Prevention of Recurrence of Crohn's Disease by Fecal Microbiota Therapy (FMT)
Phase: PHASE2
Conditions: Crohn's Disease
Sponsor: Boston Medical Center

Protocol 1 
 
1 
 
Protocol for Prevention of Recurrence of Crohn’s Disease by Fecal 
Microbiota Therapy (FMT) 
 
Version 1.3 Amendment 9, 11/10/2017 
 
NCT02417974 
 
 
Study Sites:  Beth Israel Deaconess Medical Center (BIDMC), Boston 
 
 
Brigham & Women’s Hospital, Boston 
 
 
Boston Medical Center, Boston 
 
Principal Investigator: Alan C Moss MD 
 
 
 
    Boston Medical Center 
 
 
 
    alan.moss@bmc.org 
 
 
 
     617 638 6116 
 
 
Statistical Plan see pages 15-16 
 
 
 
     
 
 
 
 
 
 
    

Protocol 2 
 
2 
 
 
TABLE OF CONTENTS 
 
 
 
Protocol 
Section 
Contents 
Protocol Page 
1 
General Information 
3 
2 
Background Information 
5 
3 
Trial Objectives & Purpose 
8 
4 
Trial Design 
9 
5 
Selection & Withdrawal of Subjects 
11 
6 
Treatment of Subjects 
13 
7 
Assessment of Efficacy 
14 
8 
Assessment of Safety 
14 
9 
Statistics 
15 
10 
Direct Access to Source Data / Documents 
16 
11 
Quality Control & Quality Assurance 
16 
12 
Ethics 
16 
13 
Data Handling & Recordkeeping 
16 
14 
Financing & Insurance 
16 
15 
Publication Policy 
17 
 
 
 

Protocol 3 
 
3 
 
1. General Information 
Protocol title 
Prevention of Recurrence of Crohn’s Disease by Fecal Microbiota Therapy (FMT) 
 
Identifying number 
IND 16373 
 
Date 
9/12/2017  
 
Name and Address of the Sponsor  
Alan C Moss MD 
Beth Israel Deaconess Medical Center 
330 Brookline Ave 
Boston, MA 02215 
 
Name and title of the person(s) authorized to sign the protocol and the 
protocol amendment(s) for the sponsor. 
Alan C Moss MD 
Director of Translational Research 
 
Name, title, address, and telephone number(s) of the sponsor's medical 
expert (or dentist when appropriate) for the trial. 
Alan C Moss MD 
Beth Israel Deaconess Medical Center 
330 Brookline Ave 
Boston, MA 02215 
617-667-3197 
 
Name and title of the investigator(s) who is (are) responsible for conducting 
the trial, and the address and telephone number(s) of the trial site(s) 
Alan C Moss MD 
Beth Israel Deaconess Medical Center 
330 Brookline Ave 
Boston, MA 02215 
617-667-3197 
 
Joshua Korzenik MD 
Brigham & Women’s Hospital 
Division of Gastroenterology 
45 Francis Street ASB-II 
Boston, MA  02115  
Phone: (617) 732-6389 
Fax: (617) 566-0338 
 
Francis A. Farraye, MD, MSc  
Boston University School of Medicine  
85 East Concord Street, 7th floor  
Boston, MA 02118  
Ph:   617-638-8339  
Fax: 617-638-6529 

Protocol 4 
 
4 
 
 
Name, title, address, and telephone number(s) of the qualified physician (or 
dentist, if applicable) who is responsible for all trial-site related medical (or dental) 
decisions (if other than investigator). 
Alan C Moss MD 
Beth Israel Deaconess Medical Center 
330 Brookline Ave 
Boston, MA 02215 
617-667-3197 
 
Joshua Korzenik MD 
Brigham & Women’s Hospital 
Division of Gastroenterology 
 
45 Francis Street, ASB-II 
Boston, MA  02115  
Phone: (617) 732-6389 
Fax: (617) 566-0338 
 
Francis A. Farraye, MD, MSc  
Boston University School of Medicine  
85 East Concord Street, 7th floor  
Boston, MA 02118  
Ph:   617-638-8339  
Fax: 617-638-6529 
 
Name(s) and address(es) of the clinical laboratory(ies) and other medical 
and/or technical department(s) and/or institutions involved in the trial. 
Center for Life Sciences 
Beth Israel Deaconess Medical Center 
3 Blackfan Circle 
Boston, MA 02215 
 
Gastrointestinal Unit 
Beth Israel Deaconess Medical Center 
330 Brookline Ave 
Boston, MA 02215 
 
Brigham & Women’s Hospital 
Division of Gastroenterology 
45 Francis Street, ASB-II 
Boston, MA  02115 
 
Boston Medical Center 
Division of Gastroenterology 
85 East Concord Street, 7th floor  
Boston, MA 02118  
Ph:   617-638-8339  
Fax: 617-638-6529 
 
 
 

