Fecal Microbiota Transplantation (FMT) of FMP30 in Relapsing-Remitting Multiple Sclerosis (MS-BIOME)

January 15, 2026 updated by: Jeffrey Gelfand

Fecal Microbiota Transplantation (FMT) of FMP30 in Relapsing-Remitting Multiple Sclerosis: A Phase 1b Clinical Trial to Evaluate Feasibility, Safety, Tolerability and Effects on Immune Function

In this Phase 1b open-label prospective clinical trial, patients with relapsing-remitting MS will undergo FMT of FMP30 (donor stool) via colonoscopy and immunological efficacy endpoints will be assessed at various time points. The active phase of the study will continue for 12 weeks post-FMT with safety and biomarker (engraftment) follow-up for 48 weeks. A parallel observational control arm of MS patients who otherwise satisfy study inclusion criteria based on their MS phenotype, demographics, disease duration and prior use of allowable MS therapies, will be recruited as a comparison observational group to measure stability of stool and serum immunological measures. The study duration for the Observational Control Arm is 12 weeks.

Study Overview

Detailed Description

In this Phase 1b open-label prospective clinical trial, patients with relapsing- remitting MS will undergo FMT of FMP30 (donor stool) via colonoscopy and immunological efficacy endpoints will be assessed at various time points. The active phase of the study will continue for 12 weeks post-FMT with safety and biomarker (engraftment) follow-up for 48 weeks. A parallel observational control arm of MS patients who otherwise satisfy study inclusion criteria based on their MS phenotype, demographics, disease duration and prior use of allowable MS therapies, will be recruited as a comparison observational group to measure stability of stool and serum immunological measures.

The primary hypotheses are that:

  1. FMT will be safe and tolerable in patients with MS.
  2. FMT preceded by antibiotic preconditioning will lead to a change in fecal microbiota community structure.

Secondary hypotheses are that:

  1. FMT preceded by antibiotic preconditioning will induce a favorable shift from pro-inflammatory to immunomodulatory T cell profiles in patients with relapsing-remitting MS.
  2. That engraftment will not appreciably decay over time.
  3. That FMT will favorably change humoral function.
  4. That FMT will favorably influence short-term clinical and radiological endpoints.

FMP30 donor stool will be obtained from OpenBiome (Somerville, Massachusetts; OpenBiome.org), an established nonprofit stool bank with stringent safety protocols and quality control. Donor stool will be obtained from donors without Multiple Sclerosis (MS) and without other known autoimmune diseases and will be screened for transmissible pathogens. In collaboration with OpenBiome, University of California, San Francisco (UCSF) will additionally screen donor stool using in vitro assays for immunological properties thought to be favorable in Multiple Sclerosis (MS), including decreasing T helper 17 cells (TH17) and increasing T regulatory cells, in order to select the final donor stool to be used in this study for FMT. UCSF will obtain an investigational new drug (IND) from the FDA for FMT of FMP30 donor stool in MS.

After providing written informed consent and reviewing inclusion and exclusion criteria, participants will participate in either the FMT Treatment Arm or the Observational Control Arm.

Participants in the FMT Treatment Arm will first undergo screening assessments according to the study schedule of activities and provide blood samples for eligibility and research, and stool samples for research. Participants who pass screening will have their pre-treatment baseline visit with 21 days of their screening visit where they will have an MRI, safety and biomarker research blood sample collection, stool sample collection for research, complete study activities according to the study visit schedule, be given antibiotics, bowel preparation, a medication compliance diary and directions on when and how to start the antibiotics and bowel preparation before their scheduled FMT colonoscopy procedure.

The week before their Baseline FMT visit, participants will be contacted by study staff to initiate an oral antibiotic regimen for 5 days to precondition the gut for FMT and optimize engraftment of the donor microbiome. Study staff will ensure that the participants understand how to complete their oral antibiotic regimen, compliance diary, and bowel preparation correctly.

