCT (2025, n=41) confirmed lower MDRO carriage at all timepoints in the FMT arm with no unanticipated harms. Colonisation resistance — competitive exclusion by a diverse microbiome — is the primary mechanism.

Chronic constipation is associated with depletion of SCFA-producing bacteria and enrichment of methanogens that slow transit. A 2025 meta-analysis of 9 studies (~250 patients) found pooled remission of 50.7% and improvement in 64.8%, with transit time reduced by an average of 20.3 hours and no serious adverse events. The largest RCT (Tian et al., 2017, n=60) found a cure rate of 36.7% FMT vs 13.3% control (P=0.04).

Benefits may fade over several months — one prospective cohort (Ding et al., 2018) showed efficacy declining from 50% at week 4 to 32.7% at week 24, suggesting repeated treatments may be needed. FMT was well-tolerated with only mild temporary side effects.

Severe alcoholic hepatitis is life-threatening with limited treatment options. Pande et al. (2023) conducted an open-label RCT of 120 patients showing 90-day survival of 75% FMT vs 56.6% prednisolone (P=0.044), with infection deaths dramatically lower: 3.6% vs 19.3% (P=0.01). A meta-analysis of 6 studies (371 patients) confirmed a pooled odds ratio for 90-day survival of 3.07 (95% CI 1.81–5.20, P<0.0001).

Important caveats: all major studies are from India, most are open-label, and survival benefit attenuates beyond 90 days. No blinded multicentre RCT has been published. The mechanism centres on restoring eubiosis, reducing endotoxaemia, and decreasing infection risk — a major cause of death where steroids are immunosuppressive.

A few small studies have explored whether FMT could help the immune system clear hepatitis B. Chauhan et al. (2021) reported HBeAg clearance in 16.7% (2/12) of FMT recipients versus 0% controls after 6 cycles via nasoduodenal tube. A Chinese prospective study found 36.4% (4/11) HBeAg-positive patients achieved negative conversion with decreased inflammatory markers. No HBsAg loss has been achieved in any study.

Only approximately 30 patients have been studied across all trials, all from India and China. The mechanism centres on restoring immune tolerance mechanisms and enhancing T-cell responsiveness to HBV antigens through the gut-liver axis. This remains a very early research area.

Cirrhosis features profound gut dysbiosis with "oralisation" of the faecal microbiome, depletion of SCFA-producing bacteria, and disrupted bile acid metabolism. Multiple Phase I/II trials have confirmed FMT is safe in cirrhosis and can restore healthier gut bacteria, reduce blood inflammation markers, and decrease antibiotic-resistant germs. Bajaj et al. (2021) showed alcohol craving reduced 90% in FMT recipients vs 30% placebo (P=0.02) in patients with alcohol-related cirrhosis, with fewer serious adverse events (2 vs 8, P=0.02).

The THEMATIC trial (2025, n=60) confirmed safety across all doses, routes, and donor types. Pooled analysis showed FMT significantly reduced gut microbial antibiotic resistance genes in cirrhosis patients — an important finding for this population prone to infections.

FMT has been shown to effectively treat diarrhoea caused by TKI cancer drugs. In an open-label RCT (Ianiro et al., 2019), 100% of FMT patients had diarrhoea resolved within a week vs 54.5% control (P=0.02), with 90% vs 0% resolution by day 15–30 (P=0.0001). Zero FMT patients needed cancer drug dose reductions.

The TACITO trial (Porcari et al., 2025, Nature Medicine) showed that FMT from immunotherapy responders combined with standard treatment more than doubled progression-free survival: median PFS 24.0 vs 9.0 months (HR 0.50, P=0.035), with an overall response rate of 52% vs 32%. This is one of the most clinically significant FMT findings in oncology.

The gut-liver axis is central to HCC development — chronic liver disease causes "leaky gut," allowing microbial products to drive inflammation and carcinogenesis. Kim et al. (2024) reported one HCC patient with remarkable tumour shrinkage after a donor switch in a Phase 2 trial of mixed tumours. Preclinical studies show FMT suppresses tumour-promoting IL-17A production and repolarises tumour-associated macrophages.

The FAB-HCC pilot (Pomej et al., 2025) is testing FMT combined with atezolizumab/bevacizumab in HCC patients failing first-line immunotherapy. This remains an early-stage, experimental area — FMT for HCC is not available outside of clinical trials.

For patients with chronic radiation damage to the bowel after radiotherapy, FMT is showing promise. The largest study (Li et al., 2019) of 127 radiation enteritis patients found 77.3% symptom improvement at 3 months, declining to ~60% at 36 months. Individual case reports document dramatic improvement in rectal bleeding and pain after multiple treatment rounds.

Preclinical work (Ding et al., 2025) identified Blautia wexlerae restoration and tryptophan metabolism as a key mechanism. Symptoms may recur over time, suggesting repeated treatments may be needed. No serious complications have been reported, but larger clinical trials are still needed.

When the body receives very high doses of radiation, it can severely damage the gut lining in a potentially life-threatening condition. Animal studies have consistently shown that FMT from healthy mice significantly improves survival, repairs the gut lining, and helps the immune system recover (Cui et al., 2017). The protective effect comes from beneficial bacteria producing tryptophan metabolites (indole-3-carboxaldehyde, kynurenic acid) that shield the gut.

Guo et al. (2020) identified that radiation survivors develop a distinct, protective microbiome enriched in Lachnospiraceae. FMT from metformin-treated mice conferred radiation resistance via FXR activation (Cui et al., 2022). While results are promising and robustly reproduced across multiple laboratories, FMT for acute radiation injury has not yet been tested in humans.

For chronic pouchitis after colectomy for UC, a meta-analysis of 9 studies (103 patients) found a pooled clinical response of 42.6% and remission of 29.8% with significant heterogeneity between protocols. A key challenge is that the ileal pouch environment differs substantially from a native colon, making it difficult for transplanted bacteria to establish.

Two RCTs showed limited benefit — one was stopped early due to low remission (1/6). An innovative trial (NCT05829109) is testing stool from patients with healthy pouches rather than from individuals with native colons as donors, which may improve engraftment.

CIPO is a rare, severe condition where the bowel fails to move its contents despite no physical blockage. Bercik et al. (2025) demonstrated that mice given gut bacteria from CIPO patients developed similar bowel problems — and a single CIPO patient who received FMT experienced improvement lasting 8 years. A pilot of 9 patients (Gu et al., 2017) found FMT reduced bloating and eliminated SIBO in 71% (5/7).

Only approximately 10 patients have been treated with FMT for CIPO in published literature worldwide. Evidence is extremely limited, and FMT for CIPO should only be considered in a research setting.

Suez et al. (2018, Cell) showed that autologous FMT (using banked pre-antibiotic stool) achieved near-complete microbiome recovery within days — outperforming both probiotics (which actually delayed recovery) and spontaneous reconstitution. Taur et al. (2018) confirmed autologous FMT rapidly restored diversity in immunocompromised stem cell transplant patients.

No RCTs exist for FMT specifically in symptomatic non-CDI antibiotic-associated diarrhoea, which typically resolves spontaneously. Research may eventually identify severe or prolonged cases where FMT could help, but this remains an unproven application — likely overtreatment for typical cases.