Small Intestinal Bacterial OvergrowthPhase 1NCT05967871
Pilot Feasibility Study of Fecal Microbiota Transplant for the Treatment of Small Intestinal Bacterial Overgrowth
A Phase 1 study testing Fecal Microbiota Transplant in people with Small Intestinal Bacterial Overgrowth, run by McMaster Children's Hospital at 2 sites in Canada.
Trial summary
The objective of the study is to assess feasibility, and clinical efficacy of a novel Fecal Microbiota Transplantation protocol for the treatment of pediatric small intestinal bacterial overgrowth (SIBO). Read more about this study
- Who is it for?
- Ages 3 to 18 years
- Conditions the study is for
- Small Intestinal Bacterial Overgrowth
- What is being tested?
- Fecal Microbiota Transplant
- Type of treatment
- Injection or infusion
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 20 participants
- Where
- 2 sitesCanada
- Study dates
- 11 Mar 2024to 31 Dec 2026
- Phase
- Phase 1
- Are there results?
- Not yet: the study is under way
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 3 to 18 years
- All sexes
- No healthy volunteers
- Child, Adult
Who may be able to join
- Patients 3-18 years old
- Patients will discontinue antibiotics for at least 1 week prior to FMT
- A diagnosis of SIBO established through lactose breath test (LBT), and showing of symptoms of SIBO
Who cannot join
- Participants will not be permitted to start any new treatments (including antibiotics, probiotics, antacid treatments, or antimotility treatments) until Week 8, unless clinically indicated
- We will exclude participants <3yo to avoid potential concerns of microbial transmission in young children, and to ensure participants are developmentally able to perform LBT
- All potential participants should request a referral through their primary, or subspecialty physician. We would be pleased to help facilitate this contact if needed, provided the appropriate contact information can be sent.
Trial locations and contacts
2 sites in 1 country. Contact the study team or a site near you to ask about taking part.
Canada2 sites, 2 recruiting
- Recruiting
McMaster Children's Hospital
Hamilton, Ontario, L8N 3Z5
Nikhil Pai, MD, 905-521-2100 ext. 73587, pailab@mcmaster.ca
Fariha Chowdhury, BASc, MSc, PhD(c)
- Not yet recruiting
Hospital for Sick Children (SickKids)
Toronto, Ontario, M5G 1X8
Varsha Lillman, BSc, 416-813-1500, varsha.lilman@sickkids.ca
Yaron Avitzur, MD, 416-813-1500, yaron.avitzur@sickkids.ca
About this study
The objective of the study is to assess feasibility, and clinical efficacy of a novel Fecal Microbiota Transplantation protocol for the treatment of pediatric small intestinal bacterial overgrowth (SIBO).
Read the detailed description
BACKGROUND AND RATIONALE Fecal microbiota transplant (FMT) is an established treatment for the management of recurrent Clostridioides difficile (CDI) infection in children and adults, including children with underlying immunodeficiency syndromes and extensive surgical resection. While CDI is the most common indication for FMT, this intervention has also been studied for Crohn's disease, ulcerative colitis, autism, and small intestinal bacterial overgrowth (SIBO). SIBO is a disorder in which the small bowel is colonized by excessive aerobic and anaerobic microbes normally present in the colon. This condition may cause malabsorption, bloating, bloodstream infections (BSI), and D-lactic acidosis (DLA). Treatment traditionally involves broad-spectrum antibiotic use yet this approach may promote persistent dysbiosis, multidrug resistant organisms (MDROs), and often lacks clinical efficacy. Patients with short bowel syndrome (SBS), which involves intestinal resection, dysmotility, and altered enteral feeding are at highest risk for SIBO. Pediatric SBS SIBO patients face significant impacts on quality of life, and higher rates of bacteremia and liver disease.
