Please select the eligibility criteria that correspond to the clinical trial below.
Title: Manipulating the Microbiome in IBD by Antibiotics and Fecal Microbiota Transplantation (FMT): a Randomized Controlled Trial
Brief Summary: the etiology of Inflammatory Bowel Diseases (IBD) is closely associated with the gut microbiome. The results of previous studies on the effectiveness of antibiotics and fecal macrobiota transplantation (FMT) are contradicting.

Aims: to evaluate the effectiveness of wide-spectrum antibiotic regimens in acute severe colitis in an addition to standard corticosteroid therapy (UC and isolated "UC-like" Crohn's colitis). The secondary aim is to assess the outcome of FMT in those not responding to five days of therapy (in either arm). As an exploratory aim, any IBD patient with a resistant disease to at least two immunosuppressive medications, may be treated with either interventions.


Options:
A: Inclusion Criteria:

1. Children 5-17 years of age.
2. Diagnosis of active Crohn's Disease.4. Patients with a PCDAI≥10 ≤40 (mild to moderate disease).
3. Have involvement of the colon and/or terminal ileum.
4. Disease defined as L1, L2, L3 or any of the above and may have gastric, duodenal or esophageal disease (L4a) according to the Paris classification for site of disease.
5. The CRP ≥ 0.6 mg/dL.
6. Duration of disease since diagnosis \< 3 years.
7. Negative stool culture, Clostridium Difficile Toxin from current flare.

Exclusion Criteria:

1. Duration of disease since diagnosis \> 3 years.
2. Positive stool culture or O\&P last 30 days.
3. Presence of clostridium difficile toxin in stool.
4. Azithromycin or Metronidazole allergy or known intolerance.
5. Diagnosis of IBD -U.
6. Presence of macroscopic disease involving the proximal ileum or jejunum (L4b).
7. Continuous macroscopic disease of the colon appearing as typical ulcerative colitis and Crohns diagnosed only by focality or granuloma on biopsies.
8. Presence of extraintestinal manifestations (such as arthritis, uveitis, or sclerosing cholangitis).Apthous lesions of mouth can be included.
9. Presence of fibrostenotic disease (strictures with prestenotic dilatation).
10. Presence of penetrating disease (fistulas or abscess).
11. Presence of current perianal disease defined as fistula or abscess.
12. Patients receiving concurrent corticosteroids or biologics.
13. Patients who have received steroids in the past 14 days.
14. Immune deficiency (CGD, GSD1, IL10R etc).
15. Known allergy or intolerance to any of the study medications.
16. Concurrent diseases such as hepatitis, ALT \>2 times UNL, renal failure.
17. Pregnancy.
18. Patients with known heart disease.
19. Prolonged QTc by E.C.G at baseline.
20. Patient after surgical resection.
B: Inclusion Criteria:

* Ulcerative colitis diagnosed by routine clinical, radiographic, endoscopic and pathologic criteria (preferably confirmed by colonoscopy and pathology records within last 2 years or if unavailable, will need approval by medical monitor) Active mild-moderate UC as determined by sigmoidoscopy within approximately 3 days of randomization to study

Exclusion Criteria:

1. Fever \> 38.3°C
2. Known or suspected toxic megacolon and/or known small bowel ileus
3. Known history of Crohn's disease
4. Subjects with serum albumin \<2.5 g/dL at baseline
5. CMV polymerase chain reaction (PCR) positive from blood plasma at screening
6. Known stool studies positive for ova and/or parasites or stool culture within the 30 days before enrollment
7. Subjects on cyclosporine or triple immunosuppression, Triple immunosuppression will include any three of the following classes of drugs taken in combination: steroids (i.e., prednisone/budesonide/budesonide MMX), immunosuppressant (i.e., methotrexate/azathioprine/6-mercaptopurine), and/or other immunosuppressant (i.e., tacrolimus, cellcept).
8. Biologic medication (infliximab/ adalimumab/ golimumab/ certolizumab/vedolizumab/ustekinumab/natalizumab) use within 3 months prior to screening
9. Known active malignancy except for basal cell skin cancer, squamous cell skin cancer
10. Subjects with previous colectomy, ostomy, J-pouch, or previous intestinal surgery (excluding cholecystectomy, appendectomy)
11. Subjects with known history of celiac disease or gluten enteropathy
12. Subjects with Clostridium difficile positive stool at Screening Visit
13. Antibiotic use within the prior 1 month before randomization
14. Expected to receive antibiotics within 8 weeks of signing the Informed Consent Form (ICF) (i.e., for planned/anticipated procedure)
15. Received an investigational drug within 1 month before study entry
16. Received an investigational antibody or vaccine within 3 months before study entry
17. Previously enrolled in a SER-109/SER-287 study
18. Received an FMT within the last 6 months
19. Subjects with anatomic or medical contraindications to flexible sigmoidoscopy, including but not necessarily limited to toxic megacolon, gastrointestinal (GI) fistulas, immediate post-operative status from abdominal surgery, severe coagulopathy, large or symptomatic abdominal aortic aneurysm, or any subject where study physician deems subject at significant risk of complications of flexible sigmoidoscopy
20. Unable to stop steroid enemas or suppositories or mesalamine enemas or suppositories before screening visit
21. Unable to stop opiate treatment unless on a stable dose and no increase in dose planned for the duration of the study
22. Unable to stop probiotics before screening visit
23. Concurrent intensive induction chemotherapy, radiotherapy, or biologic treatment for active malignancy (subjects on maintenance chemotherapy may only be enrolled after consultation with medical monitor)
24. Known allergy or intolerance to oral vancomycin

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C: Inclusion Criteria:

* Children over the age the 2 years and adults of all ages with established diagnosis of UC using standard criteria (26, 27).
* Admission for IV steroid therapy
* PUCAI of at least 65 points at admission (i.e. severe attack)
* PUCAI\>45 at enrollment
* Ability to swallow antibiotics (pills or syrup)

Exclusion Criteria:

* Change in dose or intervals of anti-TNF within the past 2 months prior to admission.
* Disease confined to the rectum (Proctitis).
* Antibiotic use in the past 4 weeks.
* Any known erosive inflammation anywhere in the small bowel or esophagus.
* Any proven infection such as positive stool culture, parasite or C. difficile, urinary tract infection, cellulitis, abscess, pneumonia, line-infections etc.
* Fever \>38.5, or \>38.0c thought to be unrelated to the inflammatory process of active UC.
* The probable need for second line medical therapy (infliximab, cyclosporine, tacrolimus) or colectomy within 5 days of enrollment, as judged by the caring physician.
* Known allergy to more than one antibiotic regimen from the list below.
* Pregnancy.
D: Inclusion Criteria:

* Acute severe ulcerative colitis as described in European Crohn's and Colitis Organisation (ECCO) guidelines (adapted from Truelove and Witts)

Exclusion Criteria:

* Patients who deny consent
* Age\<=12 years
* Pregnant or lactating women
* Severe uncontrolled comorbidities like diabetes mellitus, hypertension, coronary artery disease, chronic liver disease, chronic kidney disease, etc
* History of antibiotic use in the past one month, excluding those who may have received a single dose of antibiotic in past 24 hrs
* History of hypersensitivity or contraindication to steroids or the test drugs
* Presence of toxic megacolon as defined by transverse colon diameter more than 5.5cm on abdominal X-ray
* Patients with evidence of sepsis or active infection

Answer: C