This page is the reference background for the IBS and IBD page. It goes through twenty-four papers — but not disease by disease, rather aspect by aspect: at every question, what we know about inflammatory bowel disease and what we know about irritable bowel syndrome stand side by side. The two are not in the same weight class, and that is exactly what this page shows.
IBS and IBD often appear on the same page, because in both the patient experiences the same thing: abdominal pain, unpredictable stools, exhaustion. The evidence, however, differs radically. Anyone who blurs this is not simplifying, but misleading.
In ulcerative colitis four independent randomised controlled trials have been carried out — Canadian, Dutch, Australian and the Costello trial — and all four found a higher remission rate in the group receiving donor stool than in the placebo group.371, 796, 392, 188 The Cochrane review confirms this direction, while rating the quality of the evidence as moderate.790 There is also data that remission can be maintained with repeat dosing.801
In IBS a single large, well-designed trial showed a marked effect: 89.1% of the patients receiving the 60-gram dose improved, against 23.6% on placebo.390 This figure is strong in itself — but it does not stand alone, and it does not all point one way.
In another, likewise Norwegian, randomised trial placebo performed betterthan donor stool.779 This is not a matter of detail: the opposite results of two similarly designed trials mean that the effect is not robust. That is exactly why the meta-analyses are cautious: pooled, they find a modest but strongly heterogeneous effect, and the source of the heterogeneity — donor, dose, route of delivery, patient group — has not been clarified.783, 784 The guideline of the American College of Gastroenterology therefore does not recommend faecal transplantation in routine care in IBS;785 nor does the British NICE guideline include it in the treatment sequence.788
In Crohn's disease there is even less data: on the basis of a single smaller randomised pilot trial478 and the pooled picture from the systematic reviews,793 routine use cannot be recommended. Coeliac disease and microscopic colitis do not even belong here: there is no study for these that would support microbiota transfer.
In the studies, mild, transient complaints are common — bloating, abdominal discomfort, transient diarrhoea or constipation, slightly raised temperature — and serious events are rare. In inflammatory bowel disease, however, flare-ups have also been described after the procedure, which is why tracking the inflammatory parameters cannot be omitted. The literature discusses the minimum requirements of donor screening separately;816, 817 we describe our own procedure below, in the Safety section.
The data listed here relate to the MTT (FMT) method and not to a specific product. The trials differ substantially in route of delivery, preparation, number of donors and dose — multi-donor, intensive protocols give a different result from a single-donor, one-off procedure.392, 462 This difference alone may explain the divergence between the trials.
Below we ask six questions. For each of them we give the answer first for inflammatory bowel disease, then for irritable bowel syndrome — in the same breakdown, side by side. This way the differences also become visible that would be lost in a text organised disease by disease.
Objective remission. The endpoint of the trials is clinical and endoscopic remission: the patient's symptoms resolve and the endoscopy also shows healing mucosa. This endpoint is measurable, it does not depend on the patient's judgement, and the treating physician sees the same thing as the investigator.371, 188
Symptom severity. The endpoint is the IBS-SSS score or “adequate symptom relief” — that is, a change measured on a questionnaire and judged by the patient. This is not a faulty measure, but it is sensitive to the placebo effect, which is well known to be large in functional conditions. An objective endpoint that could be checked by endoscopy does not even exist here.390, 189
A consistent but modest advantage. All four randomised trials tipped in favour of the donor group; the multi-donor, intensive Australian protocol gave the strongest signal.392 The size of the effect is nevertheless modest: the proportion reaching remission is typically one patient in four or five. This is not a miracle cure but one further chance alongside the existing treatment.
