Standardized Microbiota Transplant Therapy in Crohn's Disease

Standardized Microbiota Transplant Therapy in Crohn's Disease (NCT06631586) is a Phase 2 interventional studying Crohn Disease, sponsored by University of Minnesota. RECRUITING as of the most recent ClinicalTrials.gov update. Talk to your doctor before contacting the trial site.

About This Trial

Crohn's disease (CD) develops because of a disruption of homeostasis between the gut microbiota and the host immune system resulting in excessive inflammation in the intestinal tract. Current drug therapies for CD are directed at the immune system. The emergence of fecal microbiota transplantation (FMT) for the treatment of recurrent C. difficile infections (rCDI) has opened a frontier of restorative therapies targeting the gut microbiome. This study aims to assess if two forms of encapsulated FMT material (MTP101C and MTP101S) can effectively engraft in the ileum and colon of individuals with CD. This study will also assess how the impact of CD phenotype impacts engraftment. Finally this study will explore symptom and endoscopic changes before and after these two therapies.

What Stage of Research Is This?

Phase 2 trials evaluate whether a treatment actually works against Crohn Disease and continue monitoring side effects. Phase 2 enrolls larger groups (typically 100–300 patients) and produces the first real efficacy signal. A successful Phase 2 readout is what unlocks the much larger Phase 3 confirmatory trials needed for FDA approval.

This trial is currently recruiting participants. The sponsor has registered the study with ClinicalTrials.gov as actively enrolling, which means new applicants who meet the eligibility criteria can be considered for screening. Trial status can change between updates — confirm current recruiting status with the study contact before traveling for a screening visit.

Target enrollment of 120 participants puts this in the typical range for a Phase 2-style efficacy study or a moderate Phase 3 trial in a focused Crohn Disease subpopulation. At this scale, the study has enough statistical power to detect a clear treatment effect but is not the largest cohort in the field.

Who May Be Eligible (Plain English)

Who May Qualify: - Able and willing to provide willing to sign a consent form. - 18-89 years of age. - English speaking. - Diagnosis of CD based on typical clinical and histologic features. - Active disease on endoscopy: - SES-CD \>= 6 - SES-CD \>= 4 for isolated ileal disease - Current CD therapies are in the maintenance phase of dosing at the time of randomization. - Any ongoing CD therapy (apart from steroid use) must be at stable doses for 4 weeks prior to randomization and remain stable over study course. - Steroid use 20mg or less by 5 days prior to randomization. - Steroid use stipulations: - Prednisone must be tapered below 20mg after 7 days. - Any use of budesonide over the study period is allowed although tapering is encouraged. - Rescue medications: Steroid courses (up to 40mg for two weeks with a planned taper) are allowed at the discretion of the treating provider. Study drug therapy will be stopped on a case-by-case basis on discussion with the participant and treating provider. - Women who are not post-menopausal (at least 12 months of non-therapy induced amenorrhea) or surgically sterile (e.g., absence of ovaries and/or uterus) must remain abstinent or use a highly effective form of birth control (e.g., oral contraception, transdermal patch, barrier, intrauterine device). o Periodic abstinence and early withdraw are not acceptable methods. - Able to comply with study measures in the opinion of the investigator. Who Should NOT Join This Trial: - Extensive bowel resection: i.e., subtotal colectomy or substantial removal of small bowel where short bowel syndrome could be a concern. - Documented gastroparesis - History of pylorus non-preserving gastric surgery, e.g., Roux-en-Y gastric bypass. - Symptomatic stricture defined as a stricture that: - Cannot be traversed by the colonoscope, - Requires intervention to be traversed, - Is otherwise responsible for the predominant clinical picture, in the opinion of the investigator. ...See full criteria on ClinicalTrials.gov Always talk to your doctor about whether this trial is right for you.

These are translations of the protocol\'s inclusion and exclusion criteria, simplified for patients and caregivers. The original clinical text appears below. Eligibility is ultimately confirmed by the trial site\'s screening process — this summary is a starting point for a conversation with your doctor, not a final determination.