Specific Aims i. To determine the feasibility, and safety of administering an FMT based treatment to pediatric SBS patients with SIBO. This aim will include measures of adverse events, acceptability to children and parents, ease of administration and sample collection.
ii. To determine short-term clinical efficacy of FMT for the treatment of SIBO. This aim will include measures of time to symptom resolution, completeness of symptom resolution, change in enteral feeding tolerance, and development of any new clinical gastrointestinal symptoms after FMT. Weeks 1-4 after FMT.
iii. To determine long-term clinical efficacy of FMT for the treatment of SIBO. This aim will include measures of durability of remission, including time to recurrence of symptom resolution, severity of clinical symptoms if recurrence, sustained changes in feeding tolerance, and efficacy of repeat FMT administration (second treatment). Week 8 after FMT.
iv. To assess changes in intestinal microbial composition and function before and after FMT. This aim will attempt to identify functional changes in the intestinal microbiome that correlate with symptom resolution. These data will support future translational and clinical studies with our collaborators and support the development of new therapeutic innovations.
- TRIAL OBJECTIVES Our objectives are to assess feasibility, and clinical efficacy of this intervention in children (Table 2).
Feasibility Objectives:
Acceptability of this intervention for patients and families, ability of patients and families to conduct the required screening to monitor efficacy and recruitment rate of patients to the study.
Clinical Objectives:
Clinical efficacy of treating SIBO in our patient population using FMT. These outcomes will be collected at the following timepoints: baseline (pre-FMT), one-, four-, and eight-weeks post-FMT administration
- STUDY DESIGN AND DURATION We will recruit 5-17-year-old patients with intestinal resection (any length), experiencing an active episode of SIBO (diagnosed through lactose breath testing and gastrointestinal symptom scores). Patients will discontinue antibiotics for >1 week prior to FMT. FMT infusions will be administered through patients' existing enteral tubes (gastrostomy, jejunostomy), or potentially via endoscopy (duodenal infusion).
Patients will receive a single FMT (Week 0). They will then have outcomes (including a combination of clinical symptom scores, blood, stool and urine testing) measured one week after FMT, four weeks after FMT, and eight weeks after FMT.
As this is an open-label trial, there will be no randomization or blinding required.
A placebo / comparative treatment will not be assessed.
All FMT treatments will be conducted at MCH, using local pediatric stool bank materials. Patients will have follow-up monitoring, per protocol through their local institution (MCH/HSC). Serial measurements of biological, clinical and microbial outcomes will occur, per protocol.
- Conditions
- Small Intestinal Bacterial Overgrowth
- Being tested
- Fecal Microbiota Transplant
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Fecal Microbiota TransplantBiological
Participants will receive approximately 50 grams of human stool/150mL (approximately 107 microbes/mL of suspension) in saline, prepared as per standard collection, preparation, and screening protocols for FMT infusion developed by our institutional stool bank in accordance with recognized standards. Fecal microbiota transplant infused via existing enteral feeding tube or upper elective endoscopy (with infusion into the duodenum) x1.
| Study group | Role | What they receive |
|---|---|---|
| Fecal Microbiota Transpant | Experimental | Participants will receive a Fecal Microbiota transplant Infusion via participants' existing enteral feeding tubes or via elective upper endoscopy (with infusion into the duodenum). Most patients with SBS at MCH and HSC have an existing enteral feeding tube (gastrostomy or jejunostomy tube). Receives: Biological: Fecal Microbiota Transplant |
What is being measured
The primary outcome is the main question the study is designed to answer.
Change in Clinical Symptoms (pre/post fecal microbiota transplant)
SIBO Clinical Symptom Scores will be measured using the PedsQL Gastrointestinal Symptoms Scale. This validated instrument has strong age-specific test-retest properties and has been used for functional GI disorders, which have symptoms that strongly overlap with SIBO. Participants will also report symptoms using a Likert scale (Izumo scale). Results of both will be compared.
Measured: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Rate of Clinical Remission (post fecal microbiota transplant)
Absence of SIBO symptoms
Measured: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Urine Metabolomics Analysis
Collected urine will be assessed by multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS), using previously described protocols. This technique will offer additional data on microbiome functional changes. Samples will be measured centrally through the Britz-McKibbin laboratory (PBM). Urine metabolomics outcomes are exploratory.
Measured: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Change in Microbiome Composition, Function (pre/post fecal microbiota transplant)
Stool will be collected for microbiome 16S rRNA and shotgun metagenomic sequencing. Samples will be obtained from either stool (per rectum), or distal ostomy outputs (ostomy in continuity with proximal bowel). All samples will be sequenced centrally through the McMaster Genomics Centre (MGC). Samples will be stored in -80 freezers. Participants unable to bring stool samples to MCH or HSC will receive funding support for temperature-controlled courier services from home. Costs of microbiome analyses will be partially subsidized by collaborators (MS).
