Efficacy and safety of fecal microbiota transplantation for the treatment of diseases other than Clostridium difficile infection: a systematic review and meta-analysis

Figures & data

Figure 1. PRISMA flowchart of included studies

Table 1. Summary of FMT methodological factors

Study details	Methodological factors	Dosing regimen (ie. dosage, frequency, duration)	Donor factors	Adjunctive treatment	Control intervention
Saidani et al, 2019	Route of administration: NGT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: once-off Initial dosage: 50 g stool Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): not stated Type of donor (e.g. Relative vs. non-related): not stated Donor screening for mental illness or metabolic risk factors: Unclear, stated used “French authorities’ recommendations”	Antibiotic pre-treatment of recipients: yes (colistin 6-MUI and aminoglycoside (either gentamycin or amikacin) if sensitive, or other antibiotics if resistant Bowel cleanse: bowel preparation 5 days prior, and day before FMT Other: nasopharangeal decolonization using chlorhexidine gluconate gargle and nose swab, and pantoprazole	Description of control intervention: treatment as usual
Huttner et al, 2019	Route of administration: NGT (two sites – Israel and The Netherlands) or encapsulated FMT (two sites – Switzerland and France) Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: NGT as once off, followed by daily encapsulated FMT for 2 consecutive days Initial dosage: 40 g stool via NGT, unclear dosing for encapsulated FMT Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple):single Type of donor (e.g. Relative vs. non-related): not related Donor screening for mental illness or metabolic risk factors: Screened for “chronic diseases or medical history” but not mental health or metabolic risk factors specifically	Antibiotic pre-treatment of recipients: yes (colistin sulfate and neomycin sulfate) Bowel cleanse: no Other: N/A	Description of control intervention: treatment as usual
Sokol et al, 2020	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: once-off Initial dosage: 50–100 g fresh stool Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple):single Type of donor (e.g. Relative vs. non-related):non-related Donor screening for mental illness or metabolic risk factors: states excluded if “chronic disease, long term treatment” or BMI > 27, but screening for mental illness or risk factors not specifically described.	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation with polyethylene glycol Other: N/A	Description of control intervention: same but placebo (physiological serum) used in sham group
Bajaj et al, 2017	Route of administration: retention enema Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: once-off Initial dosage: 90 mL frozen aliquot of fecal suspension Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – yes	Antibiotic pre-treatment of recipients:yes (metronidazole, ciprofloxacin, amoxicillin) Bowel cleanse: no Other: N/A	Description of control intervention: treatment as usual
Bajaj et al, 2019	Route of administration: encapsulated FMT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: once-off Initial dosage: 15 capsules (unclear dosage per capsule) Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – yes	Antibiotic pre-treatment of recipients: no Bowel cleanse: no Other: N/A	Description of control intervention: same but placebo capsules used (containing a sterile solution of cocoa butter, glycerol and brown food color).
Aroniadis et al, 2019	Route of administration: encapsulated FMT Aerobic vs. anaerobic preparation: Not specified Fresh vs. frozen: frozen	Duration of intervention: 3 days Initial dosage: 25 capsules containing 9.5 g fresh stool each Maintenance regimen: two further doses of 25 capsules over the next 2 days	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – yes	Antibiotic pre-treatment of recipients: no Bowel cleanse: no Other: esomeprazole	Description of control intervention: same, but placebo capsules used (containing nontoxic brown pigment)
El-Salhy et al, 2019	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: once-off Initial dosage: 30 or 60 g feces Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – screened for “metabolic disorders” mental illness – no	Antibiotic pre-treatment of recipients: no Bowel cleanse: no Other: N/A	Description of control intervention: same but autologous FMT used
Holster et al, 2019	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: once-off Initial dosage: 30 g feces Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple):single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – yes	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation prior to procedure Other: N/A	Description of control intervention: same but autologous FMT used
Vrieze et al, 2012	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: once-off Initial dosage: 500 mL aliquot of FMT suspension Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – screened for diabetes and obesity, but did not specify other metabolic risk factors mental illness – no	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel lavage the night before Other: fasting the night before	Description of control intervention: same but autologous FMT used
Smits et al, 2019	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: once-off Initial dosage: 500 mL aliquot of FMT suspension Maintenance regimen: N/A	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – no	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel lavage Other: N/A	Description of control intervention: same but autologous FMT used