Several independent research groups, in four countries. This is the most important quality indicator: the result is not peculiar to a single centre or a single donor bank. The Cochrane review nevertheless rates the evidence as of moderate quality, because the trials are small and the protocols are not uniform.790
Few trials, with contradictory results. Most of the positive data come from the same Norwegian research group, and independent confirmation is missing. When an effect is not reproduced in other hands, that in itself is information.784
Promising, but not yet standard. The guidelines do not count microbiota transfer among the established treatments in IBD; the practical reviews discuss it as an experimental or complementary procedure, with an unambiguous message: it does not replace maintenance drug treatment.794
In the protocol. We do not know how many donors, what dose, what frequency and which route of delivery is right. The multi-donor, intensive scheme appears better, but we do not know why — certain bacteria and metabolites are enriched in responders, yet this has not yet become a usable prediction.462 In Crohn's disease the uncertainty is greater still.478, 793
In the patient group. Under the “IBS” label there are very different patients: post-infectious IBS,303 the form involving small intestinal overgrowth, and complaints of predominantly psychosocial origin. We do not know which subgroup responds — and the durability of the effect is also a question: in three-year follow-up it persists, but fades.782
Established drug treatment. Aminosalicylates, steroids, immunosuppression, biological therapy: there is no alternative to these, and microbiota transfer does not compete with them. Its place — if it has one — is alongside them, on stable baseline treatment, with the agreement of the gastroenterologist in charge.
Diet and treatment of the gut–brain axis. The evidence for the low-FODMAP diet,070 fibre supplementation, antispasmodics and gut–brain neuromodulators,787 and psychological therapies789 is strongerthan that for MTT. That is why in IBS MTT is not a first and not a second step: it comes into question only once these have been exhausted.
| Aspect | IBD (ulcerative colitis, Crohn's) | IBS |
|---|---|---|
| What was measured? | clinical and endoscopic remission | questionnaire-based symptom severity (IBS-SSS) |
| What came out? | four RCTs, all in favour of the donor; modest effect | one strongly positive, one negative RCT |
| Reliability | several independent research groups; moderate quality | few trials, without independent confirmation |
| Guidelines | not standard, but its experimental/complementary role is recognised | not recommended in routine care |
| Uncertainty | the protocol: number of donors, dose, route, frequency | the heterogeneity of the patient group, and durability |
| Alternative | baseline drug treatment — cannot be replaced | diet, neuromodulators, psychotherapy — with stronger evidence |
| For whom might it come into question? | mild to moderate ulcerative colitis, subject to the treating physician's judgement | only once the established routes have been exhausted |
The safety data measured in the published studies are set out above: a large pooled review, several years of follow-up, and the caveat that mild, transient complaints are common. What goes into the capsule, however, does not follow from the literature but from our own procedure.
Donor screening. Every donor goes through our DSQ donor screening framework: bacteriological, virological, parasitological and serological testing, a stool test and a detailed questionnaire.
The window period. A recent infection is not necessarily detectable at the moment the sample is taken. The donation is therefore held frozen in quarantine: for at least eight weeks, and it is never released before the result of the repeat test performed after the eighth week has arrived. The repeat test covers those infections that could already have occurred before the sample was taken but became detectable only during those eight weeks.
Always take the capsules under the guidance of your treating physician.
The facts and figures on this page come from twenty-four papers in all: nine randomised controlled trials, six systematic reviews and meta-analyses, two international professional guidelines, two review papers, one three-year follow-up, one microbiological mechanism analysis, and three papers dealing with donor screening and post-infectious IBS.