Measured: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Change in Breath Test Results (pre/post fecal microbiota transplant)
Lactulose breath test
Measured: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Bloodwork
Bloodwork will include complete blood count (CBC), C-reactive protein (CRP), ferritin, folic acid, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), serum cytokine profiles (including IL-2, IL-6, IL10, IL-18, TNF) and serum bile acids. Routine institutional testing protocols will be followed at MCH and HSC. Bloodwork outcomes are exploratory. Data will support the development of primary and secondary objectives for future studies.
Measured: Baseline and Week 8 (post-FMT)
Secondary outcomes (3)
Monthly Rate of Recruitment
Recruitment/month. ≥2 participants/month.
Measured: 30 weeks
Adverse Events
Adverse and serious events will be recorded using the Common Terminology Criteria for Adverse Events. <10% participants
Measured: 30 Weeks
Blood, stool specimens, breath tests, clinical symptom scores
Participant provides all required blood, stool, lactulose breath tests, and symptom scores per protocol. >80% participants
Measured: 30 Weeks
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted1 Aug 2023
- Study start11 Mar 2024
- Primary completion31 Dec 2026 (estimated)
- Study completion31 Dec 2026 (estimated)
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Publications (26)Papers the sponsor has linked to this study.
- Other trials for Small Intestinal Bacterial OvergrowthStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Interventional
- Phase
- Phase 1
- Primary purpose
- Treatment
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Enrolment
- 20 participants (estimated)
Sponsor and investigators
- Lead sponsor
- McMaster Children's Hospital
- Sponsor type
- University, hospital or other
- Collaborators
- The Hospital for Sick Children
- Responsible party
- Principal investigator, Nikhil Pai, Hamilton Health Sciences Corporation
- Investigators
- Nikhil Pai, MD, Principal investigator, McMaster Children's Hospital (McMater University)
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT05967871
- Sponsor's protocol ID
- 16581
- Status last verified
- Aug 2025
- First submitted
- 13 Jul 2023
- Last updated
- 21 Aug 2025
- Results posted
- No
- Data monitoring committee
- No
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- Yes: Only de-identified individual participant data (IPD) may be shared. No directly identifying information (such as names, dates of birth, contact information, or medical record numbers) will ever be disclosed. If data are shared, they will be limited to variables relevant to the outcomes reported in the trial and will be made available in de-identified form for secondary research purposes under appropriate data use agreements.
Publications
Davidovics ZH, Michail S, Nicholson MR, Kociolek LK, Pai N, Hansen R, Schwerd T, Maspons A, Shamir R, Szajewska H, Thapar N, de Meij T, Mosca A, Vandenplas Y, Kahn SA, Kellermayer R; FMT Special Interest Group of the North American Society of Pediatric Gastroenterology Hepatology, Nutrition, the European Society for Pediatric Gastroenterology Hepatology, Nutrition. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection and Other Conditions in Children: A Joint Position Paper From the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. J Pediatr Gastroenterol Nutr. 2019 Jan;68(1):130-143. doi: 10.1097/MPG.0000000000002205.
PubMed 30540704Nicholson MR, Mitchell PD, Alexander E, Ballal S, Bartlett M, Becker P, Davidovics Z, Docktor M, Dole M, Felix G, Gisser J, Hourigan SK, Jensen MK, Kaplan JL, Kelsen J, Kennedy M, Khanna S, Knackstedt E, Leier M, Lewis J, Lodarek A, Michail S, Oliva-Hemker M, Patton T, Queliza K, Russell GH, Singh N, Solomon A, Suskind DL, Werlin S, Kellermayer R, Kahn SA. Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children. Clin Gastroenterol Hepatol. 2020 Mar;18(3):612-619.e1. doi: 10.1016/j.cgh.2019.04.037. Epub 2019 Apr 19.
PubMed 31009795Pai N, Popov J, Hill L, Hartung E. Protocol for a double-blind, randomised, placebo-controlled pilot study for assessing the feasibility and efficacy of faecal microbiota transplant in a paediatric Crohn's disease population: PediCRaFT Trial. BMJ Open. 2019 Nov 28;9(11):e030120. doi: 10.1136/bmjopen-2019-030120.
