A Phase I/II, Double Blinded, Placebo Controlled, Single-center Study of Fecal Microbiota Transplant (FMT) for the Treatment of Active Pediatric Ulcerative Colitis and Pediatric Active Crohn's Colitis
Phase: PHASE1
Conditions: Inflammatory Bowel Diseases, Ulcerative Colitis, Crohn Disease
Sponsor: Stacy A. Kahn

 
 
 
 
 
 
PROTOCOL 
 
 
 
A Phase I/II, double blinded, placebo controlled, single-center Study of Fecal 
Microbiota Transplant (FMT) for the Treatment of Active Pediatric Ulcerative 
Colitis 
 
 
 
 
 
 
 
 
Protocol version: 11MAY2018 
 
Stacy Kahn, MD 
Boston Children’s Hospital – Division of Gastroenterology & Nutrition 
300 Longwood Ave. – Hunnewell 103 
Boston, MA  02115 
617-355-6058 
 
 
CONFIDENTIAL

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
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TABLE OF CONTENTS 
1. 
INTRODUCTION ...........................................................................................................4 
1.1. Background.............................................................................................................4 
1.2. Rationale .................................................................................................................6 
2. 
OBJECTIVES ..................................................................................................................7 
2.1. Primary Objective ...................................................................................................7 
2.2. Secondary Objectives .............................................................................................7 
3. 
STUDY DESIGN ............................................................................................................8 
3.1. Study Schema .........................................................................................................8 
Description.......................................................................................................................9 
3.2. Study Population ....................................................................................................9 
3.2.1. 
Inclusion Criteria .................................................................................................................. 9 
3.2.2. 
Exclusion Criteria ............................................................................................................... 10 
3.2.3. 
Subject withdrawal criteria ................................................................................................. 11 
3.2.4. 
Screen Failure ..................................................................................................................... 11 
4. 
STUDY TREATMENT .................................................................................................12 
4.1. Investigational Agent............................................................................................12 
4.1.1. 
Fecal Microbiota Transplant (FMT) and placebo .............................................................. 12 
4.1.2. 
Storage and Accountability ................................................................................................. 12 
4.1.3. 
Administration and Dispensing ........................................................................................... 13 
4.1.4. 
Blinding and Randomization ............................................................................................... 13 
4.1.5. 
Drug Related Risks .............................................................................................................. 13 
5. 
STUDY SCHEDULE AND PROCEDURES ...............................................................15 
5.1. Schedule of Events ...............................................................................................16 
5.2. Study treatment and procedures ...........................................................................18 
5.2.1. 
Screening and Enrollment ................................................................................................... 18 
5.2.2. 
Fecal microbiota or placebo transplantation (8 weeks)...................................................... 19 
5.2.3. 
Open-label FMT or Follow-up ............................................................................................ 19 
5.2.4. 
Post-treatment follow up ..................................................................................................... 20 
5.2.5. 
End of Study or Early Termination Visit ............................................................................. 20 
5.3. Assessments ..........................................................................................................21 
5.3.1. 
Stool analysis ...................................................................................................................... 21 
5.3.2. 
Microbial analysis ............................................................................................................... 21 
5.3.3. 
Clinical Outcomes ............................................................................................................... 22 
6. 
SAFETY ASSESSMENT..............................................................................................23 
6.1. Adverse Event Assessment and Reporting ...........................................................23 
6.2. Safety and Data Monitoring .................................................................................24 
6.3. Clinical Monitoring ..............................................................................................24 
7. 
STATISTICAL CONSIDERATIONS ..........................................................................25 
7.1. Power Calculation ................................................................................................25 
7.2. Simon’s Two Stage Design ..................................................................................25 
 

FMT transplant in Ulcerative Colitis 
Protocol version:11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
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7.3. Data Analysis........................................................................................................26 
8. 
DATA CAPTURE AND RECORD KEEPING ............................................................27 
9. 
PROTECTION OF HUMAN STUDY SUBJECTS ......................................................28 
9.1. Declaration of Helsinki and Ethical Review ........................................................28 
9.2. Informed Consent .................................................................................................28 
9.3. Inclusion of Women, Minorities, and Children (Special Populations) ................28 
10. 
REFERENCES ..............................................................................................................29 
 