Protocol 5 
 
5 
 
2. Background Information 
Name and description of the investigational product 
Fecal Microbiota Therapy (FMT) 
 
Summary of Findings from Relevant Studies  
Ulcerative colitis (UC) and Crohn’s Disease (CD) are the two forms of inflammatory bowel disease 
(IBD) that lead to chronic intestinal inflammation. The natural history of these conditions is marked 
by recurrent episodes of disease exacerbation, leading to abdominal pain, diarrhea, weight loss and 
rectal bleeding. The inflammation in CD is confined predominantly to the ileum and colon, geographic 
sites with the highest concentrations of commensal bacteria in the body. This association has led to 
many questions about the role of intestinal bacteria in the pathogenesis of this chronic disease.  In 
patients with Crohn’s Disease (CD), a change in the ecology of this bacterial flora is observed, when 
compared to healthy individuals (1). This presence of a so-called “colitogenic flora may play a key 
role in propagating the intestinal inflammation seen in CD. Patients with CD develop less microbial 
diversity, and an overgrowth of species such as Proteobacteria and Bacillus Firmicutes, and patients 
with active CD flares have been shown to have predominantly more Streptococcus spp. and 
Lactobacillus spp. and less bifidobaceria in the inflamed tissue (2). It has been proposed that a 
spectrum of “colitogenic” flora in susceptible individuals triggers a sustained inflammatory response 
that leads to tissue destruction and disease.  
 
Currently-approved therapies for CD are selected to suppress the immune response to dysbiosis, 
rather than address the triggers themselves. Despite advances in therapy over the last 20 years, 
there remain a significant number of patients who live with active symptoms and have a poor quality 
of life.  In addition, available therapies do not provide sustained remission, leading up to 60% of 
patients with Crohn’s disease to require surgery during their disease course (3). Annually, 10,000 
patients with Crohn’s disease (CD) undergo intestinal resection in the U.S., and many of them will 
later experience disease recurrence (4). Patients who require surgery at an early age, smokers 
and those with perforating phenotype are all at highest risk for recurrence; in recent trials this 
occurred in up to 85% of patients within 12 months of surgery (5). Human and animal studies 
have reported that dysbiosis occurs in the intestine after surgery, and reduced bacterial species 
diversity is associated with the subsequent risk of disease recurrence (6,7). An intervention at the 
microbiome level, before chronic inflammation is re-established, may diminish the ecological 
niche that some pro-inflammatory bacteria may acquire due to host defects in bacterial sensing. 
Supporting this concept is the evidence that post-operative antibiotics reduce the risk of 
endoscopic and clinical recurrence in patients with CD (8). Although anti-TNF agents have been 
shown to be highly effective at preventing resumption of inflammation, not every patient needs, 
or wants, to commit to continuous prophylactic anti-TNF therapy after surgery. Given the 
significant costs, and rare serious side-effects, of anti-TNF therapy, alternative effective strategies 
are also needed that target other instigators of post-operative recurrence. Our prior work 
highlighted the efficacy of antimicrobial therapy, and the limitations of anti-TNF agents, as post-
operative prophylaxis (9,10). 
 
Fecal Microbiota Therapy (FMT) is a microbiome-based treatment that could correct the intestinal 
dysbiosis in CD. FMT, also known as “fecal transplantation”, "human probiotic infusion", "stool 
transplant," or "fecal transfer," involves collecting stool from healthy pre-screened donors and 
administering the components of this material to an individual with disease. Case series and reports 
of almost 400 patients since 1958 suggest that FMT is not only safe, but may be effective for a variety 
of gastrointestinal conditions including IBD (11). Fecal transplantation, by oral delivery, has been 
reported to enhance microbial diversity and restore ecological homeostasis in patients with 
C.difficile-associated colitis. Therefore, FMT could provide a safe and effective means of 
correcting ileal dysbiosis in the post-surgical setting, and preventing recurrence of CD. patients 

Protocol 6 
 
6 
 
with IBD (Crohn’s disease or Ulcerative Colitis) who have undergone FMT have experienced 
sustained clinical, endoscopic, and histologic remission in case series and open label trials (12). An 
expert group recently recommended that well-designed clinical studies of FMT in patients with CD 
should also be undertaken. There is much enthusiasm in the CD community for FMT, and many 
patients are already opting to try FMT for their CD as an alternative to immunosuppressants. There 
have been a number of website bulletin boards on which there are active discussions by patients 
who have received fecal microbiota transplantation.  In our review, these discussions reveal that 
some patients are now trying this treatment strategy at home without medical supervision or from 
unlicensed clinics. Cumulatively, these data highlight the need for a thoughtfully designed study of 
fecal microbiota transplantation for Crohn’s disease, to provide data on its effects on the host 
microbiome, safety and tolerability. 
 
We recently completed a pilot study of FMT to treat active Crohn’s disease (IND#15409), and have 
presented the results at an international meeting (13). In this 12-month study at one site, we enrolled 
20 patients with active Crohn’s disease, refractory to conventional therapy, and treated them with 
open-label FMT (from frozen donor pool) via colonoscopy (NCT01847179). Following FMT, there 
was a significant change in HBI (p < 0.0001, Figure 1 A); fifty-four percent (6/11) of patients were 
in clinical remission at week 12 defined as an HBI < 5 and no escalation in CD related 
medications3. Following FMT, there was a shift in recipient microbiome towards donor samples 
with fewer disease-associated taxa present.  Deep shotgun metabolomics sequencing of a single 
donor:recipient pair demonstrated that 99.5% of the donor microbiome was found in 56% of the 
recipient’s microbiome post FMT, while only 10% of the pre-FMT microbiome remained (Figure 
1B). This study confirmed the safety of administering FMT in patients with active CD. 
 
