The purpose of this study is to compare the effect of two procedures - the Kono-S procedure and the side-to-side functional end to end anastomosis - on the microbiome (the bacteria that live in our gut) and on the intestinal immune system. The investigators are hypothesizing that there are differences in the microbiome environment and the immune environment between the two procedural groups.

These are two are different ways to re-connect the intestines after a portion of it is removed during surgery. Patients will be randomly assigned to either be re-connected with a procedure called the Kono-S anastomosis or with a side-to-side anastomosis during their surgery. This study will look at the microbiome and immune environment in the piece of intestine that is removed during surgery. Then, at the follow colonoscopies (3-6 month, 12-18 month, 60 month), biopsies (small pieces of tissue) will be taken near the connection between the small intestine and colon. This will be used to see how the microbiome and immune system in that area changed since the surgery. Genetic tests will be used to measure the microbiome and the levels of immune proteins in the intestines.

Inclusion Criteria:

1. Patients with Crohn's ileitis/ileocolitis requiring surgical resection OR patients previously enrolled in the "Kono-S anastomosis versus side-to-side functional end anastomosis in the prevention of post-operative recurrence of Crohn's Disease (WC IRB #1303013645)" trial.
2. Patients age 18 years and older.
3. All phenotypes will be included: nonstricturing nonpenetrating (B1), stricturing (B2), and penetrating (B3) according to the Vienna classification.
4. Patients will be included regardless of preoperative medications (untreated, steroids, biologics)

Exclusion Criteria:

1. Patients under 18 years of age.
2. Pregnant patients.
3. Patient does not speak English
4. Patients that may need a different surgical procedure as per the surgeon at the time of intraoperative evaluation