Allegretti et al, 2019	Route of administration: encapsulated FMT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: 8 weeks (3 doses given 4 weeks apart) Initial dosage: 30 capsules, containing 0.75 g stool per capsule Maintenance regimen: 12 capsules given at 4 and 8 weeks	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related):non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – yes	Antibiotic pre-treatment of recipients: no Bowel cleanse: no Other: N/A	Description of control intervention: same but placebo capsules used, containing normal saline, food color and glycerol)
Costello et al, 2019	Route of administration: colonoscopy followed by retention enemas Aerobic vs. anaerobic preparation: anaerobic Fresh vs. frozen: frozen	Duration of intervention: 3 doses given in 1 week Initial dosage: 50 g stool Maintenance regimen: two enemas containing 25 g stool within first week	Number of donors (i.e. single vs. multiple): pooled (3–4 donors, mixed) Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes mental illness – screened for depression, but not other mental illnesses	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation with polyethylene glycol the night before Other: loperimide immediately prior to procedure	Description of control intervention: same but autologous FMT used
Sood et al, 2019	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: 42 weeks (6 doses, 8 weeks apart) Initial dosage: 100 g feces Maintenance regimen: same	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – no mental illness – no	Antibiotic pre-treatment of recipients: no Bowel cleanse: polyethylene glycol bowel lavage the night before Other: N/A	Description of control intervention: same but placebo FMT (normal saline with food color) used
Herfarth et al, 2019	Route of administration: endoscopic route (unspecified whether NGT, NDT or NJT), followed by encapsulated FMT Aerobic vs. anaerobic preparation: not specified Fresh vs. frozen: not specified	Duration of intervention: 14 days (endoscopic FMT, followed by daily encapsulated FMT) Initial dosage: 24 g stool Maintenance regimen: 6 capsules daily for 14 days (total dose 4.2 g stool/day)	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – Screened for BMI but unclear if screened for other metabolic risk factors mental illness – yes	Antibiotic pre-treatment of recipients: not specified Bowel cleanse: not specified Other: not specified	Description of control intervention: same but inert placebo FMT used
Philips et al, 2018^Citation14	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: daily for 7 days Initial dosage: 100 mL of strained and filtered stool Maintenance regimen: same	Number of donors (i.e. single vs. multiple): single Type of donor (e.g. Relative vs. non-related): related Donor screening for mental illness or metabolic risk factors: metabolic risk factors – yes, mental illness – no	Antibiotic pre-treatment of recipients: antibiotics were continued if the person was already on them Bowel cleanse: no Other: fasting 4 hours before and after	Description of control intervention: control groups consisted of alternative treatments (steroids, nutrition or pentoxifylline therapy)
Ishikawa et al, 2017^Citation39	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: once off Initial dosage: 150–250 g fresh donor stool Maintenance regime: N/A	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): related (spouses or relative) Donor screening for mental illness or metabolic risk factors: not comprehensively described – states “medical history”	Antibiotic pre-treatment of recipients: yes (amoxicillin, fosfomycinand metronidazole) Bowel cleanse: bowel preparation given, in addition to bowel lavage with poloyethylene glycol given prior to treatment Other: Scopolamine given post-treatment to slow gastric transit time	Description of control intervention: 2 weeks antibiotics only (Amoxicillin, Fosfomycin, metronidazole)
Tian et al, 2017^Citation40	Route of administration: NJT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: daily for 6 days Initial dosage: 100 mL fresh stool Maintenance regime: same	Number of donors (ie. single vs multiple): single Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: screened for metabolic syndrome and “any ongoing diseases”	Antibiotic pre-treatment of recipients: no Bowel cleanse: nil specified Other: N/A	Description of control intervention: Rx as usual (12 weeks of education, behavioral strategies and oral laxatives), avoidance of probiotics.
Vujkovic-Cvijin et al, 2017^Citation30	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: frozen	Duration of intervention: once-off Initial dosage: 250 mL of stool suspension Maintenance regime: N/A	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: yes (Openbiome protocol used)	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation used (Golytely) Other: N/A	Description of control intervention: treatment as usual
Johnsen et al, 2017^Citation41	Route of administration: colonoscopy Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh or frozen (1:1 ratio)	Duration of intervention: once-off Initial dosage: not described Maintenance regime: same Frequency of doses aerobic	Number of donors (ie. single vs. multiple): pooled (2 donors) and these were mixed. Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: screened for metabolic syndrome, and chronic fatigue but not specifically for mental illness	Antibiotic pre-treatment of recipients: no Bowel cleanse: Picoprep bowel preparation used Other: loperamide used prior to procedure	Description of control intervention:same but with autologous FMT.
