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.

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.

Inclusion Criteria:

• 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.

Exclusion Criteria:

• 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
• 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

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.

Adverse event data was collected over the 7 day diet intervention period

The COVID pandemic posed a significant challenge that impeded the accrual of patients. The first participant was enrolled in 2019. However due to COVID, further participant enrollment only recommenced in 2021