Figure 1. HBI scores in 11 patients with 12 week follow-up to date (A). Composition of the gut microbiome 
in a donor:recipient pair before and after FMT (B) 
Given the clinical unmet need for safe, cost-effective interventions to prevent recurrence of Crohn’s 
disease after surgery, we propose a randomized controlled trial to evaluate the efficacy of FMT to 
prevent recurrence of Crohn’s disease in adult patients. 
 
Summary of the Known and Potential Risks and Benefits to Human Subjects 
Almost 400 patient outcomes have been reported from case series and case reports of patients who 
received FMT for colitis, and no serious adverse events have been noted. This included patients with 
Inflammatory Bowel Disease followed for up to 13 years. No infections transmitted from donor to 
recipient have been reported (14).  
 

Protocol 7 
 
7 
 
A recent randomized controlled trial of 17 patients treated with FMT (given by duodenal lavage) for 
Clostridium difficile infection reported their short-term adverse events. Immediately after the 
duodenal lavage, patients had diarrhea (in 94%), cramping (in 31%) or belching (in 19%) which all 
resolved within 3 hours in all cases (15). During follow-up, three patients who were treated with donor 
feces (19%) had constipation. These adverse events have not been noted when FMT is administered 
by colonoscopy. In our pilot study in patients with active Crohn’s disease, no serious adverse events 
have been noted, over 6 months of follow-up (13). No other adverse events related to study treatment 
were reported. On the basis of these data, the following risks can be assumed for FMT; 
 
Known Risks of FMT 
• 
Altered bowel pattern (diarrhea, constipation) 
• 
Cramping 
• 
Belching 
• 
Colonoscopy risks – intestinal perforation (1:5000), bleeding, altered bowel habit 
 
Potential Risks of FMT 
• 
Transmission of pathogenic bacteria, viruses, fungi 
• 
Transmission of allergens 
• 
Alteration in intestinal metabolism 
 
Potential Benefits 
• 
Restoration of fecal diversity 
• 
Prevention of intestinal inflammation 
• 
Prevention of clinical symptoms 
 
Description of and justification for the route of administration, dosage, 
dosage regimen, and treatment period 
Route of Administration 
Donor fecal microbiota material will be administered in two formats; via colonoscopy as a solution, 
and encapsulated with glycerol and cocoa butter in HMCP capsules. For the initial dose, FMT in 
solution will be sprayed in the terminal ileum via a colonoscope. This route of administration for the 
initial dose has been selected for a number of reasons; 
• 
Recurrence of inflammation in CD always develops in the region of the anastomosis 
between the ileum and colon (~2 inches long). This is the area where dysbiosis has been 
noted as a precursor to macroscopic inflammation. Colonoscopic delivery ensures delivery 
of FMT to the sites of disease recurrence. The rate of engraftment of donor microbiota when 
delivered via the oral route is unknown. 
• 
The colonoscopic route of administration has been associated with ~80% efficacy in treating 
patient with Clostridium difficile colitis.  
 
Prior studies, including ours (see above) have reported that changes in luminal microbiota diversity 
after a single colonoscopic delivery of FMT are not sustained. In order to enhance the probability of 
sustained changes in luminal microbiota post loading FMT, we propose weekly ingestion of an oral 
form of fecal-derived microbiota for the 6 months of the trial. This approach has been used 
successfully in a recent trial to treat Clostridium difficile colitis, where fecal matter from healthy donors 
were pipetted into acid-resistant hypromellose capsules for delivery to the colon (Youngster I 2014). 
This was associated with a 70% success rate in treating Clostridium difficile colitis 
 
Dosage Form 

Protocol 8 
 
8 
 
1. Initial dose - filtered solution of donor stool (50 g) homogenized with sterile saline 90 mL. 
2. Maintenance dose – six capsules of fecal material taken once per week (550µl of fecal 
material in size 00 gelatin capsule)  
 
Dosing Regimen 
Single initial dose of 90mL of fecal solution. This will be administered at least 30 days after the 
ileo-cecal resection, but within 50 days of the surgery. 
Weekly dose of 6 capsules of fecal material (total 3300µl of fecal material per week) 
 
Statement that the trial will be conducted in compliance with the protocol, 
GCP, and the applicable regulatory requirements 
This trial will be conducted in compliance with the protocol, good clinical practice, and FDA 
requirements. 
 
Description of the Population to be Studied 
Adult patients with ileo-colonic Crohn’s disease who have undergone recent ileo-cecal resection. 
 