Kootte et al, 2017^Citation36	Route of administration: NDT Aerobic vs. anaerobic preparation: partially anaerobic Fresh vs. frozen: fresh	Duration of intervention: once-off Initial dosage: not clearly described Maintenance regime: N/A	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: not screened for mental illness but screened for metabolic risk factors	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel lavage prior to procedure Other: fasting prior to procedure	Description of control intervention: same plus autologous FMT prepared in same way. Taken 6 hours prior to FMT
Rossen et al, 2015^Citation37	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: two FMTs given 3 weeks apart Initial dosage: 120 g fresh stool (average) Maintenance regime: same	Number of donors (ie. single vs. multiple): single, except for 6 recipients Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: no	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation (Moviprep) evening before and morning of FMT Other: N/A	Description of control intervention: same plus autologous FMT prepared in same way. Taken on morning of FMT
Kump et al, 2017^Citation42	Route of administration: colonoscopy (for 1^st FMT), and via sigmoidoscopy for subsequent FMTs Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: 5 FMTs given 14 days apart (8 weeks total duration) Initial dosage: 250–500 mL fecal suspension Maintenance regime: same	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): 6 donors were related, 2 were partners and 3 were relatives Donor screening for mental illness or metabolic risk factors: screened for BMI but no other metabolic risk factors or mental illness.	Antibiotic pre-treatment of recipients: yes (vancomycin, paromomycin and nystatin) Bowel cleanse: bowel preparation (Moviprep) given prior to first FMT but not subsequent FMTs Other: N/A	Description of control intervention: antibiotics only
Moayyedi et al, 2015^Citation43	Route of administration: retention enema Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh or frozen (method of selection not described)	Duration of intervention: weekly for 6 weeks Initial dosage: 50 g of fresh stool in fecal suspension Maintenance regime: same	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): not specified Donor screening for mental illness or metabolic risk factors: not clearly described	Antibiotic pre-treatment of recipients: no Bowel cleanse: no Other: N/A	Description of control intervention: same but with placebo (water enema)
Paramsothy et al, 2017^Citation44	Route of administration: colonoscopy (1^st treatment) colonoscopically followed by self-administered enemas) Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: fresh	Duration of intervention: 8 weeks Initial dosage: 37.5 g fresh stool in 150 mL of suspension Maintenance regime: 5 enemas/week for 8 weeks. Same dosage	Number of donors (ie. single vs. multiple): multiple (3–7 donors, and these were mixed) Type of donor (eg. Relative vs. non-related): non-related Donor screening for mental illness or metabolic risk factors: yes – for metabolic syndrome, not specifically for mental illness but did screen for chronic pain syndrome and neurologic/neurodevelopmental disorders	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation used prior to procedure Other: N/A	Description of control intervention: same but with placebo enema (isotonic saline, brown food colorouant, odourant and glycerol cryoprotectant 10%
Halkjaer et al, 2018^Citation45	Route of administration: orally (capsules) Aerobic vs. anaerobic preparation: partially anaerobic Fresh vs. frozen: frozen	Duration of intervention: daily for 12 days Initial dosage: 25 capsules (12 g frozen fecal matter derived from 50 g fresh feces) Maintenance regime: same	Number of donors (ie. single vs. multiple): multiple (4 donors) Type of donor (eg. Relative vs. non-related): not specified Donor screening for mental illness or metabolic risk factors: excluded if family history of GI diseases, cancer, diabetes, obesity, autoimmune diseases, allergy, asthma, eczema, cardiovascular diseases, neurologic or mental illnesses; however, does not describe if excluded if past hx of these diseases	Antibiotic pre-treatment of recipients: no Bowel cleanse: bowel preparation (picoprep) given prior to procedure Other: fasting prior to procedure	Description of control intervention: placebo capsules containing saline, 30% glycerol and food coloring (E150)
Ren et al, 2017^Citation46	Route of administration: NDT Aerobic vs. anaerobic preparation: aerobic Fresh vs. frozen: not described	Duration of intervention: every 4 weeks for 1–7 treatments Initial dosage: 80 mL of bacterial suspension Maintenance regime: same	Number of donors (ie. single vs. multiple): single Type of donor (eg. Relative vs. non-related): not specified Donor screening for mental illness or metabolic risk factors: not described	Antibiotic pre-treatment of recipients: participants were already on Hep B treatment, but nil specific pre-treatment described Bowel cleanse: not described Other: not described	Description of control intervention: treatment as usual

