People with Crohn's disease often need surgery. The gut bacteria of people with Crohn's is associated with Crohn's disease coming back after surgery. Fecal microbiota transplant (FMT) after surgery might be a way to prevent Crohn's disease from coming back after surgery.

This study aims to determine if fecal microbiota transplant (FMT) taken by capsules results in the same amount of good bacteria in the guts as FMT by colonoscopy in people with Crohn's disease who have had surgery.

Participants will be randomized to get FMT by capsules or colonoscopy. Colonoscopy with biopsies 8-weeks after the FMT will be used to assess the good bacteria in the gut.

Inclusion Criteria:

• Able and willing to sign informed consent form
• Age 18 or older
• English speaking
• Established CD for at least 6-months based on typical clinical, endoscopic, and histopathic evidence.
• Prior ileocecal resection for CD
• Stable medications for 30 days
• Women of reproductive age: Agree to remain abstinent or use effective birth control
• Able and willing to comply with all study procedures

Exclusion Criteria:

• Antibiotic therapy within 15 days
• Probiotic therapy within 15 days
• Adenomatous polyps that have not been removed
• Anticipated antibiotic use over the study period
• Subtotal or total colectomy
• Current ostomy (ileostomy or colonoscopy)
• Anticipated surgical procedure over study period
• Pregnancy
• Severe food allergy
• Diagnosis of end stage liver disease or cirrhosis
• Absolute neutrophil count < 500 cell / uL
• Life expectancy < 6 months

Placebo capsules are indistinguishable from study FMT capsules.