PubMed 31784432Pai N, Popov J, Hill L, Hartung E, Grzywacz K, Moayyedi P; McMaster Pediatric Fecal Microbiota Transplant Research Collaboration. Results of the First Pilot Randomized Controlled Trial of Fecal Microbiota Transplant In Pediatric Ulcerative Colitis: Lessons, Limitations, and Future Prospects. Gastroenterology. 2021 Aug;161(2):388-393.e3. doi: 10.1053/j.gastro.2021.04.067. Epub 2021 May 4. No abstract available.
PubMed 33961887Bakker GJ, Nieuwdorp M. Fecal Microbiota Transplantation: Therapeutic Potential for a Multitude of Diseases beyond Clostridium difficile. Microbiol Spectr. 2017 Aug;5(4):10.1128/microbiolspec.bad-0008-2017. doi: 10.1128/microbiolspec.BAD-0008-2017.
PubMed 28840809Fiorentino M, Sapone A, Senger S, Camhi SS, Kadzielski SM, Buie TM, Kelly DL, Cascella N, Fasano A. Blood-brain barrier and intestinal epithelial barrier alterations in autism spectrum disorders. Mol Autism. 2016 Nov 29;7:49. doi: 10.1186/s13229-016-0110-z. eCollection 2016.
PubMed 27957319Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.
PubMed 28122648Davidovics ZH, Vance K, Etienne N, Hyams JS. Fecal Transplantation Successfully Treats Recurrent D-Lactic Acidosis in a Child With Short Bowel Syndrome. JPEN J Parenter Enteral Nutr. 2017 Jul;41(5):896-897. doi: 10.1177/0148607115619931. Epub 2015 Nov 29.
PubMed 26616138Gu L, Ding C, Tian H, Yang B, Zhang X, Hua Y, Zhu Y, Gong J, Zhu W, Li J, Li N. Serial Frozen Fecal Microbiota Transplantation in the Treatment of Chronic Intestinal Pseudo-obstruction: A Preliminary Study. J Neurogastroenterol Motil. 2017 Apr 30;23(2):289-297. doi: 10.5056/jnm16074.
PubMed 27840368Bulik-Sullivan EC, Roy S, Elliott RJ, Kassam Z, Lichtman SN, Carroll IM, Gulati AS. Intestinal Microbial and Metabolic Alterations Following Successful Fecal Microbiota Transplant for D-Lactic Acidosis. J Pediatr Gastroenterol Nutr. 2018 Oct;67(4):483-487. doi: 10.1097/MPG.0000000000002043.
PubMed 29901551McGrath KH, Pitt J, Bines JE. Small intestinal bacterial overgrowth in children with intestinal failure on home parenteral nutrition. JGH Open. 2019 Apr 4;3(5):394-399. doi: 10.1002/jgh3.12174. eCollection 2019 Oct.
PubMed 31633044Thanert R, Thanert A, Ou J, Bajinting A, Burnham CD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes. 2021 Jan-Dec;13(1):1940792. doi: 10.1080/19490976.2021.1940792.
PubMed 34264786Xu F, Li N, Wang C, Xing H, Chen D, Wei Y. Clinical efficacy of fecal microbiota transplantation for patients with small intestinal bacterial overgrowth: a randomized, placebo-controlled clinic study. BMC Gastroenterol. 2021 Feb 6;21(1):54. doi: 10.1186/s12876-021-01630-x.
PubMed 33549047Allegretti JR, Kassam Z, Chan WW. Small Intestinal Bacterial Overgrowth: Should Screening Be Included in the Pre-fecal Microbiota Transplantation Evaluation? Dig Dis Sci. 2018 Jan;63(1):193-197. doi: 10.1007/s10620-017-4864-8. Epub 2017 Nov 29.
PubMed 29188472Pai N, Popov J. Protocol for a randomised, placebo-controlled pilot study for assessing feasibility and efficacy of faecal microbiota transplantation in a paediatric ulcerative colitis population: PediFETCh trial. BMJ Open. 2017 Aug 21;7(8):e016698. doi: 10.1136/bmjopen-2017-016698.