Table 2. Summary of primary outcomes of included studies

Author/date	Study details	Population details	Description of Intervention	Primary outcome measure (POM) relating to clinical efficacy (or relevant secondary outcome measures where POM did not relate to efficacy)	Results for outcome measures of clinical efficacy
Functional gut disorders
Tian et al, 2017^Citation40	Study design: Randomized, single-blind controlled trial Country: China Sample size (n): N = 60 (FMT = 30, control = 30) Follow-up period: 12-weeks	Specific disorder: Slow transit constipation Age in years (mean): FMT group: 53.1 Control group: 55.4	Intervention: Frozen FMT delivered daily via NJT for 6 days plus TAU. Control: TAU	POM: Clinical cure rate (proportion of participants with an average of 3 or more complete spontaneous bowel movements per week during the 12-week follow-up).	Favors FMT The cure rate for the FMT group was 36.7% compared with 13.3% for the control group, (P = .04).
Johnsen et al, 2017^Citation41	Study design: Double blind, randomized placebo controlled parallel group, single center trial. 2:1 randomization Country: Norway Sample size (n): N = 83 (FMT = 45, control = 29) Follow-up period: 12-months	Specific disorder: IBS (excluded dominating constipation group) Age in years (median): FMT group: 43 Control group: 45	Intervention: bowel preparation and loperamide given prior to frozen FMT via colonoscopy. Control: Autologous FMT.	POM: Clinical response, defined as symptom relief of more than 75 points assessed by IBS-SSS, 3 months after FMT.	Favors FMT 36/55 (65%) participants in the FMT group compared with12/28 (43%) in the placebo showed a clinical response at 3 months (p = 0 · 049).
Halkjaer et al, 2018^Citation45	Study design: double blind placebo controlled trial for FMT capsules in IBS. 1:1 randomization Country: Denmark Sample size (n): n = 52 (FMT = 26, control = 26) Follow-up period: 6-months	Specific disorder: IBS Age in years (mean): FMT group: 37.28 Control group: 35.54	Intervention: 25 capsules of frozen encapsulated FMT daily for 12 days while fasting. Bowel preparation given the day prior to first treatment. Control: As above, but with placebo capsules used	POM: Reduction of IBS-SSS between baseline and 3-month follow up in the treatment group compared with the placebo group.	Favors placebo There was a significant difference in change in IBS-SSS groups between the FMT and placebo groups favoring the placebo group (p = .012).
Aroniadis et al, 2019	Study design: double blind, randomized, placebo controlled crossover trial Country: America Sample size (n): n = 48 (FMT = 25, control = 23) Follow-up period: 12–24 weeks	Specific disorder: IBS Age in years (mean): FMT group: 33 Control group: 42	Intervention: 25 capsules of FMT (daily) for 3 days plus TAU. Proton pump inhibitor prior to FMT. Control: Treatment as usual, plus placebo.	POM: Difference in IBS-SSS between the groups at 12 weeks	No significant result The difference in IBS-SSS and psychiatric outcome measures (HADS) scores between the FMT group and the control group were not significant.
El-Salhy et al, 2019	Study design: a double blind, randomized, placebo-controlled study Country: Norway Sample size (n): N = 165 (30 g FMT = 55, 60 g FMT = 55, control = 55) Follow-up period: 3 months	Specific disorder: IBS Age in years (mean): 30 g FMT group: 39.2 60 g FMT group: 39.3 Control group: 41.2	Intervention: TAU plus NGT FMT of 30 or 60 g. Control: As above, but 30 g autologous FMT used.	POM: Reduction in the IBS-SSS total score of ≥50 points at 3 months following transplantation	Favors FMT Responses occurredafter 3 months 30 g FMT and 60 g FMT groups (p < .0001). There was a significant improvement in the mental health sub-score of FAS in both groups at 3 months compared with placebo (p < .05).
Holster et al, 2019	Study design: a double blind, randomized, placebo-controlled study Country: Sweden Sample size (n): N = 16 (FMT = 8, control = 8) Follow-up period: 6 months	Specific disorder: IBS Age in years (median): FMT group: 34 Control group: 39	Intervention: Bowel preparation followed by colonoscopic FMT. Control: As above, but autologous FMT.	POM: Effect on IBS symptoms using the IBS version of the GSRS-IBS.	No significant result No significant differences in GSRS-IBS scores, anxiety or depression symptoms (HADS) between the allogenic and autologous groups were found.
Hepatic disorders
Philips et al, 2018^Citation14	Study design: Retrospective cohort study Comments on study design: four arms of study and unclear allocation of groups Country: India Sample size (n): N = 51 (FMT = 16, steroids 8, nutritional support 17, pentoxifylline 10) Follow-up period: 90 days	Specific disorder: Severe alcoholic hepatitis Age in years (mean): FMT group: 47.6 Control groups: steroids 44.3, nutrition 49.6, pentoxifylline 48.7	Intervention: Fresh FMT daily for 7 days via NDT. Fasting before and after procedure. Control: Three control groups consisting of alternative treatments were used (steroids, nutrition or pentoxifylline therapy)	POM: Survival at 90 days.	No significant result There was no significant difference in 90-day survival between the groups.