References 
1. Willing B.P., Dicksved J., Halfvarson J., Andersson A.F., Lucio M., Zheng Z., Jarnerot G., Tysk C., Jansson 
J.K., & Engstrand L. (2010) A pyrosequencing study in twins shows that gastrointestinal microbial profiles 
vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844-1854. 
2. Papa E., Docktor M., Smillie C., Weber S., Preheim S.P., Gevers D., Giannoukos G., Ciulla D., Tabbaa D., 
Ingram J., Schauer D.B., Ward D.V., Korzenik J.R., Xavier R.J., Bousvaros A., & Alm E.J. (2012) Non-
invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. 
PLoS.One. 7, e39242. 
3. van Deen WK, van Oijen MG, Myers KD, et al. A nationwide 2010-2012 analysis of U.S. health care 
utilization in inflammatory bowel diseases. Inflamm Bowel Dis 2014;20:1747-1753. 
4. Bernell O, Lapidus A, Hellers G. Risk factors for surgery and recurrence in 907 patients with primary 
ileocaecal Crohn's disease. Br J Surg 2000;87:1697-1701. 
5. Regueiro M, Schraut W, Baidoo L, et al. Infliximab prevents Crohn's disease recurrence after ileal 
resection. Gastroenterology 2009;136:441-50.e1; quiz 716. 
6. Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with post-operative clinical course 
in Crohn's disease. BMC Gastroenterol 2013;13:131-230X-13-131. 
7. Devine AA, Gonzalez A, Speck KE, et al. Impact of ileocecal resection and concomitant antibiotics on the 
microbiome of the murine jejunum and colon. PLoS One 2013;8:e73140. 
8. D'Haens G.R., Vermeire S., Van Assche G., Noman M., Aerden I., Van Olmen G., & Rutgeerts P. (2008) 
Therapy of metronidazole with azathioprine to prevent postoperative recurrence of Crohn's disease: a 
controlled randomized trial. Gastroenterology 135, 1123-1129. 
9.. Doherty GA, Bennett GC, Cheifetz AS, Moss AC. Meta-analysis: targeting the intestinal microbiota in 
prophylaxis for post-operative Crohn's disease. Aliment Pharmacol Ther 2010;31:802-809. 
10. Doherty GA, Miksad RA, Cheifetz AS, Moss AC. Comparative cost-effectiveness of strategies to prevent 
postoperative clinical recurrence of Crohn's disease. Inflamm Bowel Dis 2011;. 
11. Guo B., Harstall C., Louie T., Veldhuyzen v.Z., & Dieleman L.A. (2012) Systematic review: faecal 
transplantation for the treatment of Clostridium difficile-associated disease. Aliment.Pharmacol.Ther. 35, 865-
875. 
12. Borody T.J., Warren E.F., Leis S., Surace R., & Ashman O. (2003) Treatment of ulcerative colitis using 
fecal bacteriotherapy. J Clin.Gastroenterol. 37, 42-47. 
13. Vaughn B, Gevers G, Ting A, et al. Fecal Microbiota Transplantation Induces Early Improvement in 
Symptoms in Patients with Active Crohn’s Disease. . Gastroenterology 2014;146:Mo1228. 
14.  Damman C.J., Miller S.I., Surawicz C.M., & Zisman T.L. (2012) The microbiome and inflammatory bowel 
disease: is there a therapeutic role for fecal microbiota transplantation? Am.J Gastroenterol. 107, 1452-1459. 
15. van Nood E., Vrieze A., Nieuwdorp M., Fuentes S., Zoetendal E.G., de Vos W.M., Visser C.E., Kuijper 
E.J., Bartelsman J.F., Tijssen J.G., Speelman P., Dijkgraaf M.G., & Keller J.J. (2013) Duodenal infusion of 
donor feces for recurrent Clostridium difficile. N.Engl.J Med. 368, 407-415. 

Protocol 9 
 
9 
 
16. Regueiro M, Kip KE, Baidoo L, Swoger JM, Schraut W. Postoperative therapy with infliximab prevents 
long-term Crohn's disease recurrence. Clin Gastroenterol Hepatol. 2014 Sep;12(9):1494-502 
 
 
 
3. Trial Objectives & Purpose 
Objectives 
The objective of this trial is to assess if FMT can reduce the risk of endoscopic recurrence of CD in 
patients after intestinal resection. The specific outcomes of FMT we will examine are; 
1. Endoscopic appearance 
2. Clinical symptoms 
3. Safety & tolerability 
4. Microbial diversity 
 
Hypothesis 
Our hypothesis is that FMT will prevent establishment of a “pro-inflammatory” microbiome after 
surgery, leading to a reduced probability of recurrence of macroscopic inflammation. In addition we 
hypothesize that FMT will be safe and well-tolerated in these patients. 
 
4. Trial Design 
This is an open-label trial to study the rates of endoscopic recurrence of CD in patients after ileo-
cecal resection. We will prospectively enroll 50 CD patients at least 30 days after ileo-cecal 
resection, and allow them to choose to receive either FMT or no therapy for 6 months. Subjects in 
the FMT arm will start treatment within 50 days of the surgery, but at least 30 days from the surgery, 
to ensure adequate healing has occurred at the anastomotic site, and to allow time for recognition 
of any early post-operative complications that might exclude patients from the trial. 
 
Primary Clinical Endpoint 
Proportion of patients in each arm of the trial who develop endoscopic recurrence within 6 
months of ileo-cecal resection. “Endoscopic recurrence” will be defined as a Rutgeert’s score of 
>/= to i2. 
 
Secondary Endpoints 
Microbial Endpoints; 
• 
Recipients’ fecal microbial diversity and metabolic profiles at 2, 4, 8, 10, 12, 16, 20 and 
26 weeks after FMT, when compared to baseline 
Inflammatory Endpoints; 
• 
Percentage of patients with normal anastamosis (Rutgeerts score 0) at week 26 
• 
Mean CRP at week 26 
Clinical Endpoints; 
• 
Mean Harvey Bradshaw Index (HBI) score at week 26 
• 
Percentage of patients in clinical remission (those with an HBI score at week 26 <5) 
Safety Endpoints; 
• 
Number and nature of adverse events at week 4, 12, 26 and 52 
• 
% of patients with adverse events reported at week 4, 12, 26 and 52 
 
Steps to Minimize Bias 
To minimize bias in the primary endpoint, endoscopic images from the week 26 colonoscopy will 
be reviewed and scored by a researcher who will be blinded to the treatment allocation (central 
reader).   
 

