Crohn DiseaseNCT04065048
A Dietary Intervention Study on the Microbiome in Crohn's Disease Patients
A study testing Soy based diet and Non-soy based diet in people with Crohn Disease, run by Case Western Reserve University at 1 site in United States.
Trial summary
This protocol is designed to compare the effectiveness of a soy-based diet or identical diet without soy given to patients with Crohn's disease (CD) in remission, patients with active CD, or healthy controls. Read more about this study
- Who is it for?
- Ages 18 to 65 years
- Conditions the study is for
- Crohn Disease
- What is being tested?
- Soy based diet and Non-soy based diet
- Could I receive a placebo?
- No, everyone receives an active treatment
- How many people
- 67 participants
- Where
- 1 siteUnited States
- Study dates
- 1 Nov 2019to 10 Oct 2023
- Phase
- Interventional
- Are there results?
- Yes, posted in the registrySummary in the doctors' view
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 18 to 65 years
- All sexes
- No healthy volunteers
- Adult, Older adult
Who may be able to join
- CD subjects: Documented diagnosis of Crohn's disease. Control subjects: no documented diagnosis of CD.
- CD subjects: Harvey Bradshaw Index (HBI) score <4 ('CD remission'), or with HBI score >8 ('CD moderate disease')
- Capable of providing consent to participate
- Access to technology that permits the daily completion of study related activities
- Able to receive and have an adult sign for food shipments delivered to a work or home environment.
- Negative pregnancy test at screening visit in females of childbearing potential
- Able to take oral nutrition and medication intake for 3 months prior to and at time of study enrolment.
- 'CD remission' subjects: No change in 'IBD related' medications within 8 weeks prior to normally scheduled appointment with treating gastroenterologist (pre-screening): biologics, immunosuppressants, corticosteroids.
Who cannot join
- Short bowel syndrome.
- Hospitalized patients
- Body mass Index <19 kg/m or ≥35.
- Known clinically significant liver/gallbladder/pancreatic disease/dysfunction
- Individuals who lack consent capacity, including the mentally ill, prisoners, cognitively impaired participants, dementia patients.
- Uncontrolled Diabetes Type I type II
Show all 19Show fewer
- Known drug abuse.
- Known parasitic disease of the digestive system. symptomatic intestinal stricture.
- Presence of an ostomy.
- Known concurrent malignancy.
- Other conditions that would be a contraindication to and of the study diets (e.g. Soy, peanut, wheat, gluten allergy.) or preclude the participant from completing the study
- Start of new 'IBD related' medications within 8 weeks prior to enrollment: biologics, immunosuppressants, corticosteroids.
- Documented C difficile colitis within four weeks of screening
- Well-founded doubt about the patient's cooperation.
- Existing pregnancy or lactation.
- Current participation in another diet intervention, simultaneous participation in another clinical trial, or participation in any other dietary intervention trial within the last 30 days.
- History of <3 natural bowel movements per week.
- Unable to access to technology that permits the daily completion of study related activities.
- Currently consuming a soy-based diet
Trial locations and contacts
1 site in 1 country.
United States1 site
University Hospitals Digestive Health Institute
Cleveland, Ohio, 44106
About this study
Official title: A Single-center Open-label Study to Determine the Effect of Diet on Microbiome Signatures in Crohn's Disease Patients
This protocol is designed to compare the effectiveness of a soy-based diet or identical diet without soy given to patients with Crohn's disease (CD) in remission, patients with active CD, or healthy controls. The assigned diet will be compared to participant 'baseline' (pre-diet) in terms of its ability to change the gut bacteria and fecal butyrate, an important short-chain fatty acid (SCFA) that limits bowel inflammation, a characteristic of this debilitating disease.