At the study Baseline Visit, following standard bowel preparation for colonoscopy, participants will then undergo colonoscopy with FMT of FMP30 by an experienced gastroenterologist. Participants will return for scheduled assessments of stool and blood sampling, questionnaires, physical examination, MS rating scales, and follow-up MRI for 12 weeks, with additional safety and biomarker blood sample collection, and followed at weeks 24, 36, and 48. The active study time of 12 weeks was designed to be short to minimize time off MS disease-modifying therapies (should the participant wish to go on a MS disease-modifying therapy).

Participants participating in the Observational Control Arm will not undergo the interventional FMT treatment. Participants in this arm will have a total of 5 visits over the course of 12 weeks. At the Screening/Baseline visit, participants will provide blood and stool samples for research along with other study activities, according to the study visit schedule. Participants will mail in a stool sample at week 2 and come in for follow-up visits at weeks 4, 8, and 12.

Study Type

Interventional

Enrollment (Actual)

5

Phase

  • Phase 1

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

    • California
      • San Francisco, California, United States, 94158
        • UCSF Multiple Sclerosis Center

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

18 years to 60 years (Adult)

Accepts Healthy Volunteers

No

Description

Inclusion Criteria:

  1. Age 18-60 inclusive (at time of screening).
  2. Diagnosis of relapsing-remitting multiple sclerosis (MS) by the International Panel McDonald Criteria (2010)(1), incorporating 2017 revisions, which reclassify select high-risk Clinically Isolated Syndromes under 2010 criteria as RRMS under 2017 criteria, and Lublin criteria (2014)(2). [RRMS: relapsing remitting multiple sclerosis]
  3. Recent documented MS disease activity, defined as at least 1 clinical relapse within the past 1 year prior to baseline OR 2 clinical relapses in the past 2 years prior to baseline OR at least 1 new T2/FLAIR lesion on brain or spine MRI OR at least 1 gadolinium enhancing lesion on brain or spine MRI in the past 1 year prior to baseline.
  4. Expanded Disability Status Scale (EDSS) less than or equal to 6.0; EDSS 5.5 or less if MS disease duration is greater than 15 years (no other disease duration restriction).
  5. Must have positive serology for Epstein-Barr Virus (EBV) (IgG anti-EBNA positive) at screening, indicating prior exposure. [EBNA: Epstein-Barr nuclear antigen]
  6. No prior MS disease-modifying therapy or a 12-week washout period for participants on glatiramer acetate or interferon-beta therapy.
  7. At least 4 weeks from baseline since last use of IV or oral glucocorticoids. Protocol: MS-BIOME Study.
  8. Agree to maintain a stable diet during the course of the study (over-the-counter probiotics are allowable).
  9. Premenopausal women and women <12 months after the onset of menopause must have a negative serum pregnancy test unless they have undergone surgical sterilization.
  10. Female participants of childbearing potential who are sexually active with a non-sterilized male partner must agree to use a highly effective method of contraception; non-sterilized male participants who are sexually active with a female partner of childbearing potential must agree to use a highly effective method of contraception.
  11. Not actively participating in another interventional MS clinical trial (participation in other observational research studies is allowable).

Exclusion Criteria:

  1. Prior use of fingolimod, dimethyl fumarate, teriflunomide, natalizumab, alemtuzumab, mitoxantrone, cyclophosphamide, rituximab, ocrelizumab, daclizumab, methotrexate, azathioprine, mycophenolate mofetil, cyclosporine, leflunomide, or induction chemotherapy.
  2. No use of diuretics like furosemide (Lasix) 1 week before the first dose of oral antibiotics. The use of hydrochlorothiazide (HCTZ) for hypertension at a dose < 50 mg/day is allowable.
  3. Progressive MS by Lublin criteria (2014).
  4. No oral or IV antibiotics are allowed within 8 weeks prior to screening and within 12 weeks prior to the planned FMT procedure (for participants in the FMT arm) or prior to the first stool collection (for participants in the control arm). (Note that topical, otic, ocular antibiotics are specifically allowable, which is consistent with the IMSMS.org protocol for collaborative gut microbiome research in MS). [IMSMS: International MS Microbiome Study]
  5. Hypersensitivity or allergy to study antibiotics, conscious sedation medications, or bowel preparation.
  6. Contraindication to study procedures, including MRI, anesthesia (ASA criteria IV and V), colonoscopy, and phlebotomy.
  7. History of inflammatory bowel disease (Crohn's Disease, Ulcerative Colitis) Protocol: MS-BIOME Study.
  8. Active symptomatic C. Difficile infection (colonization is not an exclusion).
  9. Active gastrointestinal condition being investigated (i.e. GI bleeding, colon cancer, active GI workup); history of known or suspected toxic megacolon and/or known small bowel ileus, major gastrointestinal surgery (e.g. significant bowel resection) within 3 months before enrollment (note that this does not include appendectomy or cholecystectomy); or history of total colectomy or bariatric surgery.
  10. History of malignancy (except excised cutaneous basal cell carcinoma or squamous cell carcinoma, which are allowable), including no concurrent induction chemotherapy, radiation therapy, or biological treatment for active malignancy.
  11. Pregnant or lactating women or intention of getting pregnant during the trial period.
  12. Active infection, including untreated latent or active tuberculosis, HIV, hepatitis, syphilis, or other major active infection.
  13. Known immunodeficiency, including Common Variable Immunodeficiency (CVID).
  14. INR>1.5, Platelets<100, Hemoglobin <8.5, WBC<2.0, Absolute lymphocyte count <0.8, Absolute Neutrophil Count <0.5, CD4<200, eGFR<45. [INR: international normalized ratio, WBC: White Blood cell, CD4: cluster of differentiation 4, eGFR: epidermal growth factor receptor]
  15. Any condition that in the opinion of the study PI could jeopardize the safety of the participant, would make it unlikely for the participant to complete the study or could confound the results of the study.
  16. Unable or unwilling to comply with study protocol requirements.

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Treatment
  • Allocation: Non-Randomized
  • Interventional Model: Parallel Assignment
  • Masking: None (Open Label)

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: Interventional FMT Treatment Arm

After providing written informed consent, participants will undergo screening and baseline assessments of stool and blood sampling, questionnaires, physical examination, MS rating scales, and MRI. Participants will then initiate an oral antibiotic regimen for 5 days to precondition the gut for the Fecal Microbiota Transplantation (FMT) of FMP30 donor stool and optimize engraftment of the FMP30 donor stool microbiome. Following standard bowel preparation for colonoscopy, participants will undergo the FMT procedure by an experienced gastroenterologist. Participants will return for scheduled assessments and follow-up MRI for 12 weeks, with additional safety and biomarker follow-up for 36 weeks.

The active study time is designed to be short (12 weeks active phase) to minimize time off on other MS disease-modifying therapy (DMT). This arm of the study will last for approximately 52 weeks total (4 weeks of screening + 12 weeks active treatment phase + 36 weeks of safety follow-up).

FMP30 is manufactured by the non-profit stool bank Openbiome. Each FMP30 filtered donor stool engraftment has approximately 12.5g of stool per 30mL of normal saline. It is homogenized in sterile normal saline.
Three doses of filtered donor stool engraftments homogenized in sterile normal saline (FMP30), obtained from the non-profit stool bank OpenBiome, will be administered via colonoscopy in patients with Relapsing-Remitting Multiple Sclerosis. FMT dosage via colonoscopy may include a lower amount of transplanted stool at the discretion of the study gastroenterologist if there are any peri-procedural safety or technical considerations. Total FMT dose (in milliliters) will be documented.
Active Comparator: Observational Control Arm

Participants, who otherwise satisfy study inclusion criteria based on their MS phenotype, demographics, disease duration, and prior use of allowable MS therapies, will be recruited as a comparison observational group to measure stability of stool and serum immunological measures.