Protocol 10 
 
10 
 
Trial Treatment 
The treatment for this trial will be an initial aliquot of donor stool in 90ml of sterile saline, followed by 
weekly ingestion of six capsules of encapsulated fecal material. These will be provided by the 
Microbiome Health Research Institute at Massachusetts Institute of Technology as described in 
their Drug Master File (15543). 
 
Dosage Form 
1. Initial dose - filtered solution of donor stool (50 g) homogenized with sterile saline 90 mL. 
2. Maintenance dose – six capsules of fecal material taken once per week (550µl of fecal 
material in size 00 gelatin capsule)  
 
Dosing Regimen 
Single initial dose of 90mL of fecal solution  
Weekly dose of 6 capsules of fecal material (total 3300µl of fecal material per week) 
 
Packaging 
Fecal solution will be acquired in plastic bottles, and enscapsulated fecal material in blister packs 
from the Microbiome Health Research Institute at Massachusetts Institute of Technology, as 
described in their Drug Master File (15543). 
 
Labeling 
See Drug Master File (15543). 
 
Sequence & Duration of Trial Periods 
An outline of the study timeline and measurements is shown in Appendix 1 
 
Recipient Procedures; 
Week -1; Screening – potential subjects will undergo the following screening procedures one 
week prior to FMT to determine if they meet the recipient selection criteria; 
• 
medical record review to confirm diagnosis and treatment history 
• 
Harvey Bradshaw Index (HBI) score to determine disease activity score (Appendix 2) 
• 
stool sample to exclude current infections (bacterial culture, ova & parasites, Clostridum 
difficule toxin) 
• 
standard of care blood tests for baseline and infection screening (CBC, LFTs, Renal 
profile, CRP, ESR) 
• 
stool sample for microbiome analysis (MIT) 
Women of child-bearing potential will be counseled by study clinicians, that those who choose to 
the treatment arm will be requested to avoid pregnancy by hormonal or barrier methods from time 
of screening for 7 months (duration of FMT therapy and one month lag afterwards). 
Eligible subjects will then have the option to be in either treatment or control arm. 
 
Week 0; Treatment & Control Arm 
• 
Urine pregnancy test (HCG) for females of child-bearing age (during admission process, 
prior to colonoscopy) 
• 
Initial Fecal Transplant via colonoscopy for treatment arm (none for control arm). Biopsies 
will be taken at the time of colonoscopy 
 
Week 1; Treatment Arm 
• 
Ingestion of first oral FMT capsules in clinic, under observation 
• 
Follow-up phone call to assess for adverse events 4 hours later 

Protocol 11 
 
11 
 
 
Week 2, 4, 8, 10, 12, 16, 20 and 26: (Treatment & Control Arms) 
• Stool sample for microbiome analysis (MIT) 
 
Weeks 4, 12, 26; (Treatment & Control Arms) ; 
Follow-up assessment of  
• 
clinical scores 
• 
adverse event screening,  
• 
standard of care blood tests screening (CBC, LFTs, Renal profile, CRP, ESR) 
 
Week 26: (Treatment & Control Arms); 
Efficacy end-point evaluation; 
• 
Urine pregnancy test (HCG) for females of child-bearing age (prior to colonoscopy) 
• 
colonoscopy and Rutgeert’s score of anastomosis images (Appendix 3). Biopsies will be 
taken at the time of the colonoscopy 
 
Week 52 (Treatment & Control Arms) 
• Final safety assessment; phone interview to screen for adverse events. 
 
Written instructions will be given to all subjects for stool collection methods (Appendix 4).  
 
Stopping Criteria 
Adverse events will be specifically monitored at 4, 12, 26 and 52 weeks after FMT by direct patient 
interviews, or by reporting from clinical sites of adverse events at any time in-between. A data safety 
and monitoring board (DSMB, Appendix 5) will review all patient data to ensure optimal patient 
safety and precautions for subjects with CD treated with FMT. A severity grade for adverse events 
(Appendix 6) and subject symptom diary used (Appendix 7). The DSMB will meet a minimum of 2 
times: after treatment of the first 20 subjects, and after treatment of all 44 subjects. Study will be 
stopped under the following circumstances; 
• 
recurrence of CD symptoms in any more than 3 of the first 10 patients treated (increase by 
>5 points from baseline of mean HBI score after FMT) 
• 
detection of new pathogenic intestinal infection in stool samples in any patient treated.  
• 
any unexpected serious adverse event that that DSMB determines is of significant clinical 
impact, and probably related to FMT 
In addition, any subject who develops a serious adverse event that is judge to be probably, possibly 
or definitely related to FMT therapy will receive no further FMT treatment. They will remain in the 
trial for adverse event follow-up. 
 