Read the detailed description
The inflammatory bowel disease (IBD) subtype, Crohn's disease (CD) is a chronic and relapsing inflammatory disorder of the gastrointestinal tract. Although the precise etiology of IBD is not known, evidence suggests that environmental factors, including diet, contribute to its pathogenesis. A soy-based diet has been demonstrated to have numerous health benefits. This single-center open-label study will compare the effectiveness of a soy-based diet or an identical diet without soy to change the gut microbiota composition and fecal butyrate concentration to that of baseline (pre-diet) in patients with CD (remission or active disease) and healthy control subjects without CD. Participants will follow either a soy-based diet or an identical diet without soy to which they will be randomized for 7 days. No data collection or other study procedures will take place until the potential participant provides written informed consent to participate in the research study. The informed consent, screening, enrollment, and baseline data collection which make up visit 1 can occur on the same day or be completed across several days.
- Conditions
- Crohn Disease
- Being tested
- Soy based diet, Non-soy based diet
- Keywords
- diet, inflammatory bowel disease, gut microbiome
- Medical subject headings
- Crohn Disease, Inflammatory Bowel Diseases
What participants receive
What participants receive. In a randomised study each person is assigned to one group by chance.
Soy based dietOther
The diet will be based on the detailed descriptions according to the American Heart Association, US Food and Drug Administration (FDA), and the Soyfoods Association of North America Website, which all promote soy products as having beneficial nutrient profiles with a daily consumption of 25 grams or more of soy protein (average serving = 6.25 grams), upper limit of 50g.
Non-soy based dietOther
Diet of identical composition to the soy diet with the exception of soy.
| Study group | Role | What they receive |
|---|---|---|
| Soy-based diet | Experimental | Participants will be randomized to follow a soy-based diet for 7 days. The diet will be preceded by a 12-hr overnight fast. Receives: Other: Soy based diet |
| Regular diet | Active comparator | Participants will be randomized to follow a diet without soy for 7 days. The diet will be preceded by a 12-hr overnight fast. Receives: Other: Non-soy based diet |
What is being measured
The primary outcome is the main question the study is designed to answer.
Maintenance of Symptomatic Remission, Without Worsening of Any Existing Disease Activity During Study Period
The primary aim will measure the Crohn's Disease Activity Index (CDAI) at the enrollment and end of study visit. CDAI scores can range from 0 to ~600 (A score of less than 150 corresponds to relative disease quiescence (remission); 150 to 219, mildly active disease; 220 to 450, moderately active disease; and greater than 450, severe disease). Herein, a cut-off value of <150 was selected so that most patients below this threshold would be rated by physicians as 'very well'. Change was calculated from two time points as the value at the later time point minus the value at the earlier time point [i.e., value at 7 days (post) minus value at baseline/enrollment (pre)].
Measured: 7 days
Change in Fecal Myleoperoxidase (MPO) Activity
Change in fecal myleoperoxidase (MPO) activity at day 7 vs day 0.
Measured: 7 days
Secondary outcomes (2)
Changes to Functional Composition of Gut Microbiota
Secondary outcome will focus on changes to the functional composition of fecal gut microbiota, including bacterial butryate production after the diet intervention.
Measured: measured after the 7-day diet intervention
Percentage of Subjects Who Continue Diet Following Completion of Study
To assess the percentage of patients who intend to continue the study diets when prepared food is no longer provided without cost, and the reasons for discontinuation of either diet (compared to resuming usual food habits).
Measured: 6 months
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted22 Aug 2019
- Study start1 Nov 2019
- Primary completion11 Sep 2023
- Study completion10 Oct 2023
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Posted resultsParticipant flow, outcome measures and adverse events reported by the sponsor.
- Publications (4)Papers the sponsor has linked to this study.