Original Eligibility Criteria

View original clinical language

Inclusion Criteria: * Able and willing to provide informed consent. * 18-89 years of age. * English speaking. * Diagnosis of CD based on typical clinical and histologic features. * Active disease on endoscopy: * SES-CD \>= 6 * SES-CD \>= 4 for isolated ileal disease * Current CD therapies are in the maintenance phase of dosing at the time of randomization. * Any ongoing CD therapy (apart from steroid use) must be at stable doses for 4 weeks prior to randomization and remain stable over study course. * Steroid use 20mg or less by 5 days prior to randomization. * Steroid use stipulations: * Prednisone must be tapered below 20mg after 7 days. * Any use of budesonide over the study period is allowed although tapering is encouraged. * Rescue medications: Steroid courses (up to 40mg for two weeks with a planned taper) are allowed at the discretion of the treating provider. Study drug therapy will be stopped on a case-by-case basis on discussion with the participant and treating provider. * Women who are not post-menopausal (at least 12 months of non-therapy induced amenorrhea) or surgically sterile (e.g., absence of ovaries and/or uterus) must remain abstinent or use a highly effective form of birth control (e.g., oral contraception, transdermal patch, barrier, intrauterine device). o Periodic abstinence and early withdraw are not acceptable methods. * Able to comply with study measures in the opinion of the investigator. Exclusion Criteria: * Extensive bowel resection: i.e., subtotal colectomy or substantial removal of small bowel where short bowel syndrome could be a concern. * Documented gastroparesis * History of pylorus non-preserving gastric surgery, e.g., Roux-en-Y gastric bypass. * Symptomatic stricture defined as a stricture that: * Cannot be traversed by the colonoscope, * Requires intervention to be traversed, * Is otherwise responsible for the predominant clinical picture, in the opinion of the investigator. * Presence of ileostomy or colostomy. * Entero-vesicular fistula (i.e., fistula from bowel to bladder). * Suspicion of ischemic colitis, radiation colitis or microscopic colitis. * Diagnosis of ulcerative colitis. * Active or untreated infection. * Adenomatous polyps that have not been removed. * Use of antibiotics within 14-days of randomization. * Current pregnancy. * Current breastfeeding or planning to breastfeed over the study period. * History of anaphylactic food allergies. * End stage liver disease or cirrhosis. * Anticipated need for antibiotics over the study period. * Anticipated surgical procedure over the study period. * An absolute neutrophil count \<500 cell/µL. * Diagnosis of a primary immunodeficiency. * Active malignancy requiring the use of chemotherapeutic agent (except for localized non-melanomatous skin cancers). * Patients receiving active cytotoxic therapy for solid tumors and hematologic malignancies. * Any solid organ transplant within 6 months of randomization. * Use of chimeric antigen receptor T-cell therapy or hematopoietic cell transplant within the past 12 months * Life expectancy \>=6 months.

Treatments Being Tested

BIOLOGICAL

MTP-101C

MTP-101C composed of double-encapsulated freeze-dried healthy donor microbiota. The fecal microbiota is frozen in the presence of a lyoprotectant (trehalose), freeze-dried, and double encapsulated into hypromellose capsules (Lonza, Morristown, NJ). Each capsule contains ≥ 1 x 10 11 and ≤ 2.0 x 10 11 bacterial cells.

BIOLOGICAL

MTP-101S

MTP-101S contains identical healthy donor microbiota double encapsulated in VCaps Plus (Lonza). These capsules are also composed of hypromellose but disintegrate in the proximal small bowel. Each capsule contains ≥ 1 x 10 11 and ≤ 2.0 x 10 11 bacterial cells.

Locations (2)

Trial sites listed on ClinicalTrials.gov for this study. Site activation status can vary — confirm with the specific site before traveling for a screening visit.