[070] Halmos, E. P., Power, V. A., Shepherd, S. J., et al. A diet low in FODMAPs reduces symptoms of irritable bowel syndrome Gastroenterology 2014. doi:10.1053/j.gastro.2013.09.046
Randomised single-blind cross-over trial in 30 IBS patients and 8 controls compared a low-FODMAP diet (<0.5 g/meal) with a typical Australian diet for 21 days each (>=21-day washout). Almost all food was provided. The low-FODMAP arm produced significantly greater reduction in IBS symptoms measured on 0-100 mm visual analogue scales, supporting the low-FODMAP diet as an effective intervention for symptom control in IBS compared with a standard Western diet.Source: references-v2.bib · ref-070
[188] Costello, S. P., Hughes, P. A., Waters, O. et al. Effect of fecal microbiota transplantation on 8-week remission in patients with ulcerative colitis: a randomized clinical trial JAMA 2019. doi:10.1001/jama.2018.20046
A multicenter, randomized, double-blind trial in three Australian centers enrolled 73 adults with mild-to-moderate ulcerative colitis. Patients received anaerobically prepared pooled donor FMT (n=38) or autologous FMT (n=35) via colonoscopy followed by 2 enemas over 7 days, with 12-month follow-up. Anaerobic stool processing was hypothesized to enhance microbial viability and allow efficacy with shorter, less intensive FMT therapy. The trial supports anaerobically prepared, short-duration FMT as an effective induction therapy in active UC.Source: references-v2.bib · ref-188
[189] Camilleri, M. Diagnosis and treatment of irritable bowel syndrome: a review JAMA 2021. doi:10.1001/jama.2020.22532
Irritable bowel syndrome (IBS) affects 7–16% of the US population, most often women and young adults, with direct annual costs over USD 1 billion. Diagnosis has traditionally been symptom-based. Validation studies of consensus symptom-based criteria favor simpler identification of the cardinal symptoms (abdominal pain, bowel dysfunction, bloating) and exclusion of alarm symptoms (unintentional weight loss, rectal bleeding, recent change in bowel function). Diagnostic accuracy is enhanced by additional history, physical examination including digital rectal examination, and basic screening tests (hemoglobin, C-reactive protein) to exclude organic disease.Source: references-v2.bib · ref-189
[303] Thabane M, Kottachchi DT, Marshall JK Systematic review and meta-analysis: The incidence and prognosis of post-infectious irritable bowel syndrome Alimentary Pharmacology & Therapeutics 2007. doi:10.1111/j.1365-2036.2007.03399.x
Meta-analysis of the incidence and prognosis of post-infectious irritable bowel syndrome. After acute infectious gastroenteritis the odds of developing IBS are several times higher than in the general population, and in a proportion of patients the symptoms persist a year later. Campylobacter and Salmonella infections carry the greatest risk. The paper supports the view that part of what is called IBS follows an identifiable trigger — one source of the heterogeneity of this patient group.Source: references-v2.bib · ref-303
[371] Moayyedi P et al Fecal microbiota transplantation induces remission in active ulcerative colitis Gastroenterology 2015.
The first large randomised, placebo-controlled trial of faecal transplantation in active ulcerative colitis. Substantially more patients in the donor-stool arm reached remission than on placebo. The trial recorded two further observations: the effect was strongly donor-dependent — most of the benefit came from the preparation of a single donor — and repeated dosing proved necessary. This paper opened the randomised evidence line for ulcerative colitis.Source: references-v2.bib · ref-371
[390] El-Salhy M, Hatlebakk JG, Gilja OH, et al Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study Gut 2020. doi:10.1136/gutjnl-2019-319630
