Up to 80% of people with ileal Crohn’s disease (CD) will require an ileocecal resection (ICR). CD recurrence following surgery is common, although antibiotics can reduce short term recurrence rates. Following an ICR, it is unknown what happens to the fecal microbiota and how the microbiota relates to CD recurrence. To further investigate this, we analyzed fecal microbiomes of patients with CD (with and without an ICR) and compared to healthy controls.