University of Minnesota

Minneapolis, Minnesota, United States

NYU Langone Health

New York, New York, United States

How to Talk to Your Doctor About This Trial

Bring the printable summary of this trial — including the NCT ID (NCT06631586), the sponsor (University of Minnesota), and the key eligibility criteria — to your next appointment. Your doctor can review the inclusion and exclusion criteria against your medical history, lab values, and current treatments to assess whether you are likely to qualify. They can also help you weigh whether trial participation makes sense alongside your existing care plan.

Useful questions to walk through together: What does the trial protocol require beyond standard care? How long is the active treatment phase, and how long is follow-up? Are there study visits at sites I can reach? Who pays for the trial-specific procedures, and who pays for standard-of-care portions? See our 25 questions to ask about clinical trials guide for a more complete checklist.

Authoritative Sources

The official record for this trial lives on ClinicalTrials.gov — the federal registry maintained by the National Library of Medicine at NIH. For background on how this trial fits into the FDA approval pathway, see the FDA drug approval process. For oncology-specific guidance for patients considering trials, the National Cancer Institute publishes patient-oriented overviews. International trial registries are aggregated by the WHO ICTRP.

Frequently Asked Questions

What is the NCT06631586 clinical trial studying?

Crohn's disease (CD) develops because of a disruption of homeostasis between the gut microbiota and the host immune system resulting in excessive inflammation in the intestinal tract. Current drug therapies for CD are directed at the immune system. The emergence of fecal microbiota transplantation (FMT) for the treatment of recurrent C. difficile infections (rCDI) has opened a frontier of restorative therapies targeting the gut microbiome. This study aims to assess if two forms of encapsulated FMT material (MTP101C and MTP101S) can effectively engraft in the ileum and colon of individuals with… The full protocol is registered on ClinicalTrials.gov and includes the primary outcome measures, eligibility criteria, and study endpoints.

Who can participate in NCT06631586?

Eligibility for this trial depends on the specific inclusion and exclusion criteria set by the sponsor. The plain-English summary above translates the most important criteria into accessible language; the official clinical text is preserved in the collapsible section underneath. Whether you fit any specific trial is a medical decision your doctor needs to confirm — bring the trial information to your treating physician for a full review against your medical history.

How do I contact the trial site for NCT06631586?

Contact information registered with ClinicalTrials.gov is shown in the sidebar of this page. Before reaching out, confirm with your treating physician that this trial is appropriate for your situation. The trial site will then walk you through the screening process to determine final eligibility.

Is participating in a clinical trial safe?

Clinical trials in the United States are regulated by the FDA and overseen by Institutional Review Boards (IRBs) that review the protocol for safety. Risk varies by trial — Phase 1 studies test new treatments in humans for the first time, while Phase 3 trials use treatments that have already passed earlier safety screening. The informed consent document for any specific trial details the known risks and what to expect. Discuss those risks with your physician before deciding whether to participate.

Where can I verify the data on this page?

Every detail on this page comes directly from the ClinicalTrials.gov API. Click "View on ClinicalTrials.gov" in the sidebar to see the official, unmodified record. The federal record is always authoritative; this page is a structured presentation with a plain-English eligibility translation. For background on how clinical trials are regulated, see the FDA drug approval process documentation.

How This Page Is Built

Every field on this page is pulled directly from the ClinicalTrials.gov API v2 — no estimates, no proxies. The plain-English eligibility translation is generated from the original protocol text and reviewed for fidelity to the underlying clinical criteria. The original clinical text remains visible in the collapsible section above so users and clinicians can verify the translation. Read the full methodology for the data pipeline and known limitations.

Source: ClinicalTrials.gov API v2 record for NCT06631586. Maintained by the National Library of Medicine at NIH. Public domain. Cite as: "TrialFinderData. NCT06631586. Data: ClinicalTrials.gov."

Medical disclaimer: This page is informational, not medical advice. Talk to your doctor about whether a clinical trial is right for you.

Last updated 2026-05-08 · Data from ClinicalTrials.gov.