Ren et al, 2017^Citation46	Study design: case controlled, single blind, open-label pilot trial Comments on study design: Data analyst blinded to study design, participants allocated into groups based on their treatment preferences (for FMT or not) Country: China Sample size (n): N = 18 (FMT = 5, control = 13) Follow-up period: 32–36 weeks	Specific disorder: Hepatitis B Age in years (median): FMT group: 27 Control group: 33	Intervention: FMT via NDT delivered every 4 weeks (for 1–7 treatments) plus TAU Control: TAU	POM: HbeAg clearance, defined as the loss of HbeAg.	Favors FMT 4/5 participants in FMT group achieved clearance of HbeAg, compared to 0/13 of the control group (p = .0002).
Bajaj et al, 2017	Study design: An open-label, randomized clinical trial Country: America Sample size (n): N = 20 (FMT = 10, control = 10) Follow-up period: 12–15 months	Specific disorder: Recurrent hepatic encephalopathy Age in years (mean): FMT group: 64.5 Control group: 62.9	Intervention: TAU, plus 5 days of pre-treatment with antibiotics (metronidazole, ciprofloxacin and amoxicillin), followed by a 12 hour washout, then FMT via retention enema. Control: TAU	POM did not relate to clinical efficacy. Relevant clinical outcomes included: changes in cognitive function at day 20, cirrhosis severity (MELD score, albumin) and changes in liver function	POM not relevant to clinical efficacy A significant improvement was observed in cognitive outcomes for FMT compared with control on both PHES total score (p = .003) and EncephalApp Stroop (p = .01). No significant changes were observed in cirrhosis severity or liver function for either group.
Bajaj et al, 2019	Study design: A Phase 1, Randomized, single-blind, Placebo-Controlled Trial Country: America Sample size (n): N = 20 (FMT = 10, control = 10) Follow-up period: 5 months	Specific disorder: Age in years (mean): FMT group: 63.3 Control group: 64.2	Intervention: 15 capsules of frozen, encapsulated FMT. Control: As above, but placebo capsules used, containing 80% cocoa butter, 20% glycerol and brown food coloring.	POM did not relate to clinical efficacy. Relevant clinical outcomes included: changes in cognitive testing on PHES and EncephalApp, serum LBP, and changes in duodenal mucosal expression of inflammatory cytokines, barrier proteins, and AMPs	POM not relevant to clinical efficacy Following intervention, a significant improvement in cognitive function was observed in FMT group, but not the control group compared to baseline for EncephalApp score (p = .02), but not PHES score. A significant post-treatment reduction in LBP was also observed in the FMT group (P < .009), but not the control group. No significant change in duodenal expression of inflammatory cytokines, barrier proteins or AMPs was observed.
Inflammatory Bowel Disease
Ishikawa et al, 2017^Citation39	Study design: open-label, non-randomized prospective control study Country: Japan Sample size (n): N = 41 (FMT = 21, control = 20) Follow-up period: 4 weeks	Specific disorder: UC Age in years (mean): FMT group: 40.4 Control group: 44.7	Intervention: 2 weeks of antibiotics followed by fresh colonoscopic FMT (bowel preparation given prior), followed by scopolamine. Control: antibiotics only	POM: Clinical response (CAI of <10, and decrease of 3 or less) and clinical remission (CAI of 3 or less) at baseline compared with the four week follow up.	No significant result No significant difference was observed either in clinical response or clinical remission between the FMT and control groups.
Rossen et al, 2015^Citation37	Study design: Single center, randomized (1:1), double blind trial Country: The Netherlands Sample size (n): N = 50 (FMT = 25, control = 25) Follow-up period: 12 weeks	Specific disorder: Active UC Age in years (mean): Data not provided	Intervention: 2 doses fresh FMT via NDT 3 weeks apart, each preceded by bowel preparation. Control: As above, but autologous FMT used.	POM: Clinical remission at 12 weeks (SCCAI score < or = 2, and > or = 1 point improvement on the combined Mayo endoscopic score of sigmoid and rectum) compared to baseline.	No significant result There was no significant difference between the FMT group and control groups regarding clinical remission at 12 weeks.
Kump et al, 2017^Citation42	Study design: Open label, prospective, non-randomized controlled study Comments on study design: means of allocation not described Country: Austria Sample size (n): N = 27 (FMT = 17, control = 10) Follow-up period: 90 days	Specific disorder: Therapy-refractory, active UC Age in years (mean): FMT group: 44 Control group: 36	Intervention: Pre-treatment with antibiotics followed by 5 treatments of fresh FMT given 14 days apart. Bowel preparation given prior to first FMT only. First FMT delivered colonoscopically, and subsequent FMTs via sigmoidoscopy. Control: Antibiotics only.	POM: Mayo Score at the 90-day follow up point between the two groups, wherein a reduction in total Mayo score by three or more was considered a clinical response, and a score of two or less was considered remission	P-values/significance not described. 10/17 (59%) of the FMT group achieved a clinical response and four participants (24%) achieved clinical remission compared to 1/10 (10%) in the control group achieving partial response. P-values not provided, hence significance unclear.