 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
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1. 
INTRODUCTION 
1.1. 
Background 
The history of fecal microbiota therapy and its success 
Fecal microbiota transplantation (FMT) has been employed in the treatment of 
gastrointestinal disorders in humans since 1958, when it was first described by Eiseman to 
treat fulminant pseudomembranous enterocolitis.(1)  Over the last several years, 
investigators have reported their experiences on over 300 patients who have received fecal 
microbiota therapy for treatment of Clostridium Difficile infection (CDI). (2) This 2012 
meta-analysis reviewed over 27 studies using FMT for the treatment of refractory and often 
fulminant CDI associated colitis with an overall success rate of 92%. A more recent study 
on the treatment of CDI published in the New England Journal of Medicine was halted 
prematurely due to the overwhelming success of patients randomized to FMT for CDI as 
compared to standard antibiotic therapy. (3) Interestingly, Hamilton and colleagues have 
recently demonstrated that a frozen inoculum from a “universal screened donor” is equal in 
efficacy for CDI to a “fresh” donation from such an individual (90% vs. 92%; not 
significantly different). (4,5) They also note that the frozen approach allows for rigorous 
donor screening in a cost effective manner. Taking into account its well-documented clinical 
efficacy, apparent cost savings and safety, FMT for CDI, despite its unconventional nature, 
is now considered standard-of-care therapy.  Research has recently shown oral frozen 
inoculum is non-inferior to colonoscopically delivered frozen donor FMT in treating 
recurrent CDI (6), thereby reducing substantial risks and costs associated with colonoscopic 
delivery of FMT.   
The use of fecal microbiota therapy in inflammatory bowel disease (IBD), a natural 
next-step  
IBD is a difficult to treat, chronic inflammatory disease, currently without a cure. IBD often 
requires life-long immune suppression and, at times, surgical intervention to keep under 
control. Even our most robust medical therapies are expensive, lack universal clinical 
efficacy, and are rife with significant risk of infection, malignancy and drug reactions. Given 
the strong microbial influence in the proposed etiopathogenesis of IBD, FMT has been used 
for the treatment of IBD in both children and adults for over a decade. Borody and 
colleagues pioneered the use of FMT in IBD as published in their initial case series in 2003, 
including six patients all of whom achieved a clinical remission following FMT. (7) A more 
recent retrospective meta-analysis reviewed 17 articles including 41 patients with IBD 
receiving FMT, many of whom also had CDI. (8) In patients treated for their IBD, the 
majority experienced a reduction of symptoms (19/25), cessation of IBD medications 
(13/17) and disease remission (15/24). While suggesting potential promise of FMT for the 
treatment of IBD, these heterogeneous retrospective reports are difficult to interpret. 
Early evidence supports multiple FMT’s 
Early data suggests single administration of FMT may be inferior to multiple doses of FMT 
given over time.  Vermeire prospectively delivered FMT by naso-jejunal tube over two days 
in 4 adult patients who suffered from refractory CD. While they reported no long-term 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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adverse effects, this group saw only temporary clinical response and microbial change in the 
gut ecosystem of these patients. (9) Kump found similar tolerability and safety in treating 6 
Ulcerative colitis (UC) patients with a single FMT delivered colonoscopically but only 
temporary clinical improvement in some of the underlying IBD activity (11). Similarly, he 
reported no long-term engraftment of donor microbiota on recipient.  Research has showed 
no apparent adverse events in 3 pediatric patients with IBD (2 of whom had CD) treated by 
single FMT all delivered colonoscopically for the primary indication of recurrent CDI but no 
improvement in underlying IBD clinical status. (12)  
 
