Biomarker-based Multidisciplinary Team (Bio-MDT) Approach to Personalized Microbial-targeted Treatment of Pouchitis and Crohn's Disease

All patients will undergo comprehensive screening by the bio-MDT. Aim 1: Antibiotic treatment- (patients with active disease) will be randomized to receive a prescription for one of two antibiotic regimens. 1. Ciprofloxacin + metronidazole 2. Doxycycline+ metronidazole Aim 2: Combination therapy ( Antibiotics+diet) After arm 1 recruitment completion, a favorable antibiotic regimen will be determined and recommended in arm 2, in which, patients with active disease will be randomized to 1. Favorable antibiotics + Mediterranean diet (MED) 2. Favorable antibiotics + The Specific Carbohydrate Diet (SCD) Aim 3: Nutritional prevention- Patients in clinical remission will be recruited to a dietary prevention study and be allocated to one of three groups: 1. Mediterranean diet (MED) 2. Control- based on the American Dietetic Association recommendations for patients with IBD. 3. Personalized nutrition group- based on prior results from study- NCT02858557 Comprehensive assessment including nutritional, clinical, inflammatory and microbial parameters will be performed at baseline and at weeks 2,3,4,8,26, 52.