FMT in Inflammatory Bowel Disease

Inclusion Criteria: * Patients with inflammatory bowel disease (Crohn's disease or Ulcerative colitis) or Microscopic Colitis proven on the basis of radiology, endoscopy or histology. * Patients with clinically and endoscopically active, Crohn's Disease, Ulcerative Colitis or Microscopic Colitis * Patient must have attempted reasonable medical therapies to control their disease without sufficient response. * All patients have to be capable of attending appointments, as well completing surveys and diagnostic tests for the duration of study follow up * The patient must be able to identify a likely stool donor Exclusion Criteria: * Patients with an enteropathy or colitis which cannot definitively be diagnosed as Ulcerative Colitis, Crohn's disease or Microscopic colitis * Patients with concurrent Clostridium difficile infection * Women who are pregnant or intending to become pregnant in the near future (less than 6 months). * Neutrophils less than 1.0 x 109/L * Albumin less than 20g/L * Active gastrointestinal infection as identified by testing * A patient on steroids (prednisolone, budesonide) at a dose that cannot be safely tapered to zero within 6 weeks of initial FMT, due to the risk of adrenal insufficiency * Short gut syndrome and/or small intestine less than 1.5m in length as measured intra-operatively * Perforation or active internal fistulising disease or enterocutaneous fistulae. * Any patient that the clinicians feel is incapable of participating in the safe use of FMT. * Current use of antibiotics for any condition