Multiple FMT administration seems to show more promising results. An adult case report by 
Kao showed complete resolution of severe Crohn’s colitis after 2 colonoscopically delivered 
FMT’s separated by 1 month  with significant alterations/engraftment in the patient’s gut 
microbial profile after FMT. (13) Similarly, Vandenplas reported improvement and 
eventually complete remission of infantile severe IBD activity with multiple FMTs from 2 
separate donors over time. (14) Kunde and colleagues recently published a larger 
prospective safety and tolerability study of daily FMT enemas for 5 days in 10 children with 
IBD showing it was safe and well tolerated. (9) Seven of nine (78%) of subjects showed 
clinical response within 1 week, six out of the nine (67%) of subjects maintained clinical 
response at 1 month, and three out of the nine (33%) subjects achieved clinical remission at 
1 week after FMT.  In a large double-blind placebo controlled trial, Moayeddi suggests that 
16/27 (60%) patients had subjective improvement of underlying UC activity after 6 weekly 
FMT therapies delivered by fecal retention enema. One third of these patients who showed 
initial subjective clinical response to an initial course of FMT eventually went into remission 
if FMT administration was maintained for a longer period of time. (15) 
 
Best Mode of Delivery 
 
There remains much uncertainty about the “best” mode of delivery of FMT. The most 
promising, prospective research using FMT for IBD to date utilized FMT delivery by 
retention enema (Moayeddi and Kunde, in adult and pediatric patients, respectively). Daily 
enema therapy for IBD colitis is routine in clinical standard practice for delivery of topical 
steroid and aminosalicylate therapy. Indeed, even in fragile, very sick adult populations with 
multiple co-morbidities and recurrent C. diff infection, where FMT is life-saving but any 
procedure is dangerous, FMT by retention enema is considered the safest and least invasive 
FMT delivery method available with minimal to no  procedurally associated risk. Therefore, 
enema or colonoscopy represents the “traditional” method by which to perform FMT. 
 
In the pediatric population, we are considerate of the invasive nature of enema therapy and 
the potential associated risks of anxiety and discomfort. An oral delivery would be an 
attractive, low risk and non-invasive alternative method of delivery for FMT therapy in this 
patient population. Based on our recent work in treating recurrent CDI successfully with oral 
inoculum by nasogastric tube delivery (16) and also by encapsulated oral inocula (work 
completed under FDA IND 15-199), the oral route of FMT seems to be non-inferior and 
obviates the need for persistent invasive delivery method. Vandenplas’ case report showing 
ultimate remission of infantile IBD after 7 FMT (6 by an upper gastrointestinal delivery 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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route) provides “proof-of-concept” that this method of FMT delivery in a pediatric 
population is feasible, and potentially helpful in the treatment of IBD. 
 
No studies to our knowledge have been done on FMT for pediatric IBD using frozen inocula 
collected from a universal donor. One might argue that given the known similarities of one’s 
microbiome to their parents, a universal donor is more likely to introduce a more desirable 
commensal inoculum. (17,18) Moreover, given the frequency of IBD and other autoimmune 
conditions in first-degree relatives, it is common that a suitable healthy donor cannot be 
identified and an unrelated donor is required.  
 
To best reflect and duplicate previous successes documented in the literature, we envision a 
hybrid FMT delivery method, using both FMT enema induction and an innovative oral 
encapsulated inoculum thereafter. We believe initial engraftment with donor stool is of 
paramount importance for eventual success of FMT therapy. 
 
Fecal Microbiota Transplant (FMT) as a therapy for Ulcerative Colitis 
Ulcerative Colitis (UC), a chronic inflammatory bowel disease (IBD) of the colon has 
similar strong microbial drivers of inflammation to CDI. FMT has been studied as a therapy 
for IBD in a number of small case series over the last three decades. (7,9,19) We propose 
that FMT would be a safe and well-tolerated therapy for pediatric UC. We further 
hypothesize that subjects will demonstrate subjective measures of clinical improvement (i.e., 
in the Pediatric  Ulcerative Colitis Activity Index), in patient related outcome variables such 
as abdominal pain and number of daily bowel movements, as well as  in objective 
inflammatory biomarkers. 
1.2. 
Rationale 
Profiling studies of the intestinal microbiome have associated the pathogenesis of IBD to 
characteristic shifts of the intestinal microbiota, reinforcing the view that IBD results from 
altered interactions between intestinal gut microbiota and the mucosal immune system. It is 
known that the microbial community in IBD patients is less diverse; enriched in 
Gammaproteobacteria and invasive E. coli species; and deficient in Faecalbacterium 
prauznitzii, certain Clostridia, Bacteroidetes, and Firmicutes. Metabolically, there is 
increased oxidative stress in these individuals, decreased presence of  short chain fatty acids 
and metabolites of short chain fatty acids, increased auxotrophy, sulfate transport, amino 
acid transport, and toxin secretion. (20) 
 
