This is a prospective observational cohort study, over 52 weeks, evaluating the the use of faecal microbiota transplantation amongst patients with Inflammatory Bowel Disease and Microscopic Colitis

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

Patients with active inflammatory bowel disease or microscopic collitis