- Other trials for Crohn DiseaseStudies 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 N/A
- Primary purpose
- Other
- Allocation
- Randomised
- Intervention model
- Parallel groups
- Model description
- This is an open label single center study to compare the effect of a soy-based diet or an identical diet without soy on the composition and metabolite production of gut bacteria in Crohn's disease (CD) patients in remission or active disease, and in healthy controls. Crohn's subjects will be pre-screened by the treating gastroenterologist for eligibility criteria during their normally scheduled appointment. The treating gastroenterologist will ask suitable patients whether they are interested in participating in the described dietary intervention study during the patient appointment. Initial verbal consent will be obtained by the treating gastroenterologist. Healthy controls will be recruited in the same manner, as well as via a hospital flyer advertisement. Subjects will then be contacted by the study investigator to schedule a screening visit (visit 1) and if study eligibility is confirmed, and informed consent provided, enrolled into the study.
- Masking
- None (open label)
- Enrolment
- 67 participants (actual)
Sponsor and investigators
- Lead sponsor
- Case Western Reserve University
- Sponsor type
- University, hospital or other
- Collaborators
- University of California, Davis, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), University Hospitals Cleveland Medical Center
- Responsible party
- Principal investigator, Abigail Basson, Case Western Reserve University
- Investigators
- Fabio Cominelli, MD, PhD, Principal investigator, Case Western Reserve University, School of Medicine, Gastroenterology
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT04065048
- Sponsor's protocol ID
- 09411
- Other IDs
- 1P30DK097948
- Status last verified
- Jun 2026
- First submitted
- 19 Aug 2019
- Last updated
- 3 Jun 2026
- Results posted
- Yes, on ClinicalTrials.gov
- Data monitoring committee
- Yes
- FDA-regulated drug
- No
- FDA-regulated device
- No
- Individual data sharing
- No: Study results or individual subject results such as investigational tests will not be shared with the research participants or others unless deemed medically necessary. Result of this research and management of intellectual property will adherence to the NIH Grant Policy on Sharing of Unique Research Resources including the Principles and Guidelines for Recipients of NIH Research Grants and Contracts on Obtaining and Disseminating Biomedical Research Resources issued March 5, 2003. Publication of data during the project and/or at the end of the project shall be consistent with normal scientific practices. Research data which documents, supports, and validates research findings will be made available after the main findings from the final research data set have been accepted for publication.
Publications
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1.
PubMed 21885731David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.
PubMed 24336217Thia K, Faubion WA Jr, Loftus EV Jr, Persson T, Persson A, Sandborn WJ. Short CDAI: development and validation of a shortened and simplified Crohn's disease activity index. Inflamm Bowel Dis. 2011 Jan;17(1):105-11. doi: 10.1002/ibd.21400.
PubMed 20629100Basson AR, Katz J, Nguyen V, Singh D, Menghini P, Gomez-Nguyen A, Sieg J, Bell M, Thamma K, Ponzani G, Osme A, Rodriguez-Palacios A, Cominelli F. A Randomized Controlled Trial Comparing Soy-Pea Protein to Animal Protein in Adults with Crohn's Disease. medRxiv [Preprint]. 2026 Jun 11:2026.05.20.26353678. doi: 10.64898/2026.05.20.26353678.
PubMed 42238434
Study at a glance
From the registry record, last updated by the sponsor on 3 Jun 2026. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- A Single-center Open-label Study to Determine the Effect of Diet on Microbiome Signatures in Crohn's Disease Patients
- ClinicalTrials.gov ID
- NCT04065048
- Acronym / sponsor ID
- 09411
- Conditions
- Crohn Disease
- Keywords
- diet, inflammatory bowel disease, gut microbiome
- Study type
- Interventional
- Recruitment status
- Completed
- Enrolment
- 67 participants (actual)
- Lead sponsor
- Case Western Reserve UniversityUniversity, hospital or other
- Collaborators
- University of California, Davis, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), University Hospitals Cleveland Medical Center
- Study start
- 1 Nov 2019 (actual)
- Primary completion
- 11 Sep 2023 (actual)
- Study completion
- 10 Oct 2023 (actual)
- First posted
- 22 Aug 2019 (actual)
- Results
- Posted 19 Sep 2024
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
This protocol is designed to compare the effectiveness of a soy-based diet or identical diet without soy given to patients with Crohn's disease (CD) in remission, patients with active CD, or healthy controls. The assigned diet will be compared to participant 'baseline' (pre-diet) in terms of its ability to change the gut bacteria and fecal butyrate, an important short-chain fatty acid (SCFA) that limits bowel inflammation, a characteristic of this debilitating disease.