Moayyedi et al, 2015^Citation43	Study design: double blind, placebo controlled, parallel design study (1:1) Country: Canada Sample size (n): N = 75 (FMT = 38, control = 37) Follow-up period: 12 months	Specific disorder: Active UC Age in years (mean): FMT group: 42.2 Control group: 35.8	Intervention: Fresh or frozen FMT given as retention enema weekly for 6 weeks. Control: As above, but water used as FMT placebo.	POM: UC remission (Mayo score <3 and endoscopic Mayo score 0) at week 7 compared with baseline.	Favors FMT At week 7, UC remission in the FMT group was 9/38 (24%) compared with 2/37 (5%) in the placebo group (p = .03).
Paramsothy et al, 2017^Citation44	Study design: multicentre, double-blind, randomized, placebo-controlled parallel design (1:1) Country: Australia Sample size (n): N = 81, FMT = 41, control = 40 Follow-up period: 8 weeks	Specific disorder: Active UC Age in years (median): FMT group: 35.6 Control group: 35.4	Intervention: Frozen FMT delivered via colonoscopy on day 1, followed by daily self-administered enemas of frozen FMT delivered 5 times per week for 8 weeks. Control: As above, but placebo colonoscopy and enema used (saline and glycerol).	POM: Steroid free clinical and endoscopic remission (total Mayo score ≤2, with all sub-scores ≤1, and ≥1 point reduction from baseline in endoscopy sub-score) at week 8 compared with baseline.	Favors FMT At week 8, remission rates in the FMT group were 27% compared with 8% in the placebo group, a RR of 3.6, (95% CI 1.1–11.9, p = .021).
Sokol et al, 2020	Study design: a multicentre, randomized, single-blind placebo-controlled trial Country: France Sample size (n): N = 17 (FMT = 8, control = 9) Follow-up period: 24 weeks	Specific disorder: Crohn’s disease Age in years (mean): FMT group: 31.5 Control group: 34	Intervention: Bowel preparation followed by colonoscopic FMT. Control: As above, but “physiological serum” used as placebo FMT.	POM did not relate to clinical efficacy. Relevant clinical outcomes included: clinical flare rate, change in CDEIS, CRP level, leukocyte level, or fecal calprotectin.	POM not relevant to clinical efficacy The CDEIS decreased significantly 6 weeks after FMT (p = .03) but not after sham. There was no significant difference in clinical fare rate, fecal calprotectin, leukocyte level or CRP level between groups.
Costello et al, 2019	Study design: a multi-center, double blind, randomized, controlled trial Country: Australia Sample size (n): N = 73 (FMT = 38, control = 35) Follow-up period: 12 months	Specific disorder: Active UC Age in years (median): FMT group: 38.5 Control group: 35	Intervention: 3 L polyethlene glycol bowel preparation given the night before, and 2 mg loperimide immediately prior. FMT consisted of frozen pooled donor stool via colonoscopy followed by 2 enemas on day 3 or 4 and one on day 6 or 7. Control: As above, but with autologous FMT	POM: Steroid-free remission at week 8 defined as 1. Total Mayo score of ≤ 2 AND 2. Mayo endoscopic score of ≤ 1	Favors FMT The primary outcome was achieved in 12/38 (32%) of the donor FMT group compared with 3/35 (9%) of autologous FMT group (p = .03).
Sood et al, 2019	Study design: a pilot double blind, randomized, placebo controlled study Country: India Sample size (n): N = 61 (FMT = 31, control = 30) Follow-up period: 48 weeks	Specific disorder: Inactive UC (maintenance) Age in years (mean): FMT group: 33 Control group: 34.6	Intervention: FMT delivered via colonoscopy every 8 weeks for 6 treatments plus TAU. Bowel preparation with polyethylene glycol lavage the night prior. Control: As above, but placebo colonoscopy given (saline with food dye).	POM: Maintenance of steroid-free clinical remission (Mayo score ≤2, all sub scores ≤ 1) at week 48. Relevant secondary clinical end points included: achievement of endoscopic remission (endoscopic Mayo score 0), histological remission (Nancy grade 0, 1) and change in inflammatory markers (ESR and CRP) at week 48.	No significant result for POM Nil significant difference in maintenance of steroid free clinical remission between groups. However, significant results were achieved for endoscopic remission (p = .026), histological remission (p = .033), and change in inflammatory markers (p < .001).
Antibiotic-resistant organisms
Saidani et al, 2019	Study design: A matched case-control retrospective study (2 controls per case) Country: France Sample size (n): N = 30 (FMT = 10, control = 20) Follow-up period: 6 months	Specific disorder: CPE Age in years (mean): FMT group: 59.2 Control group: 60.3	Intervention: FMT via NGT, plus a nasopharangeal decolonization (8 days prior), bowel wash (5 days prior and 1 day prior), antibiotics for 5 days prior, and proton pump inhibitor (1 day prior and day of FMT). Control: TAU	POM: Delay in negativation of rectal-swab cultures.	Favors FMT At day 14 post-FMT, 8/10 treated patients (80%) achieved the POM, compared with 2/20 (10%) of the control group (p < .001) in the clearance rate between both groups.
Huttner et al, 2019	Study design: A multi-center (International) randomized, open-label, superiority trial Country: International (Swizerland, France, Israel, The Netherlands) Sample size (n): N = 39 (FMT = 22, control = 17) Follow-up period: 150–210 days	Specific disorder: CPE and ESBL Age in years (median): FMT group: 70 Control group: 64	Intervention: Colistin sulfate and neomycin sulfate tablets for 5 days followed by FMT (either capsules or NGT). Control: TAU	POM: Detectable intestinal carriage of ESBL/CPE by stool culture 35–48 days after randomization	No significant result for POM Nil significant difference between groups in intestinal ESBL or CPE rates following treatment.