PubMed 28827258
Study at a glance
From the registry record, last updated by the sponsor on 21 Aug 2025. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Pilot Feasibility Study of Fecal Microbiota Transplant for the Treatment of Small Intestinal Bacterial Overgrowth
- ClinicalTrials.gov ID
- NCT05967871
- Acronym / sponsor ID
- 16581
- Conditions
- Small Intestinal Bacterial Overgrowth
- Phase
- Phase 1
- Study type
- Interventional
- Recruitment status
- Recruiting
- Enrolment
- 20 participants (estimated)
- Lead sponsor
- McMaster Children's HospitalUniversity, hospital or other
- Collaborators
- The Hospital for Sick Children
- Study start
- 11 Mar 2024 (actual)
- Primary completion
- 31 Dec 2026 (estimated)
- Study completion
- 31 Dec 2026 (estimated)
- First posted
- 1 Aug 2023 (actual)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
The objective of the study is to assess feasibility, and clinical efficacy of a novel Fecal Microbiota Transplantation protocol for the treatment of pediatric small intestinal bacterial overgrowth (SIBO).
Detailed description
BACKGROUND AND RATIONALE Fecal microbiota transplant (FMT) is an established treatment for the management of recurrent Clostridioides difficile (CDI) infection in children and adults, including children with underlying immunodeficiency syndromes and extensive surgical resection. While CDI is the most common indication for FMT, this intervention has also been studied for Crohn's disease, ulcerative colitis, autism, and small intestinal bacterial overgrowth (SIBO). SIBO is a disorder in which the small bowel is colonized by excessive aerobic and anaerobic microbes normally present in the colon. This condition may cause malabsorption, bloating, bloodstream infections (BSI), and D-lactic acidosis (DLA). Treatment traditionally involves broad-spectrum antibiotic use yet this approach may promote persistent dysbiosis, multidrug resistant organisms (MDROs), and often lacks clinical efficacy. Patients with short bowel syndrome (SBS), which involves intestinal resection, dysmotility, and altered enteral feeding are at highest risk for SIBO. Pediatric SBS SIBO patients face significant impacts on quality of life, and higher rates of bacteremia and liver disease.
Specific Aims i. To determine the feasibility, and safety of administering an FMT based treatment to pediatric SBS patients with SIBO. This aim will include measures of adverse events, acceptability to children and parents, ease of administration and sample collection.
ii. To determine short-term clinical efficacy of FMT for the treatment of SIBO. This aim will include measures of time to symptom resolution, completeness of symptom resolution, change in enteral feeding tolerance, and development of any new clinical gastrointestinal symptoms after FMT. Weeks 1-4 after FMT.
iii. To determine long-term clinical efficacy of FMT for the treatment of SIBO. This aim will include measures of durability of remission, including time to recurrence of symptom resolution, severity of clinical symptoms if recurrence, sustained changes in feeding tolerance, and efficacy of repeat FMT administration (second treatment). Week 8 after FMT.
iv. To assess changes in intestinal microbial composition and function before and after FMT. This aim will attempt to identify functional changes in the intestinal microbiome that correlate with symptom resolution. These data will support future translational and clinical studies with our collaborators and support the development of new therapeutic innovations.
- TRIAL OBJECTIVES Our objectives are to assess feasibility, and clinical efficacy of this intervention in children (Table 2).
Feasibility Objectives:
Acceptability of this intervention for patients and families, ability of patients and families to conduct the required screening to monitor efficacy and recruitment rate of patients to the study.
Clinical Objectives:
Clinical efficacy of treating SIBO in our patient population using FMT. These outcomes will be collected at the following timepoints: baseline (pre-FMT), one-, four-, and eight-weeks post-FMT administration
- STUDY DESIGN AND DURATION We will recruit 5-17-year-old patients with intestinal resection (any length), experiencing an active episode of SIBO (diagnosed through lactose breath testing and gastrointestinal symptom scores). Patients will discontinue antibiotics for >1 week prior to FMT. FMT infusions will be administered through patients' existing enteral tubes (gastrostomy, jejunostomy), or potentially via endoscopy (duodenal infusion).
Patients will receive a single FMT (Week 0). They will then have outcomes (including a combination of clinical symptom scores, blood, stool and urine testing) measured one week after FMT, four weeks after FMT, and eight weeks after FMT.
As this is an open-label trial, there will be no randomization or blinding required.
A placebo / comparative treatment will not be assessed.