Randomised, double-blind, placebo-controlled trial in 164 patients with IBS, comparing two doses of donor stool (30 g and 60 g) with placebo. The IBS-SSS symptom score fell significantly and dose-dependently in the donor arms: 23.6% responded on placebo, 76.9% at 30 g and 89.1% at 60 g. Donor selection proved decisive — the donor with an exceptionally diverse microbiota produced the best results. This is the strongest positive dataset in IBS, but it comes from a single research group and lacks independent confirmation.Source: references-v2.bib · ref-390
[392] Paramsothy S, Kamm MA, Kaakoush NO, et al Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial Lancet 2017. doi:10.1016/s0140-6736(17)30182-4
Randomised, double-blind trial in active ulcerative colitis using an intensive, multidonor protocol: five enemas a week for eight weeks. About three times as many patients in the treatment arm reached steroid-free clinical and endoscopic remission as on placebo. The multidonor design was intended to prevent differences between donors from deciding the outcome — this trial showed that dose intensity and the number of donors matter in their own right. It is the most cited randomised FMT trial in ulcerative colitis.Source: references-v2.bib · ref-392
[462] Paramsothy, S., Nielsen, S., Kamm, M. A. et al. Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis Gastroenterology 2019. doi:10.1053/j.gastro.2018.12.001
Double-blind RCT in 81 patients with active ulcerative colitis randomized to intensive multidonor FMT or placebo enemas 5 days/week for 8 weeks after an initial colonoscopic infusion. FMT patients received blended stool from 3–7 unrelated donors; placebo patients were eligible for open-label FMT afterward. 314 fecal samples were collected across screening, treatment, and 8 weeks post-therapy to identify bacterial taxa and metabolic functions associated with response. The study identifies microbial and metabolite signatures that predict FMT response in UC, supporting donor selection and response stratification.Source: references-v2.bib · ref-462
[478] Sokol, H., Landman, C., Seksik, P. et al. Fecal microbiota transplantation to maintain remission in Crohn's disease: a pilot randomized controlled study Microbiome 2020. doi:10.1186/s40168-020-0792-5
Randomized, single-blind, sham-controlled pilot trial of FMT in adults with colonic or ileo-colonic Crohn's disease in steroid-induced clinical remission. Patients were randomized at remission to receive FMT or sham transplantation during colonoscopy; corticosteroids were tapered and follow-up colonoscopy performed at week 6. The trial provides the first randomized data on FMT for maintaining remission in CD, with modest signals supporting microbial engraftment as a candidate driver of clinical response and informing larger confirmatory studies.Source: references-v2.bib · ref-478
[779] Johnsen, P., Hilpüsch, F., Cavanagh, J., et al. Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial The lancet. Gastroenterology & hepatology 2018. doi:10.1016/S2468-1253(17
FMT achieves a significantly better symptomatic response rate in IBS (65% vs. 43%) than placebo — the first positive, high-evidence RCT in the IBS-FMT field — 83 moderate-to-severe IBS patients, colonoscopic FMT vs. autologous placebo. IBS-SSS >75-point reduction: 65% (35/55) FMT vs. 43% (12/28) placebo (p=0.049). Both fresh and frozen stool transplants. First double-blind, placebo-controlled trial shown to be effective in IBS.Source: references-v2.bib · ref-779
[782] El-Salhy, M., Winkel, R., Casen, C., et al. Efficacy of Fecal Microbiota Transplantation for Patients With Irritable Bowel Syndrome at 3 Years After Transplantation Gastroenterology 2022. doi:10.1053/j.gastro.2022.06.020
FMT remained significantly more effective than placebo in IBS 3 years after treatment; no long-term adverse events or safety concerns emerged — 125 patients, 3-year follow-up. Response at 3 years: 27.0% (placebo) vs. 64.9% (30 g) and 71.8% (60 g). IBS symptoms, fatigue, and QoL durably better in both FMT groups. Dysbiosis index durably lower. 10 bacterial taxa correlated with symptom reduction. No long-term adverse events.Source: references-v2.bib · ref-782