Obesity or metabolic syndrome
Kootte et al, 2017^Citation36	Study design: Double blind, randomized controlled trial of obese metabolic syndrome subjects Country: The Netherlands Sample size (n): N = 44 (FMT = 26, control = 12) Follow-up period: 18 weeks	Specific disorder: Metabolic Syndrome Age in years (median): FMT group: 54 Control group: 54	Intervention: Participants were fasted and received bowel preparation prior to fresh FMT via NDT. Control: As above, but participants received autologous FMT.	POM did not relate to clinical efficacy. Relevant clinical outcomes included: metabolic changes, insulin sensitivity and plasma metabolites at 6 and 18 weeks following FMT.	POM not related to clinical efficacy Significant improvement in insulin sensitivity was observed in FMT group at 6 weeks (p < .05), but not at 18 weeks.
Vrieze et al, 2012	Study design: a double blind, randomized controlled pilot study Country: The Netherlands Sample size (n): N = 18 (FMT = 9, control = 9) Follow-up period: 6 weeks	Specific disorder: metabolic syndrome (insulin sensitivity) Age in years (mean): FMT group: 47 Control group: 53	Intervention: Participants were fasted from the night before. Bowel lavage with polyethylene glycol solution given prior to FMT via NDT. Control: As above, but autologous FMT used.	POM: Change in insulin sensitivity at 6 weeks.	Favors FMT Peripheral insulin sensitivity improved at week 6 compared with baseline for the FMT group (p < .05), but not the control group. There was no significant change in hepatic insulin sensitivity at week 6, diet composition, resting energy expenditure, or counter-regulatory hormones.
Smits et al, 2019	Study design: a double blind, randomized controlled pilot study Country: The Netherlands Sample size (n): N = 20 (FMT = 10, control = 10) Follow-up period: 2 weeks	Specific disorder: metabolic syndrome (TMAO production) Age in years (mean): FMT group: 52.3 Control group: 57.7	Intervention: Bowel lavage, followed by FMT via NDT. Control: As above, but autologous FMT used.	POM: TMAO production (as a possible indicator for cardiovascular disease risk)	No significant change in POM At 2 weeks, there was no significant difference from baseline in fasting plasma TMAO, 24 hour urinary TMA excretion, 24 hour urinary TMAO excretion, plasma d3-carnitine appearance or 24 hour urinary d3-TMA excretion for FMT or control groups.
Allegretti et al, 2019	Study design: a double blind, randomized, placebo-controlled, pilot study Country: America Sample size (n): N = 22 (FMT = 11, control = 11) Follow-up period: 26 weeks	Specific disorder: obesity without metabolic syndrome Age in years (mean): FMT group: 44.5 Control group: 43.2	Intervention: Initial dose of 30 FMT capsules and a maintenance dose of 12 capsules at week 4 and week 8. Control: As above, but placebo capsules used.	POM did not relate to clinical efficacy. Relevant clinical outcomes included: Obesity related biomarkers such as change in weight or short-chain fatty acids, and change in area under the curve for GLP1 or leptin at week 12	POM not related to clinical efficacy There was a significant between group change in area under the curve for leptin, with a larger increase in the placebo group at week 12 compared with baseline (p = .001). There was no significant change in mean BMI, or area under the curve for GLP1, or short chain fatty levels at week 12 for either group.
Other disorders
Vujkovic-Cvijin et al, 2017^Citation30	Study design: open label, non-randomized, prospective controlled study Comments on study design: Participants were selected for having low CD4 counts on ART (but excluded if they were too low) Country: America Sample size (n): N = 8(FMT = 6, control = 2) Follow-up period: 24 weeks	Specific disorder: HIV Age in years (median): FMT group: 61 Control group: 64	Intervention: Bowel preparation given prior to frozen colonoscopic FMT. Control: TAU	POM is not clearly stated. Relevant clinical outcomes included: HIV-associated markers of inflammatory activation (CD38, HLA-DR, CD8 + T-cells, plasma rations of kynurenine to tryptophan, IL-6, sCD14) over time (from baseline up to 24 week follow up).	No significant result Nil significant changes in any of the inflammatory markers between FMT and control groups was observed at any of the follow up points compared with baseline.
Herfarth et al, 2019	Study design: a prospective, placebo controlled, double blind randomized, controlled trial Country: America Sample size (n): n = 6 (FMT = 4, control = 2) Follow-up period: 16 weeks	Specific disorder: antibiotic-dependant pouchitis Age in years (mean): FMT group: 39.25 Control group: 33.5	Intervention: Two boluses of endoscopic FMT followed by daily dosing of 6 FMT capsules for 14 days. Control: As above, but placebo FMT used.	POM did not relate to clinical efficacy. Relevant clinical outcomes included: clinical remission (defined as an mPDAI < 4 and no need for antibiotics in weeks 4, 8, and 16) and change in fecal calprotectin level	POM not related to clinical efficacy All patients experienced relapse (ie. remission rate of zero for both groups). There was no significant change in fecal calprotectin levels as data were only available for 5 participants.