After providing written informed consent, participants will undergo screening and baseline assessments, including collection of blood and stool samples, demographic data collection, concomitant medication review, and an MS Relapse assessment. At week 2, participants will mail in stool samples with a prepaid air bill and packaging. Weeks 4, 8, and 12 assessments will include concomitant medication review, relapse assessment, and blood and stool collection.

The duration of the study for the observational control arm will last for 12 weeks. All study procedures will be performed at the University of California, San Francisco.

Participants, who otherwise satisfy study inclusion criteria based on their MS phenotype, demographics, disease duration, and prior use of allowable MS therapies will be recruited as a comparison observational group to measure stability of stool and serum immunological measures.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Participants Who Complete the Study Protocol
Time Frame: Baseline through week 48
This includes the proportion of participants who completed the study protocol, including the completion of the study visits at baseline, 2 weeks, 4 weeks, 8 weeks, 12 weeks, and a safety follow-up through week 48.
Baseline through week 48
Change in Fecal Microbiota
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.

Engraftment: Change in fecal microbiota community structure at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, 12 weeks by 16S ribosomal RNA amplicon sequencing (as a measure of the diversity of fecal microbiota by detecting sequence variations).

Comment on unit of measure: The Shannon Index is used to assess changes in fecal microbiota diversity, with higher values indicating greater microbial diversity. Changes in the Shannon index over time will reflect the impact of the intervention on gut microbial composition.

Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Number of Treatment-Emergent Serious Adverse Events [Safety and Tolerability]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Treatment-emergent serious adverse events from baseline through week 12. The proportion of participants who develop an adverse event (AE) of severity grade 2 or more by NIH CTCAE criteria V4.0 is considered serious. NIH CTCAE is a standardized classification and severity grading scale for adverse events used in clinical trials. The CTCAE displays Grades 1 through 5 with unique clinical descriptions of severity for each AE. Grade 1 is considered mild, Grade 2 as moderate, Grade 3 as severe or medically significant, Grade 4 as life-threatening, and Grade 5 as death related to AE.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Number of Treatment-Emergent Non-Serious Adverse Events [Safety and Tolerability]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Treatment-emergent non-serious adverse events from baseline through week 12. The proportion of participants who develop an adverse event (AE) of severity grade 2 or more by NIH CTCAE criteria V4.0 is considered serious. NIH CTCAE is a standardized classification and severity grading scale for adverse events used in clinical trials. The CTCAE displays Grades 1 through 5 with unique clinical descriptions of severity for each AE. Grade 1 is considered mild, Grade 2 as moderate, Grade 3 as severe or medically significant, Grade 4 as life-threatening, and Grade 5 as death related to AE.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Change in Plasma CD19+ B Cells in Interventional Arm [CD19: Cluster of Differentiation Antigen 19]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Plasma CD19+ B cell count will be measured as absolute cell counts (cells/uL) at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Change in Plasma CD19+ B Cells in Observational Arm
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Plasma CD19+ B cell count will be measured as absolute cell counts (cells/uL) at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Change in Serum IgA Immunoglobulin Levels in Interventional Arm [IgA: Immunoglobulin A]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Serum Immunoglobulin levels of IgA will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Change in Serum IgA Immunoglobulin Levels in Observational Arm
Time Frame: Baseline Visit, 2 weeks, 4 weeks, and 12 weeks.
Serum Immunoglobulin levels of IgA will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, and 12 weeks.
Change in Serum IgM Immunoglobulin Levels in Interventional Arm [IgM: Immunoglobulin M]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks.
Serum Immunoglobulin levels of IgM will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks.
Change in Serum IgM Immunoglobulin Levels in Observational Arm
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks.
Serum Immunoglobulin levels of IgM will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks. The percentage of change from baseline for each time point is also reported.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks.
Change in Serum IgG Immunoglobulin Levels in Interventional Arm [IgG: Immunoglobulin G]
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks
Serum Immunoglobulin levels of IgG will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks
Change in Serum IgG Immunoglobulin Levels in Observational Arm
Time Frame: Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks
Serum Immunoglobulin levels of IgG will be measured in mg/dL at Baseline Visit, 2 weeks, 4 weeks, 8 weeks, and 12 weeks.
Baseline Visit, 2 weeks, 4 weeks, 8 weeks and 12 weeks
Incidence of New T2/FLAIR Lesions
Time Frame: At pre-treatment visit and week 12.
The number of new or enlarging T2/FLAIR lesions will be counted at pre-treatment and week 12.
At pre-treatment visit and week 12.
Treatment-emergent Gadolinium Enhancing Lesions
Time Frame: At pre-treatment visit and week 12.
New treatment-emergent gadolinium-enhancing lesions on brain MRI.
At pre-treatment visit and week 12.
Clinical Relapse
Time Frame: From baseline to week 12
Clinical relapse through week 12 (treatment phase)
From baseline to week 12
Percentage of Induced T-regulatory Cells
Time Frame: Pre-screening, Screening, Baseline, Week 2, Week 4, Week 8, Week 12, Week 24, Week 36, Week 48
Flow cytometric analysis of peripheral blood mononuclear cells (PBMC) from each participant and at each time point. T-regs were induced by stimulation of PBMCs with anti-CD3 and anti-CD28 antibodies in the presence of IL2 and TGFb. The percentage of T-regs before and after FMT was analyzed. FMT was performed during the baseline visit. [CD3: cluster of differentiation 3, CD28: cluster of differentiation 28, IL2: interleukin2, TGFb: Transforming growth factor beta]
Pre-screening, Screening, Baseline, Week 2, Week 4, Week 8, Week 12, Week 24, Week 36, Week 48

