This is a prospective unblinded, randomized trial for the use of Fecal Microbiota Transplantation (FMT) for the treatment of Ulcerative Colitis (UC), in combination with or without antibiotic pretreatment.

This is a prospective open-label, randomized trial for the use of Fecal Microbiota Transplantation (FMT) for the treatment of Ulcerative Colitis (UC), in combination with or without antibiotic pretreatment.

This trial involves 11 study visits at UCSF in San Francisco, CA.

The routes of administration will be via colonoscopy for all subjects with maintenance therapy administered orally (i.e. using encapsulated FMT) for half of the subjects and per rectum by enema in the other half of the subjects. Additionally, the utility of pretreatment antibiotics will be assessed.

Inclusion Criteria:

• Patients with history of mild to moderate Ulcerative Colitis confirmed by endoscopy and pathology.
• Total Mayo score 4-9, endoscopic subscore ≥1; patients who have not had endoscopic evaluation within one year of enrollment will have flexible sigmoidoscopy for evaluation.
• Age 18 - 64 and deemed otherwise healthy at the discretion of the investigator.
• Concurrent therapies with mesalamine (stable x 4 weeks), immunomodulators (stable x 3 months), and biologic agents (stable x 3 months) will be allowed to continue during study.
• If patient is on prednisone, the dose must be ≤ 10mg/day at the time of treatment and will be weaned by 2.5mg/week during the study period.

Exclusion Criteria:

• Severe or refractory UC defined as Mayo score ≥10, endoscopic disease activity score 3
• Untreated enteric infection (positive stool test for any of the following: Clostridium difficile, Salmonella, Shigella, Yersinia, Campylobacter, enteropathogenic E. coli or other enteric infection at the discretion of the investigator.
• History of colectomy
• Disease limited to distal proctitis
• Patients taking probiotics within 6 weeks of planned FMT therapy.
• Severe immunodeficiency, inherited or acquired (e.g. HIV, chemotherapy or radiation therapy)
• Patients with the following laboratory abnormalities: absolute neutrophil count (ANC) < 1000 / µl, platelets <50 x 10^9 /L,, hemoglobin <6.5 g/dL..
• History of anaphylaxis (severe allergic reaction) to food allergens (e.g. tree nuts, shellfish)
• Dysphagia (oropharyngeal, esophageal, functional, neuromuscular)
• History of recurrent aspiration episodes
• Documented severe gastroparesis
• Active intestinal obstruction
• Patients with renal insufficiency (GFR < 50ml/min)
• Allergy to the following generally regarded as safe ingredients (GRAS): glycerol, acid resistant HPMC, gellan gum, cocoa butter, titanium dioxide
• Adverse event attributable to any previous FMT
• Allergy/intolerance to proton pump inhibitor therapy
• Allergy/intolerance to vancomycin, metronidazole, or neomycin.
• Non-steroidal inflammatory medications (NSAIDs) as long-term treatment, defined as use for at least 4 days a week each month.
• Cholestyramine use
• Any condition in which the investigator thinks the FMT treatment may pose a health risk (e.g. severely immunocompromised)
• Simultaneous participation in another interventional clinical trial
• Patients who are pregnant, breast feeding or planning pregnancy during study trial period.
• During the trial period until one week after the trial end: Non-use of appropriate contraceptives in females of childbearing potential (e.g. condoms, intrauterine device (IUD), hormonal contraception, or other means considered adequate by the responsible investigator) or in males with a child-fathering potential (condoms, or other means considered adequate by the responsible investigator during treatment) or well-founded doubt about the patient's cooperation
• Patients with any other significant medical condition that could confound or interfere with evaluation of safety, tolerability or prevent compliance with the study protocol at the discretion of the investigator
• Life expectancy <6 months