POM – Primary Outcome Measure, TAU – treatment as usual, UC- Ulcerative Colitis, ASD – Autism Spectrum Disorder, RCT – Randomized Controlled Trial, NDT – Nasoduodenal Tube, NJT – Nasojejunal Tube, NGT – Nasogastric Tube, FMT – Fecal Microbiota Transplant, ESR – Erythrocyte sedimentation rate, CRP – C-Reactive Protein, IBS – Irritable Bowel Syndrome, CDEIS-Crohn’s Disease Endoscopic Index of Severity, CPE – Carbapenemase-Producing Enterobacteriaceae, ESBL – Extended spectrum beta-lactamase, HIV – Human Immunodeficiency Virus, HADS – Hospital Anxiety and Depression Scale, FAS – Fatigue Assessment Scale, GSRS – Gastrointestinal Symptom Rating Scale, DSR – Daily Stool Records, SCCAI – Simple Clinical Colitis Activity Index, CAI – Clinical Activity Index, IBS-SSS – Irritable Bowel Syndrome Severity Scoring System, HbeAg – Hepatitis B-e Antigen, mPDAI – modified pouch activity

Figure 2. Clinical remission results

Figure 3. Clinical response results

Figure 4. Endoscopic remission results

Table 3. Completeness of reporting of AE

Completeness of reporting of AE	Number reported (total studies, n = 26)
Mild-moderate AE
Detailed reporting of AE	9 (34.6%)
Generic statement only or limited reporting of AE	9 (34.6%)
Not reported at all	8 (30.8%)
SAE
Clearly described	23 (88.5%)
Not reported at all or not clearly reported	3 (11.5%)

Table 4. Summary of “engraftment” of FMT

Study	Does the microbiome change in recipients following FMT?	Were the changes toward the donor microbiome?	Duration of microbiome changes	Was an association observed between microbiome changes and clinical outcomes?
Holster et al, 2019^Citation52	Yes	Yes	Changes appeared to persist for 8 weeks (final data point).	Yes
El Salhy et al, 2019^Citation49	Yes	Not described	Appeared changed at one month (only data point).	Yes
Aroniadis et al, 2019^Citation34	Yes	Yes	Changes appeared to persist for 12 weeks (final data point).	No
Costello et al, 2019^Citation48	Yes	Yes	Changes appeared to persist for 8 weeks, reduced by 12 months.	Yes
Sood et al, 2019^Citation54	Not measured	N/A	N/A	N/A
Herfarth et al, 2019^Citation35	Yes	Only in one of six recipients	Not clearly described.	Yes
Allegretti et al, 2019^Citation65	Yes	Yes	Changes appeared to persist for 12 weeks (final data point).	Not described
Vrieze et al, 2012^Citation47	Yes	Not described	Appeared changed at six weeks (only data point).	Yes
Smits et al, 2018^Citation38	Yes	Yes, “in some but not all participants” – further detail not provided.	Appeared changed at two weeks (only data point).	Not described
Bajaj et al, 2017^Citation32 and long term data reported in Bajaj et al, 2019^Citation56	Yes	Yes	Changes appeared to persist for over one year (reported in long term paper).	Not described
Bajaj et al, 2019^Citation33	Yes	Not measured	Appeared changed at day 30 (only data point).	Not described
Sokol et al, 2020^Citation51	Not significant overall. However when data from 2 participants was removed, a significant change was observed in the remaining 8 participants	Not significant	Not significant overall, however when data was corrected for 2 participants who were considered “treatment failures”, duration of changes were significant at 6 weeks for the FMT group, but microbiota were considered back to baseline at week 14.	Yes
Vujkovic-Cvijin et al, 2017^Citation30	Yes	Yes	Changes in microbiota were most significant between 2–4 weeks, and less significant by week 8.	Not described
Ren et al, 2017^Citation46	Yes	Not described	Not described.	Not described
Philips et al, 2018^Citation14	Yes	Not described	Changes appeared to persist for up to 90 days (study duration).	Not described
Kump et al, 2017^Citation42	Yes	Yes	Changes appeared to persist for 90 days (final data point).	No
Ishikawa et al, 2017^Citation39	Yes	Not described	Appeared changed at 4 weeks, but not measured beyond that.	Yes
Tian et al, 2017^Citation40	Not measured	N/A	N/A	N/A
Kootte et al, 2017^Citation36	Yes	Not described	Changes demonstrated at 6 weeks. No changes apparent at 18 weeks.	Yes
Paramsothy et al, 2017^Citation44	Yes	Yes	Changes persisted for 8 weeks after intervention finished (final data point).	Yes
Johnsen et al, 2017^Citation41	Not measured	N/A	N/A	N/A
Halkjaer et al, 2018^Citation45	Yes	Yes	3 months (final data point).	Not significant
Rossen et al, 2015^Citation37	Yes	Yes, but only in responders	Changes were observed at 12 weeks (final data point).	Yes
Moayyedi et al, 2015^Citation43	Yes	Not significant	Changes were observed at 6 weeks (only data point).	Not significant

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