Pilot Study of Fundamental Modification of the Gut Microbiota in the Treatment of Refractory Crohn's Disease

Group 1 Inclusion Criteria: * Males or females 6-18 years of age * Current weight \>10 kg (or 22 lb) * Ability to swallow pills * Normal kidney function * Normal Aspartate transaminase (AST), Alanine transaminase (ALT), and alkaline phosphatase * Active CD or IBDU defined as PCDAI ≥ 30 * C-Reactive Protein (CRP) ≥ 15mg/L (or 1.5mg/dL) or fecal calprotectin (FCP)\>350mcg/g (within one month of enrollment) * Have been treated with one of the following therapies for at least 8 weeks with primary nonresponse or an initial response, followed by loss of response \[LOR\] (self-reported worsening of symptoms for ≥ 7 days): azathioprine, 6-mercaptopurine, methotrexate, adalimumab, certolizumab, golimumab, infliximab, natalizumab, vedolizumab, or ustekinumab \*\*These medications must have been administered at standard, therapeutic dosages. Exclusion Criteria: * Known allergy or intolerance to aminoglycosides or any of the medications used in this study * Current use of one or more of the following medications: 5-fluorouracil, digoxin, anticoagulants, theophylline, phenytoin, probenecid, duloxetine, clozapine, sildenafil, hydrochlorothiazide, cyclosporine, hypoglycemics, terfenadine, tacrolimus, rifabutin, midazolam, and voriconazole * Known diagnosis of diabetes mellitus * Known or suspected structuring disease producing obstructive symptoms * Active Clostridium difficile infection * Prolonged QTc interval as seen on enrollment EKG * Current use of antibiotics * Starting or increasing the dose of an IBD related medication within 4 weeks of screening Group 2 Inclusion Criteria * Males or females 10 years of age and older. * Patients undergoing a clinical GI endoscopy due to suspicion for active intestinal inflammation determined by physician global assessment (PGA). * Undergoing a bowel preparation as part of clinical care. * Parental/guardian permission (informed consent) and if appropriate, child assent. Exclusion Criteria * Antibiotic use within the past 30 days. * Current presence of an ostomy bag. * Patients undergoing a non- polyethylene glycol 3350 cleanout. * Unwillingness to provide informed consent. * Parents/guardians or subjects who, in the opinion of the Investigator, may be non-compliant with study schedules or procedures.