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Investigators

  • Principal Investigator: Jeffrey Gelfand, MD, MAS, UCSF Multiple Sclerosis Center

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

November 16, 2018

Primary Completion (Actual)

December 16, 2024

Study Completion (Actual)

December 16, 2024

Study Registration Dates

First Submitted

June 7, 2018

First Submitted That Met QC Criteria

July 18, 2018

First Posted (Actual)

July 20, 2018

Study Record Updates

Last Update Posted (Actual)

February 3, 2026

Last Update Submitted That Met QC Criteria

January 15, 2026

Last Verified

January 1, 2026

More Information

Terms related to this study

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

YES

IPD Plan Description

Outcome data as well as study data related to diagnosis, disease presentation, and date of birth, along with biological specimens collected as part of the study, may be shared (in coded form) in the future with other qualified researchers on a case by case basis at the discretion of the PI and Co-PIs. Any such investigator will be required to provide appropriate documentation that the research being conducted has been approved by an Institutional Review Board and demonstrate that it will be of value in determining the cause of MS or a related disorder, and as allowed by the UCSF Institutional Review Board.

IPD Sharing Time Frame

After initial study results are published and on a case by case basis.

IPD Sharing Access Criteria

Limited data to include demographic and clinical information and biological specimens collected as part of the study, may be shared (in coded form) in the future with other qualified researchers on a case by case basis at the discretion of the PI and Co-PIs. Any such investigator will be required to provide appropriate documentation that the research being conducted has been approved by an Institutional Review Board and demonstrate that it will be of value in determining the cause of MS or a related disorder, and as allowed by the UCSF Institutional Review Board.

IPD Sharing Supporting Information Type

  • STUDY_PROTOCOL

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

Yes

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

Clinical Trials on Relapsing Remitting Multiple Sclerosis

Clinical Trials on FMP30 Donor Stool

Subscribe