All FMT treatments will be conducted at MCH, using local pediatric stool bank materials. Patients will have follow-up monitoring, per protocol through their local institution (MCH/HSC). Serial measurements of biological, clinical and microbial outcomes will occur, per protocol.
Study design
- Primary purpose
- Treatment
- Allocation
- Not applicable
- Intervention model
- Single group
- Masking
- None (open label)
- Number of arms
- 1
| Arm | Type | Receives |
|---|---|---|
| Fecal Microbiota Transpant | Experimental | Biological: Fecal Microbiota TransplantParticipants will receive a Fecal Microbiota transplant Infusion via participants' existing enteral feeding tubes or via elective upper endoscopy (with infusion into the duodenum). Most patients with SBS at MCH and HSC have an existing enteral feeding tube (gastrostomy or jejunostomy tube). |
Who may qualify
- Ages
- 3 to 18 years
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Child, Adult
Key inclusion criteria (3 listed)
- Patients 3-18 years old
- Patients will discontinue antibiotics for at least 1 week prior to FMT
- A diagnosis of SIBO established through lactose breath test (LBT), and showing of symptoms of SIBO
Key exclusion criteria (3 listed)
- Participants will not be permitted to start any new treatments (including antibiotics, probiotics, antacid treatments, or antimotility treatments) until Week 8, unless clinically indicated
- We will exclude participants <3yo to avoid potential concerns of microbial transmission in young children, and to ensure participants are developmentally able to perform LBT
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Interventions
| Intervention | Type | Arms |
|---|---|---|
| Fecal Microbiota TransplantParticipants will receive approximately 50 grams of human stool/150mL (approximately 107 microbes/mL of suspension) in saline, prepared as per standard collection, preparation, and screening protocols for FMT infusion developed by our institutional stool bank in accordance with recognized standards. Fecal microbiota transplant infused via existing enteral feeding tube or upper elective endoscopy (with infusion into the duodenum) x1. | Biological | Fecal Microbiota Transpant |
Primary outcome
Change in Clinical Symptoms (pre/post fecal microbiota transplant)
Time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
SIBO Clinical Symptom Scores will be measured using the PedsQL Gastrointestinal Symptoms Scale. This validated instrument has strong age-specific test-retest properties and has been used for functional GI disorders, which have symptoms that strongly overlap with SIBO. Participants will also report symptoms using a Likert scale (Izumo scale). Results of both will be compared.
Rate of Clinical Remission (post fecal microbiota transplant)
Time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Absence of SIBO symptoms
Urine Metabolomics Analysis
Time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Collected urine will be assessed by multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS), using previously described protocols. This technique will offer additional data on microbiome functional changes. Samples will be measured centrally through the Britz-McKibbin laboratory (PBM). Urine metabolomics outcomes are exploratory.
Change in Microbiome Composition, Function (pre/post fecal microbiota transplant)
Time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Stool will be collected for microbiome 16S rRNA and shotgun metagenomic sequencing. Samples will be obtained from either stool (per rectum), or distal ostomy outputs (ostomy in continuity with proximal bowel). All samples will be sequenced centrally through the McMaster Genomics Centre (MGC). Samples will be stored in -80 freezers. Participants unable to bring stool samples to MCH or HSC will receive funding support for temperature-controlled courier services from home. Costs of microbiome analyses will be partially subsidized by collaborators (MS).
Change in Breath Test Results (pre/post fecal microbiota transplant)
Time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.
Lactulose breath test
Bloodwork
Time frame: Baseline and Week 8 (post-FMT)
Bloodwork will include complete blood count (CBC), C-reactive protein (CRP), ferritin, folic acid, alanine transaminase (ALT), aspartate transaminase (AST), alkaline phosphatase (ALP), serum cytokine profiles (including IL-2, IL-6, IL10, IL-18, TNF) and serum bile acids. Routine institutional testing protocols will be followed at MCH and HSC. Bloodwork outcomes are exploratory. Data will support the development of primary and secondary objectives for future studies.
3 secondary outcomes
Monthly Rate of Recruitment
Time frame: 30 weeks
Adverse Events
Time frame: 30 Weeks
Blood, stool specimens, breath tests, clinical symptom scores
Time frame: 30 Weeks
Results and safety
This study is still under way. Results are not available in the source record yet.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 21 Aug 2025.