[783] Wu, J., Lv, L., Wang, C. Efficacy of Fecal Microbiota Transplantation in Irritable Bowel Syndrome: A Meta-Analysis of Randomized Controlled Trials Frontiers in cellular and infection microbiology 2022. doi:10.3389/fcimb.2022.827395
FMT via colonoscopy or gastroscopy significantly improves IBS symptoms and quality of life; capsule FMT has the opposite effect — route of administration is decisive — 7 RCTs, 472 IBS patients. Colonoscopic FMT: significantly better symptomatic response (RR 0.70, 95% CI 0.51–0.96). Gastroscopic FMT: significantly better (RR 0.37, 95% CI 0.14–0.99). Capsule FMT: inferior to placebo (RR 1.88, 95% CI 1.06–3.35). FMT significantly improves IBS-QoL (+9.39 points, p<0.01). One-year outcomes not significant. GRADE: very low evidence level — larger trials are needed.Source: references-v2.bib · ref-783
[784] Wang, M., Xie, X., Zhao, S., et al. Fecal microbiota transplantation for irritable bowel syndrome: a systematic review and meta-analysis of randomized controlled trials Frontiers in immunology 2023. doi:10.3389/fimmu.2023.1136343
A single stool-transplantation FMT durably improves IBS symptoms for 1–36 months; long-term effect is also demonstrated, but capsule FMT is not effective — Analysis of 9 RCTs, 19 reports. Single stool FMT significantly reduced IBS-SSS at 1, 3, 6, 24, and 36 months (at 24 months MD=−110 points vs. placebo). Response rate at 3 months: RR=1.91; at 24 months: RR=2.97; at 36 months: RR=2.48. No positive effect with capsule FMT. No serious adverse events. GRADE quality: moderate (in stool-FMT group).Source: references-v2.bib · ref-784
[785] Lacy, B. E., Pimentel, M., Brenner, D. M., et al. ACG Clinical Guideline: Management of Irritable Bowel Syndrome The American journal of gastroenterology 2021. doi:10.14309/ajg.0000000000001036
An ACG (American College of Gastroenterology) clinical guideline (Am J Gastroenterol) on the management of irritable bowel syndrome.Source: references-v2.bib · ref-785
[787] Ford AC et al Efficacy of soluble fibre, antispasmodic drugs, and gut-brain neuromodulators in irritable bowel syndrome: a systematic review and network meta-analysis2022;7(11):975–991 Lancet Gastroenterol Hepatol .
A systematic review and network meta-analysis by Ford et al. (Lancet Gastroenterol Hepatol, 2022) on the efficacy of soluble fibre, antispasmodic drugs and gut-brain neuromodulators in irritable bowel syndrome.Source: references-v2.bib · ref-787
[788] NICE Guideline CG61 (updated 2017) Irritable bowel syndrome in adults: diagnosis and management 2017.
The NICE CG61 guideline (updated 2017) on the diagnosis and management of irritable bowel syndrome in adults.Source: references-v2.bib · ref-788
[789] Ford AC et al Effect of antidepressants and psychological therapies in irritable bowel syndrome: an updated systematic review and meta-analysis 2019;114(1):21–39 Am J Gastroenterol 2019. doi:10.1038/s41395-018-0222-5
An updated systematic review and meta-analysis of the effect of antidepressants and psychological therapies in irritable bowel syndrome (IBS). The authors searched MEDLINE, EMBASE, PsychINFO and the Cochrane register (up to July 2017); 53 randomized controlled trials reported in 51 articles were eligible (17 compared antidepressants with placebo, 35 compared psychological therapies with control/usual management, and one compared both). They concluded that antidepressants are efficacious in reducing IBS symptoms, and psychological therapies also appear effective, although the quality of evidence is limited and treatment effects may be overestimated.Source: references-v2.bib · ref-789
[790] Imdad, A., Pandit, N., Zaman, M., et al. Fecal transplantation for treatment of inflammatory bowel disease The Cochrane database of systematic reviews 2023. doi:10.1002/14651858.CD012774.pub3
Efficacy of FMT in inflammatory bowel disease — Cochrane review (2023) — 12 RCTs, 550 participants. FMT vs. control in UC: clinical remission RR 1.79 (95% CI: 1.13–2.84). Endoscopic remission: RR 1.45. Adverse event rates similar. Uncertainty regarding CD.Source: references-v2.bib · ref-790