Accountability Procedures for the Investigational Product 
The location, volume and number of all FMT donor solutions will be maintained in a log by the 
research team. The principal investigator will be responsible for accurate record and tracking of all 
FMT solutions. Logging of FMT solution used for administration will be performed using a two-
person process. 
  
Data to be Recorded Directly on the CRFs 
Data will be obtained from patient directly, and their electronic health record as follows; 
Demographics - age, gender 
Disease history - disease phenotype, disease location, duration of disease, medication history, 
surgical history, symptoms 
Endoscopic scores 

Protocol 12 
 
12 
 
Adverse Events 
 
 
5. Selection & Withdrawal of Subjects 
Inclusion Criteria 
Patients - Patient enrollment will be done via referral of appropriate patients from the study sites.  
Patients will be included if they meet all the following criteria:  
• 
Adults (age > 18) 
• 
Confirmed diagnosis of Crohn’s disease, based on endoscopy, histology and imaging 
(confirmed by Study PI for each site) 
• 
Ileo-cecal resection or terminal ileal resection for CD at least 30 days prior to enrollment 
in the trial. 
• 
Resection margins & anastomosis free of active inflammation based on histology and 
surgical description (confirmed by Study PI for each site) 
• 
No therapy to prevent post-operative recurrence of CD. A 30-day wash-out period for anti-
TNFs, thiopurines, antibiotics will be required prior to enrollment. 
 
Risk factors for post-operative recurrence will not be a requirement for study eligibility, as we 
expect most clinicians and their high-risk patients will opt to start anti-TNF therapy post-
operatively, rather than enroll in a clinical trial. However, we expect some patients in this category 
will opt to try FMT before committing to anti-TNF prophylaxis. All enrolled subjects will be 
categorized as either ‘high-risk’ of recurrence (current smoker / perforating phenotype / prior ileal 
resection), or ‘low-risk’. 
 
Exclusion Criteria 
Patient - Patients will be excluded for any of the following: 
• 
Diagnosis of indeterminate colitis 
• 
Women who are pregnant or nursing 
• 
Patients who are unable to give informed consent 
• 
Patients who are unable or unwilling to undergo colonoscopy with moderate sedation (>ASA 
class II) 
• 
Patients who have previously undergone FMT 
• 
Patients who have a confirmed malignancy or cancer 
• 
Participation in a clinical trial in the preceding 30 days or simultaneously during this trial 
• 
Probiotic use within 30 days of start date 
• 
Decompensated cirrhosis 
• 
Congenital or acquired immunodeficiencies e.g. neutropenia 
• 
Chronic kidney disease as defined by a GFR <60mL/min/1.73m2 44 
• 
History of rheumatic heart disease, endocarditis, or valvular disease due to risk of bacteremia 
from colonoscopy 
• 
Active infections, including, but not limited to, surgical infections or abscesses 
• 
History of severe food allergies 
• 
Any condition, based on clinical judgement, that may make study participation unsafe. In 
particular, post-operative anastomotic leaks or fistula 
 
Subject Withdrawal Criteria 
Patients – patients will be withdrawn under the following circumstances; 

Protocol 13 
 
13 
 
• 
Colonoscopy for FMT cannot be completed for technical reasons due to inability by 
endoscopist to reach terminal ileum, or patient intolerance of procedure, or pregnancy. 
These patients will only be followed-up for week 2 adverse event screening, as they will 
not have received FMT. These subjects will be replaced, as they will not be considered 
“treated”. 
• 
Patient withdraws their consent for study protocols, follow-up visits or contacts 
• 
Any subject who develops a serious adverse event that is judge to be probably, possibly 
or definitely related to FMT therapy will receive no further FMT treatment. They will 
remain in the trial only for adverse event follow-up. 
 
Subjects who require rescue treatment will be censured for the analysis of primary end-point. They 
will however continue to be followed for 6 months for evaluation of safety outcomes. 
 
6. Treatment of Subjects 
Trial Treatment 
The initial treatment for this trial will be administration of an initial single infusion of fecal solution to 
the terminal ileum. Treatment will begin at least 30 days after ileo-cecal resection, but within 50 
days of surgery, in the treatment group.  
 
Subsequent FMT administration will be in the form of capsules of frozen FMT material ingested 
orally once a week. Each subject will ingest six FMT capsules once every seven days for the 6 
months of treatment in the trial. The first ingestion will be undertaken in the clinic, where subjects 
will be monitored for adverse events for 1 hour. A follow-up phone call will be undertaken 4 hours 
later to screen for adverse events. At this visit, and at weeks 4, 12 subjects will be provided with 
blister packs of FMT capsules for their subsequent doses. They will be instructed to store the blister 
packs in a sealed bag (provided) in a domestic freezer  at -200C   until each weekly ingestion. A full 
instruction document for patient is included as Appendix 8.   
 
Medications Permitted 
During the follow-up period after enrollment (6 months), subjects should not take any 
medications that may prevent recurrence of CD; antibiotics, thiopurines, anti-TNFs, 
mesalamine. Rescue pathway for CD subjects with clinical recurrence during the study period to 
be determined by the clinician investigator and based on standard of clinical practice. This may 
include, but is not limited to the following; 
i. 
Oral steroids (if not already receiving them or failing them) 
ii. 
Rectal therapy (5-ASA or steroids) 
iii. 
IV steroids 
iv. 
Hospitalization 
v. 
Anti-TNF therapy 
vi. 
Surgery 
 
7. Assessment of Efficacy 
Primary Clinical Endpoint; 
Proportion of patients in each arm of the trial who develop endoscopic recurrence within 6 
months of ileo-cecal resection. “Endoscopic recurrence” will be defined as a Rutgeert’s score of 
>/= to i2. 
 