- Background: PubMed 30540704Davidovics ZH, Michail S, Nicholson MR, Kociolek LK, Pai N, Hansen R, Schwerd T, Maspons A, Shamir R, Szajewska H, Thapar N, de Meij T, Mosca A, Vandenplas Y, Kahn SA, Kellermayer R; FMT Special Interest Group of the North American Society of Pediatric Gastroenterology Hepatology, Nutrition, the European Society for Pediatric Gastroenterology Hepatology, Nutrition. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection and Other Conditions in Children: A Joint Position Paper From the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. J Pediatr Gastroenterol Nutr. 2019 Jan;68(1):130-143. doi: 10.1097/MPG.0000000000002205.
- Background: PubMed 31009795Nicholson MR, Mitchell PD, Alexander E, Ballal S, Bartlett M, Becker P, Davidovics Z, Docktor M, Dole M, Felix G, Gisser J, Hourigan SK, Jensen MK, Kaplan JL, Kelsen J, Kennedy M, Khanna S, Knackstedt E, Leier M, Lewis J, Lodarek A, Michail S, Oliva-Hemker M, Patton T, Queliza K, Russell GH, Singh N, Solomon A, Suskind DL, Werlin S, Kellermayer R, Kahn SA. Efficacy of Fecal Microbiota Transplantation for Clostridium difficile Infection in Children. Clin Gastroenterol Hepatol. 2020 Mar;18(3):612-619.e1. doi: 10.1016/j.cgh.2019.04.037. Epub 2019 Apr 19.
- Background: PubMed 31784432Pai N, Popov J, Hill L, Hartung E. Protocol for a double-blind, randomised, placebo-controlled pilot study for assessing the feasibility and efficacy of faecal microbiota transplant in a paediatric Crohn's disease population: PediCRaFT Trial. BMJ Open. 2019 Nov 28;9(11):e030120. doi: 10.1136/bmjopen-2019-030120.
- Background: PubMed 33961887Pai N, Popov J, Hill L, Hartung E, Grzywacz K, Moayyedi P; McMaster Pediatric Fecal Microbiota Transplant Research Collaboration. Results of the First Pilot Randomized Controlled Trial of Fecal Microbiota Transplant In Pediatric Ulcerative Colitis: Lessons, Limitations, and Future Prospects. Gastroenterology. 2021 Aug;161(2):388-393.e3. doi: 10.1053/j.gastro.2021.04.067. Epub 2021 May 4. No abstract available.
- Background: PubMed 28840809Bakker GJ, Nieuwdorp M. Fecal Microbiota Transplantation: Therapeutic Potential for a Multitude of Diseases beyond Clostridium difficile. Microbiol Spectr. 2017 Aug;5(4):10.1128/microbiolspec.bad-0008-2017. doi: 10.1128/microbiolspec.BAD-0008-2017.
- Background: PubMed 27957319Fiorentino M, Sapone A, Senger S, Camhi SS, Kadzielski SM, Buie TM, Kelly DL, Cascella N, Fasano A. Blood-brain barrier and intestinal epithelial barrier alterations in autism spectrum disorders. Mol Autism. 2016 Nov 29;7:49. doi: 10.1186/s13229-016-0110-z. eCollection 2016.
- Background: PubMed 28122648Kang DW, Adams JB, Gregory AC, Borody T, Chittick L, Fasano A, Khoruts A, Geis E, Maldonado J, McDonough-Means S, Pollard EL, Roux S, Sadowsky MJ, Lipson KS, Sullivan MB, Caporaso JG, Krajmalnik-Brown R. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017 Jan 23;5(1):10. doi: 10.1186/s40168-016-0225-7.
- Background: PubMed 26616138Davidovics ZH, Vance K, Etienne N, Hyams JS. Fecal Transplantation Successfully Treats Recurrent D-Lactic Acidosis in a Child With Short Bowel Syndrome. JPEN J Parenter Enteral Nutr. 2017 Jul;41(5):896-897. doi: 10.1177/0148607115619931. Epub 2015 Nov 29.