Detailed description
The inflammatory bowel disease (IBD) subtype, Crohn's disease (CD) is a chronic and relapsing inflammatory disorder of the gastrointestinal tract. Although the precise etiology of IBD is not known, evidence suggests that environmental factors, including diet, contribute to its pathogenesis. A soy-based diet has been demonstrated to have numerous health benefits. This single-center open-label study will compare the effectiveness of a soy-based diet or an identical diet without soy to change the gut microbiota composition and fecal butyrate concentration to that of baseline (pre-diet) in patients with CD (remission or active disease) and healthy control subjects without CD. Participants will follow either a soy-based diet or an identical diet without soy to which they will be randomized for 7 days. No data collection or other study procedures will take place until the potential participant provides written informed consent to participate in the research study. The informed consent, screening, enrollment, and baseline data collection which make up visit 1 can occur on the same day or be completed across several days.
Study design
- Primary purpose
- Other
- Allocation
- Randomised
- Intervention model
- Parallel groups
- Masking
- None (open label)
- Number of arms
- 2
- Model description
- This is an open label single center study to compare the effect of a soy-based diet or an identical diet without soy on the composition and metabolite production of gut bacteria in Crohn's disease (CD) patients in remission or active disease, and in healthy controls. Crohn's subjects will be pre-screened by the treating gastroenterologist for eligibility criteria during their normally scheduled appointment. The treating gastroenterologist will ask suitable patients whether they are interested in participating in the described dietary intervention study during the patient appointment. Initial verbal consent will be obtained by the treating gastroenterologist. Healthy controls will be recruited in the same manner, as well as via a hospital flyer advertisement. Subjects will then be contacted by the study investigator to schedule a screening visit (visit 1) and if study eligibility is confirmed, and informed consent provided, enrolled into the study.
| Arm | Type | Receives |
|---|---|---|
| Soy-based diet | Experimental | Other: Soy based dietParticipants will be randomized to follow a soy-based diet for 7 days. The diet will be preceded by a 12-hr overnight fast. |
| Regular diet | Active comparator | Other: Non-soy based dietParticipants will be randomized to follow a diet without soy for 7 days. The diet will be preceded by a 12-hr overnight fast. |
Who may qualify
- Ages
- 18 to 65 years
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
Key inclusion criteria (8 listed)
- CD subjects: Documented diagnosis of Crohn's disease. Control subjects: no documented diagnosis of CD.
- CD subjects: Harvey Bradshaw Index (HBI) score <4 ('CD remission'), or with HBI score >8 ('CD moderate disease')
- Capable of providing consent to participate
- Access to technology that permits the daily completion of study related activities
- Able to receive and have an adult sign for food shipments delivered to a work or home environment.
Key exclusion criteria (19 listed)
- Short bowel syndrome.
- Hospitalized patients
- Body mass Index <19 kg/m or ≥35.
- Known clinically significant liver/gallbladder/pancreatic disease/dysfunction
- Individuals who lack consent capacity, including the mentally ill, prisoners, cognitively impaired participants, dementia patients.