Secondary Endpoints: 
Microbial Endpoints; 

Protocol 14 
 
14 
 
• 
Recipients’ fecal microbial diversity and metabolic profiles at 2, 4, 8, 10, 12, 16, 20 and 
26 weeks after FMT, when compared to baseline 
Inflammatory Endpoints; 
• 
Percentage of patients with normal anastamosis (Rutgeerts score 0) at week 26 
• 
Mean CRP at week 26 
Clinical Endpoints; 
• 
Mean Harvey Bradshaw Index (HBI) score at week 26 
• 
Percentage of patients in clinical remission (those with an HBI score at week 26 <5) 
Safety Endpoints; 
• 
Number and nature of adverse events at week 4, 12, 26 and 52 
• 
% of patients with adverse events reported at week 4, 12, 26 and 52 
 
8. Assessment of Safety 
Patient safety monitoring schedule - although there have been no reported serious adverse events  
associated with fecal microbiota transplantation (FMT) in patients with recurrent refractory  
Clostridium difficile or Crohn’s disease (CD), we will have a special data safety and monitoring  
board (DSMB) to ensure optimal patient safety and precautions for subjects with CD treated with  
FMT. Adverse events will be specifically monitored at 4, 12, 26 and 52 weeks after FMT by direct 
patient interviews, or by reporting from clinical sites of adverse events at any time in-between. The 
DSMB will meet a minimum of 2 times: after treatment of the first 20 subjects, and after treatment 
of all 44 subjects. A copy of the DSMB charter is located in Appendix 5.  
 
For this trial, an adverse event (AE) is defined as any untoward medical occurrence in a patient or  
clinical investigation patient administered a biologic product; such an occurrence does not  
necessarily have to have a causal relationship with this treatment. An AE can be any unfavorable  
and unintended sign, symptom, or disease temporally associated with the use of a medicinal  
product whether or not considered related to the medicinal product. A serious adverse event (SAE)  
is defined as any untoward medical occurrence that results in death, is life threatening, requires  
hospitalization or prolongation of existing hospitalization, results in persistent or significant  
disability/incapacity, is a congenital anomaly/birth defect, is an important medical event that may  
not be immediately life threatening or result in death or hospitalization but may jeopardize the  
patient or may require intervention to prevent one of the other outcomes previously mentioned.  
Adverse events will be determined by a toxicity grading scale (Appendix 6). In accordance with 
applicable policies of the BIDMC Institutional Review Board (IRB), the investigator-sponsor will 
report, to the IRB, any observed or volunteered Unanticipated Problem that is determined to be 
1) unexpected); 2) related or at least possibly related to study participation; and 3) suggests that 
the research places subjects or others at a risk of unknown harm or addition/increased 
frequency of harms (including physical, psychological, economic, legal, or social harm) than was 
previously known or recognized. Unanticipated problems may be adverse events, protocol 
deviations, noncompliance or other types of problems, but MUST meet all of the criteria listed 
above. Unanticipated problem reports will be submitted to the IRB in accordance with the 
respective IRB procedures.  
 
 
Patients will be asked to document their symptoms using the symptom diary card  
(Appendix 7) as a memory aide. Subjects will be asked to complete a symptom diary card 1 week  
prior to colonoscopy FMT and on the day of colonoscopy FMT treatment to assess their baseline. 
They will then be asked to complete a symptom diary card daily for the first seven days post 
colonoscopy FMT and then weekly thereafter for 26 weeks. The symptom diary card will help the 
patient monitor and keep track of adverse events. 6 months after the last dose of oral therapy, the 
patient will receive a final follow-up phone call. 

Protocol 15 
 
15 
 
 
In addition the DSMB may convene additional meetings if necessary to ensure the ongoing  
monitoring and safety of the subjects treated with FMT. The internal DSMB will include the  
following individuals: Dr Ciaran Kelly (Gastroenterology – BIDMC, Chair), 
Dr. David Yassa (Infectious Diseases – BIDMC), 
Dr. Mark Osterman (Gastroenterology – University of Pennsylvania) 
 
All events will be reported directly to the DSMB and the Institutional Review Board (IRB) in  
accordance with Harvard University policy: Investigators will promptly report to the IRB all  
unanticipated problems involving risks to human subjects or others under Title 21 of the Code of  
Federal Regulations (21 CFR 312.32) part 56 (Institutional Review Boards), part 312 
(Investigational New Drug Application), and part 812 (Investigational Device Exemptions). Harvard 
Medical School policy is consistent with guidance set forth by the Office for Human Research 
Protections (OHRP) (presented January 15, 2007)  
http://www.hhs.gov/ohrp/policy/AdvEvntGuid.htm and the FDA (presented January 14, 2009)  
http://www.fda.gov/downloads/RegulatoryInformation/Guidances/UCM126572.pdf when  
determining what related events require review by the Institutional Review Board. Any serious AEs  
also will be evaluated by the DSMB for review and determination of whether the trial should  
continue. 
 
