Fecal Microbiota Transplantation will be offered to eligible Crohn's disease patient as Investigational New Drug treatment

The following hypothesis will be tested in this study:

1. Fecal microbiota transplantation is a safe, tolerable procedure.
2. The fecal microbial diversity, composition and function in stool recipients after fecal transplantation will change to a similar microbial diversity, composition and functionality as found in donor stool.

Primary objectives:

1. To determine the short term safety and tolerability of fecal microbiota transplantation up to 12 weeks post-transplant in patients with Crohn's disease.

Secondary objectives:

1. To determine the long term safety and tolerability of fecal microbiota transplantation (FMT) up to one year post transplant in patients with Crohn's disease.
2. To compare microbial diversity in healthy donor stools compared to pre-FMT recipient stools collected from patients (recipients) with Crohn's disease.
3. To compare microbial composition in healthy donor stools compared to pre-FMT recipient stools from patients (recipients) with Crohn's disease.
4. To compare microbial function in healthy donor stools compared to pre-FMT recipient stools from patients (recipients) with Crohn's disease
5. To compare microbial diversity in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
6. To compare microbial composition in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
7. To compare microbial function in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
8. To compare microbial diversity in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
9. To compare microbial composition in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
10. To compare microbial function in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with Crohn's disease.
11. Stool calprotectin levels will be measured in the recipient at baseline pre-FMT, 1 week and 12 weeks post FMT to determine if FMT causes a statistically significant change.

Inclusion Criteria for initial Fecal Microbial Transplant for Crohn's disease:

All patients age ≥7 years of age with established diagnosis of Crohn's disease made by a primary gastroenterologist based on history, physical examination, laboratory/radiological studies, and gastrointestinal histology, with one or more of the following criteria:

1. has been treated with steroid therapy for at least a month
2. has been treated with immunomodulatory therapy for at least a month
3. has been treated with biological therapy for at leaset a month

All patients or legal guardians of patients less than 18 years of age will have to give consent. The consent form will outline that although fecal microbiota transplantation appears safe based on past studies, a theoretical risk of transmission of an unrecognized infectious agent or substance exists and could result in an unexpected disease. All patients aged ≥7 and <18 years will have to give assent

Exclusion Criteria:

1. Patients less than 7 years of age
2. Scheduled for abdominal surgery within the next 12 weeks
3. Major abdominal surgery within the past 3 months
4. Pregnancy (This will be checked through a urine test on the day of procedure)
5. Anemia: Hemoglobin < 6 g/dL,
6. Neutropenia: Absolute Neutrophil Count <1500 Both of the above criteria will be checked via screening test or blood test reports within one month prior to the procedure
7. A known diagnosis of graft vs. host disease
8. Presence of an intra-abdominal or perianal abscess.
9. Presence of intestinal cutaneous fistula
10. Presence of severe intestinal stricture and/or intestinal obstruction
11. Administration of any investigational drug within the past 2 months
12. Use of a TNF-α antagonist within 2 weeks of the proposed date of transplantation
13. Bacteremia within past 4 weeks (28 days)
14. Severe Crohn's Disease, determined by Pediatric Crohns Disease Activity Index (PCDAI) value of more than 29.
15. Individuals with severe prior allergic reaction to food;
16. Individuals with intercurrent illness including but not necessarily limited to: febrile illness, decompensated liver cirrhosis, HIV/AIDS BMT within past 150 days, malignancy, or other severe immunodeficiency.
17. Individuals at increased risk for complications of endoscopy or procedural sedation (e.g., ASA classification IV and above).
18. Previous FMT

No plans to share IPD