A disturbance in the diversity of gut bacterial composition could be linked to several immune mediated diseases including inflammatory bowel diseases (IBD). IBD can be classified into Crohn's Disease (CD) and Ulcerative Colitis (UC). Both these diseases occur from abnormal immune reaction to resident gut bacteria.The process of fecal microbiota transplantation (FMT) where fecal bacteria from a healthy individual is transferred into a recipient, has recently received attention as an alternative therapy for individuals affected with these life-altering diseases. In this study, the investigators will perform fecal transplantation on the subjects meeting inclusion criteria, to determine the efficacy and safety of this therapy in subjects with IBD (CD and UC) who are not responding to first line therapy, and are in a flare.

50 subjects (25 subjects with Crohn's Disease and 25 subjects with Ulcerative Colitis) who are 2 to 22 years of age will be enrolled in the trial over 3 years. The fecal donors, preferably a parent or sibling, will be extensively screened for infectious diseases prior to providing stool for the transplant. Patients who are failing primary therapy, are in a flare, and require restaging of their IBD by an endoscopy and colonoscopy will be approached for the study. Standard of care endoscopy and colonoscopy will be performed on each subject and 2 additional biopsies will be taken for analysis. Microbiota analysis will also be performed on both the donor and recipient stool sample prior to transplantation, and on the recipient sample at 1 week, 1 month, and 6 months post transplantation. The primary objective will be to study the safety of FMT in all enrolled subjects. The study will also correlate efficacy and patient outcomes with the fecal microbiome prior to, and after FMT. The secondary objectives are to examine the efficacy of FMT in the treatment of children with IBD using the Pediatric Ulcerative Colitis Activity Index (PUCAI) and the Pediatric Crohn Disease Activity Index (PCDAI) analysis. Correlate the patient outcomes with the fecal microbiome prior to, and after FMT.

STUDY SUBJECT INCLUSION CRITERIA:

Current IBD patients who have:

• UC patients with a flare due to failure of current therapy and have to undergo esophagogastroduodenoscopy (EGD) and colonoscopy for restaging the disease and escalation of therapy.
• CD patients with ileo colonic or colonic disease who require an EGD and colonoscopy for disease assessment due to a flare or poor control.
• The ability to safely undergo colonoscopy (physical status classification used by the American Society of Anesthesiologists).
• PUCAI score less than sixty five.
• PCDAI score less than forty.

STUDY SUBJECTS EXCLUSION CRITERIA:

• Patients with Crohn's disease: complications like an abscess, phlegmon, stricture, small bowel obstruction, perforation, internal or external fistulization or infection as causes for flare up before being deemed eligible for recruitment to the study. We will check for these complications if a recent study has not been done.
• Severe immunosuppression: Biologicals with concomitant steroids (>30 mg/day).
• Central Line.
• Pressor or ventilatory support.
• On antibiotics.
• Patients with Crohn's disease found to have complications like an abscess, phlegmon, stricture, small bowel obstruction, perforation, internal or external fistulization or infection.
• Not willing to consent or follow guidelines throughout research trial.
• Screening labs in either donor or recipient reveal problems with performing fecal microbiome transplantation because inclusion requirements are no longer met.
• Physician discretion.
• Participant request.

DONOR EXCLUSION CRITERIA:

• A history of antibiotic treatment during the 3 months preceding donation.
• A history of intrinsic gastrointestinal illnesses.
• A history of autoimmune or atopic illness or modulating therapy.
• A history of chronic pain syndromes, or neurologic or neurodevelopmental disorders.
• Metabolic syndrome or malnutrition or obesity.
• A history of exposure to infectious agents.
• Diarrhea or other symptoms of an intestinal infection within two weeks prior to, or on the day of, stool donation.
• A history of malignant illnesses or ongoing oncologic therapy.
• Weight less than 15 kgs.

6 months

small number of subjects, open label trial, fecal calprotectin not collected in every subject so response measurement was subjective