All subjects will be followed for an additional six months following the end of their treatment.   
Subjects that did not experience a AEs or SAEs will receive a telephone call to monitor their current  
symptoms and quality of life.  For subjects that did experience a AE or SAE that was found to be  
connected to the FMT treatment, we ask that they return to our medical center for an exam with  
their gastroenterologist. All treatment and outcome of AEs will be documented on the CRF and  
summarized in the CSR. All AEs will be followed to resolution or stabilization by the study  
physician. 
 
9. Statistics 
Power Calculations 
Assuming 60% endoscopic recurrence in the control arm, and 20% in the FBT arm, the study 
would require 22 patients in each arm (Total N=44) to have 80% power. These assumptions are 
based on endoscopic recurrence data from the Reguiero trial, which represents typical patient 
populations coming to ileo-colectomy at tertiary referral centers16. This cohort could be enrolled 
from 4 participating sites (N=11 per site) that perform >30 ileo-cecal resections per annum.  
 
Statistical Analysis Plan 
For the primary end-point, chi-square test (or Fisher’s exact test if any cell number <5) will be 
used to compare the proportion of patients in each arm who exhibit endoscopic recurrence 
(Rutgeerts score > i2) at 6 months. A p value <0.05 will be considered significant. 
 
For the secondary end-points, dichotomous variables will be summarized using frequency tables 
or proportions, and compared using chi-square of Fisher’s exact test. Continuous variables will 
be expressed as mean values ± standard error, and compared using unpaired, two-tailed 
Student’s t-tests and one-way analysis of variance (ANOVA) for multiple group comparisons. Data 
that lack normality will be analyzed using non-parametric tests (Mann-Whitney). P-values < 0.05 
will be considered significant, after correction for multiple tests. Data will be analyzed using JMP 
software (SAS, Cary, NC). For microbial diversity, we will apply a set of downstream statistical 
tests to the resulting microbial, viral, gene, pathway, and metabolite abundances. Transformed 
data from groups will be compared using Bray–Curtis similarity, multidimensional scaling, and 
analysis of similarity (ANOSIM) (Primer E, Plymouth,UK). ANOSIM will also be used to compare 

Protocol 16 
 
16 
 
intersubject and intrasubject TRFLP profile similarities. Analysis of variance (ANOVA) will be used 
to compare relative abundance of specific TRFLP pattern elements between each group of 
subjects. These tests will take into account covariates included in available or collected sample 
metadata (age, family history, treatment, environmental/demographic data, and diet) by 
leveraging our LEfSe univariate biomarker discovery method and its multivariate successor 
MaAsLin. Such statistical tests will provide a measure of expected reproducibility of predicted 
microbial biomarkers that is not attainable by unsupervised ordination methods (e.g. Principle 
Coordinates Analysis) as provided by other software such as QIIME. 
 
10. Direct Access to Source Data/Documents 
The investigator will permit trial-related monitoring, audits, IRB/IEC review, and regulatory 
inspection(s) by providing direct access to source data/documents. 
 
11. Quality Control and Quality Assurance 
Good Clinical Practice will be adhered to in screening, preparation and administration of donor 
stool. All research staff are trained in Responsible Conduct of Research of clinical trials.  
 
12. Ethics 
Special Ethical Considerations: None 
Subject Confidentiality: as described above 
Placebo Use: N/A 
Exclusion of Children and Women of Childbearing Capacity: This is a pilot study to establish 
safety and tolerability in adults and women who are not pregnant or nursing. Future studies will 
potentially include children and childbearing-women 
Exclusion of Vulnerable Populations: N/A 
Plans for Scientific Review: The PI and co-investigators will be responsible for overseeing 
scientific review. 
In accordance with Harvard Medical School policy, all investigators have completed a COI 
statement. There are no relevant COI for this study. 
 
13. Data Handling and Recordkeeping 
Electronic data will be uploaded to a secure server hosted at the primary study site. Electronic 
data will be stored in the site’s shared drive on a secure server behind the site’s  firewall.  Only 
those individuals granted access to the CD research shared drive will have access to this data.  
Patient information will be coded and the coding legend will be maintained in a password-
protected PC in the investigator’s locked office. Only investigators  will retain the electronic code 
linking samples to PHI for  patients.  Original consent forms and other paper charts will be kept 
in a secured locked cabinet in the study coordinators office . Data will be stored through the 
Harvard-affiliated RedCap program.  This will allow security of data and accuracy of clinically 
collected information.   
Research stool samples will be shipped on the day of collection with unique study numbers 
that do not identify patients by name, date of birth or medical record number (completely de-
identified). Once received, researchers at the Broad Institute will re-code samples for an additional 
level of security.  Analyzed stool products will be stored at the Broad Institute for the duration of 
the study. Only investigators at BIDMC will retain the code linking blood samples to PHI. There is 
very minimal risk of loss of confidentiality relating to the shipment or storage of stool samples. 
 
14. Financing and Insurance 
This clinical trial is funded by a grant from the Harvard Institute for Translational Immunology 
(HITI) and Finch Therapeutics.  
 

Protocol 17 
 
17 
 
15. Publication Policy 
The PI will be responsible for publishing any findings. Results are expected to be published six 
months following the conclusion of the study. The study team will be responsible for compiling 
all necessary results in preparation for publication.