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 |
|---|---|---|
| Soy based dietThe diet will be based on the detailed descriptions according to the American Heart Association, US Food and Drug Administration (FDA), and the Soyfoods Association of North America Website, which all promote soy products as having beneficial nutrient profiles with a daily consumption of 25 grams or more of soy protein (average serving = 6.25 grams), upper limit of 50g. | Other | Soy-based diet |
| Non-soy based dietDiet of identical composition to the soy diet with the exception of soy. | Other | Regular diet |
Primary outcome
Maintenance of Symptomatic Remission, Without Worsening of Any Existing Disease Activity During Study Period
Time frame: 7 days
The primary aim will measure the Crohn's Disease Activity Index (CDAI) at the enrollment and end of study visit. CDAI scores can range from 0 to ~600 (A score of less than 150 corresponds to relative disease quiescence (remission); 150 to 219, mildly active disease; 220 to 450, moderately active disease; and greater than 450, severe disease). Herein, a cut-off value of <150 was selected so that most patients below this threshold would be rated by physicians as 'very well'. Change was calculated from two time points as the value at the later time point minus the value at the earlier time point [i.e., value at 7 days (post) minus value at baseline/enrollment (pre)].
Change in Fecal Myleoperoxidase (MPO) Activity
Time frame: 7 days
Change in fecal myleoperoxidase (MPO) activity at day 7 vs day 0.
2 secondary outcomes
Changes to Functional Composition of Gut Microbiota
Time frame: measured after the 7-day diet intervention
Percentage of Subjects Who Continue Diet Following Completion of Study
Time frame: 6 months
Results and safety
Loading the posted results from ClinicalTrials.gov…
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 3 Jun 2026.
- Posted resultsParticipant flow, baseline, all outcome measures and adverse events.
- Background: PubMed 21885731Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7;334(6052):105-8. doi: 10.1126/science.1208344. Epub 2011 Sep 1.
- Background: PubMed 24336217David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11.
- Background: PubMed 20629100Thia K, Faubion WA Jr, Loftus EV Jr, Persson T, Persson A, Sandborn WJ. Short CDAI: development and validation of a shortened and simplified Crohn's disease activity index. Inflamm Bowel Dis. 2011 Jan;17(1):105-11. doi: 10.1002/ibd.21400.
- Derived from this study: PubMed 42238434Basson AR, Katz J, Nguyen V, Singh D, Menghini P, Gomez-Nguyen A, Sieg J, Bell M, Thamma K, Ponzani G, Osme A, Rodriguez-Palacios A, Cominelli F. A Randomized Controlled Trial Comparing Soy-Pea Protein to Animal Protein in Adults with Crohn's Disease. medRxiv [Preprint]. 2026 Jun 11:2026.05.20.26353678. doi: 10.64898/2026.05.20.26353678.
- Individual participant dataSharing planned: No. Study results or individual subject results such as investigational tests will not be shared with the research participants or others unless deemed medically necessary. Result of this research and management of intellectual property will adherence to the NIH Grant Policy on Sharing of Unique Research Resources including the Principles and Guidelines for Recipients of NIH Research Grants and Contracts on Obtaining and Disseminating Biomedical Research Resources issued March 5, 2003. Publication of data during the project and/or at the end of the project shall be consistent with normal scientific practices. Research data which documents, supports, and validates research findings will be made available after the main findings from the final research data set have been accepted for publication.
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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. This study is not recruiting at the moment.
Fabio Cominelli, MD, PhD principal investigator
Case Western Reserve University, School of Medicine, Gastroenterology
1 site in 1 country: see every site and its status.
Questions about this trial
What is this clinical trial studying?
A study testing Soy based diet and Non-soy based diet in people with Crohn Disease, run by Case Western Reserve University at 1 site in United States.
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 8 inclusion and 19 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: finished, as of the sponsor's last update on 3 Jun 2026. Status can change between updates, so confirm with the study contact before making plans.
Where is the study taking place?
The record lists 1 site in United States. 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.
Are results available for this study?
Yes. Results are posted in the registry (first posted 19 Sep 2024). A summary is in the For doctors view, and the full results are on ClinicalTrials.gov.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Maintenance of Symptomatic Remission, Without Worsening of Any Existing Disease Activity During Study Period (time frame: 7 days). The study lists 2 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 NCT04065048, which also lists 4 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 3 Jun 2026.