[793] Fehily, S., Basnayake, C., Wright, E., Kamm, M. Fecal microbiota transplantation therapy in Crohn's disease: Systematic review Journal of gastroenterology and hepatology 2021. doi:10.1111/jgh.15598
FMT in Crohn's disease — systematic review — 15 studies (2 RCTs, 13 cohorts). Multiple FMT showed higher early response rate. Upper GI route early efficacy 75–100% vs. lower 30–58%. No serious adverse events occurred.Source: references-v2.bib · ref-793
[794] Arora, U., Kedia, S., Ahuja, V. The practice of fecal microbiota transplantation in inflammatory bowel disease Intestinal research 2024. doi:10.5217/ir.2023.00085
Practice of FMT application in IBD — Frozen preparation, antibiotic pretreatment, and short donor-to-recipient time improve efficacy. Proven effect in UC by RCTs; data on Crohn's are promising. Safety is adequate.Source: references-v2.bib · ref-794
[796] Rossen, N., Fuentes, S., van der Spek, M., et al. Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis Gastroenterology 2015. doi:10.1053/j.gastro.2015.03.045
FMT in UC — early double-blind RCT, relationship between microbiota composition and clinical response — 50 patients, double-blind RCT (nasoduodenal infusion). FMT (healthy donor): 30.4% (7/23) vs. autologous FMT: 20.0% (5/25) reached the composite primary endpoint at 12 weeks (p=0.51). Not significant, but the microbiota of responders differed significantly from non-responders. Key early RCT in UC.Source: references-v2.bib · ref-796
[801] Sood, A., Mahajan, R., Singh, A., et al. Role of Faecal Microbiota Transplantation for Maintenance of Remission in Patients With Ulcerative Colitis: A Pilot Study Journal of Crohn's & colitis 2019. doi:10.1093/ecco-jcc/jjz060
FMT maintenance therapy (every 8 weeks) keeps UC patients in remission — endoscopic and histological remission improve vs. placebo — 87.1% FMT vs. 66.7% placebo maintained clinical remission at 48 weeks; endoscopic remission: 58.1% vs. 26.7% (p=0.026); histological: 45.2% vs. 16.7% (p=0.033); relapse: 9.7% FMT vs. 26.7% placebo (J Crohns Colitis, 2019).Source: references-v2.bib · ref-801
[816] Kassam, Z., Dubois, N., Ramakrishna, B. et al. Donor Screening for Fecal Microbiota Transplantation N Engl J Med 2019. doi:10.1056/NEJMc1913670
Kassam and colleagues' 2019 New England Journal of Medicine correspondence on 'Donor Screening for Fecal Microbiota Transplantation' was written in the wake of an FDA safety alert reporting two cases of extended-spectrum beta-lactamase (ESBL)-producing E. coli bacteremia — one fatal — transmitted via FMT from a donor not screened for MDROs. The OpenBiome team, the leading US stool bank, summarises updated donor-screening protocols, including ESBL/CRE PCR and culture, and discuss broader implications for biosafety, donor recruitment, and stool-bank operations. The letter directly informed updated FDA, ESCMID and EBP donor-screening recommendations and is the canonical citation for AMR-driven screening intensification.Source: references-v2.bib · ref-816
[817] Rondinella, D., Quaranta, G., Rozera, T., et al. Donor screening for fecal microbiota transplantation with a direct stool testing-based strategy: a prospective cohort study Microbes and infection 2024. doi:10.1016/j.micinf.2024.105341
Direct stool identity testing-based donor screening strategy — Of 277 donations, 99 (36%) were discarded due to pathogen positivity (most common: EPEC n=37, Blastocystis n=20). Among 337 approved aliquots used in FMT: no serious adverse events occurred over 12 weeks.Source: references-v2.bib · ref-817
If you want to find out whether your case is suitable, what happens when and what it costs, you will find that on the service page.
The MicroBiome Bank service is not a substitute for professional medical advice, diagnosis or treatment. The decision to use it rests in every case with the treating physician.