- Background: PubMed 27840368Gu L, Ding C, Tian H, Yang B, Zhang X, Hua Y, Zhu Y, Gong J, Zhu W, Li J, Li N. Serial Frozen Fecal Microbiota Transplantation in the Treatment of Chronic Intestinal Pseudo-obstruction: A Preliminary Study. J Neurogastroenterol Motil. 2017 Apr 30;23(2):289-297. doi: 10.5056/jnm16074.
- Background: PubMed 29901551Bulik-Sullivan EC, Roy S, Elliott RJ, Kassam Z, Lichtman SN, Carroll IM, Gulati AS. Intestinal Microbial and Metabolic Alterations Following Successful Fecal Microbiota Transplant for D-Lactic Acidosis. J Pediatr Gastroenterol Nutr. 2018 Oct;67(4):483-487. doi: 10.1097/MPG.0000000000002043.
- Background: PubMed 31633044McGrath KH, Pitt J, Bines JE. Small intestinal bacterial overgrowth in children with intestinal failure on home parenteral nutrition. JGH Open. 2019 Apr 4;3(5):394-399. doi: 10.1002/jgh3.12174. eCollection 2019 Oct.
- Background: PubMed 34264786Thanert R, Thanert A, Ou J, Bajinting A, Burnham CD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes. 2021 Jan-Dec;13(1):1940792. doi: 10.1080/19490976.2021.1940792.
- US Department of Health and Human Services. Common Terminology Criteria for Adverse Events (CTCAE). Published 2017.Link provided by the sponsor.
- Individual participant dataSharing planned: Yes. Only de-identified individual participant data (IPD) may be shared. No directly identifying information (such as names, dates of birth, contact information, or medical record numbers) will ever be disclosed. If data are shared, they will be limited to variables relevant to the outcomes reported in the trial and will be made available in de-identified form for secondary research purposes under appropriate data use agreements.
Related trials for Small Intestinal Bacterial Overgrowth
Not yet recruiting
Prevalence of Small Intestinal Bacterial Overgrowth (SIBO) in Women With Endometriosis
SIBO, Endometriosis
RecruitingObservational study
Characterization of Small Intestinal Bacterial Overgrowth and Intestinal Barrier-Related Biomarkers in Patients With Severe Periodontitis
Periodontitis (Stage 3), Periodontitis Stage IV
Enrolling by invitationPhase 2
Herbal Supplement (Biocidin REMOVE) for Bacterial Overgrowth in Irritable Bowel Syndrome
Irritable Bowel Syndrome (IBS), Small Intestinal Bacterial Overgrowth Syndrome (SIBO)
Active, not recruitingPhase 2
Comparative Efficacy of Antibiotics for Small Intestine Bacterial Overgrowth in Bangladeshi Children
Small Intestine Bacterial Overgrowth
RecruitingObservational study
Small Intestinal Bacterial Overgrowth (SIBO) in Pancreatic Adenocarcinoma (PDAC)
Pancreatic Adenocarcinoma, Weight Loss
Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part.
Nikhil Pai, MD principal investigator
McMaster Children's Hospital (McMater University)
2 sites in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A Phase 1 study testing Fecal Microbiota Transplant in people with Small Intestinal Bacterial Overgrowth, run by McMaster Children's Hospital at 2 sites in Canada.
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
The sponsor lists 3 inclusion and 3 exclusion criteria. Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: looking for participants now, as of the sponsor's last update on 21 Aug 2025. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 2 sites in Canada. Whether a site is taking part right now should be confirmed with that site. See every site.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
What does this phase mean?
Phase 1 studies test a treatment in a small group of people for the first time or in a new way, mainly to check safety and find the right dose.
Not every study follows the same path, and some studies (observational studies, device studies) have no phase.
Are results available for this study?
This study is still under way. Results are not available in the source record yet.
How can a doctor refer a patient or contact the research team?
Contact Fariha Chowdhury, BASc, MSc, PhD(c) (647-787-8297, chowdf1@mcmaster.ca), or a site near the patient. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Change in Clinical Symptoms (pre/post fecal microbiota transplant) (time frame: Baseline (pre-fecal microbiota transplant), one-, four-, and eight-weeks post-fecal microbiota transplant administration.). The study lists 6 primary outcomes in all. It is what the study was designed to measure, not a finding.
Where can I read the original study information?
On the ClinicalTrials.gov record for NCT05967871, which also lists 26 linked publications.
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 21 Aug 2025.