Recent pediatric work in multiple immunomodulator-refractory acute severe colitis has 
shown promising results in treating ill IBD children successfully with aggressive antibiotic 
regimens.  Seven of 15 (47%) of this retrospective cohort of patients achieved complete 
remission with only alteration of their microbial community via aggressive multiple 
antibiotic regimens. (21) 
 
It is entirely reasonable to assume that repopulating the gut habitat with healthy bacteria 
may alter disease activity course and progression. It is also entirely reasonable to assume 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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depleting gut flora with broad-spectrum antibiotic would be beneficial in setting the stage 
for appropriate transplant engraftment. 
 
2. 
OBJECTIVES 
2.1. 
Primary Objective 
The primary aim of this phase I/II, randomized, placebo controlled study is the assessment 
of safety and tolerability of universal donor FMT compared to placebo in pediatric and 
young adult subjects (ages 5 years through 30 years) with Ulcerative Colitis, who have 
failed, are intolerant to, or have refused first-line maintenance therapy. 
2.2. 
Secondary Objectives 
1. Identify biomarkers in both donor and recipient that may confer a clinical response. 
2. Establish whether or not ongoing FMT maintenance therapy is required for maintenance 
of clinical benefit in pediatric UC. 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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3. 
STUDY DESIGN 
3.1. 
Study Schema 
 
 
 
Antibiotic Conditioning (7 days) 
Induction: Retention Enema  
(Week 1 only) 
 
Maintenance: oral, encapsulated 
inoculum 
(Once weekly for 7 weeks) 
Maintenance: oral, 
encapsulated 
inoculum 
(Once weekly for  
8 weeks) 
48 hours 
Randomization to 
Eligible subjects 
with active 
ulcerative colitis
FMT Arm 
(N=30) 
Placebo Arm 
(N=30) 
Maintain 
Blinding 
Opt to receive Open-label FMT 
 
Received FMT in Blinded 
Arm  
 
FOLLOW UP 
(2 or 6 months) 
NO 
YES 
Antibiotic or Placebo Conditioning  
(7 days) 
FMT OR PLACEBO 
Induction: Retention Enema (Week 1 only) 
 
Maintenance: oral, encapsulated inoculum 
(Once weekly for 7 weeks) 
NO 
Yes 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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Description 
This is a single-center, phase I/II, randomized, prospective, double-blinded, placebo-
controlled study of FMT in the treatment of active pediatric UC. The primary aim is to 
assess safety and feasibility of a weekly FMT maintenance therapy. A total of 60 patients 
with active UC (as defined by PUCAI score of > 9) will be enrolled and randomized to first 
receive FMT or placebo (study treatment). 
 
For therapy/placebo induction, a retention enema will be administered according to the 
treatment arm to which the patient is assigned. FMT by retention enema will afford us the 
best delivery method equivalent to that previously described by Moayyeddi and Kunde (see 
Background) for engraftment of donor stool using FMT materials available to us. 
Subsequent administrations will occur as oral, frozen encapsulated inocula/placebo for 7 
weeks. After the first 8 weeks, subjects will have the option to continue on study treatment 
or switch to open-label FMT. Subjects will be followed by telephone to assess adverse 
events for a total of 6 months after their last FMT dose. 
 
Patient metadata and stool samples will be collected at key time points. The patient-reported 
metadata collection technique will allow for numerous clinical correlations to be parsed out 
using the random forest machine learning capabilities of synthetic learning in microbial 
ecology (SLiME) to identify taxonomic features associated with important clinical 
parameters.(22) 
 
An initial subset of 10 subjects will be enrolled in the study (will be limited to only those 
patients 12 years of age or older and to those who have mild to moderate ulcerative colitis) 
and randomized to receive FMT or placebo. We’d expect short term adverse events to occur 
within 7 days of FMT administration. Individual subject safety data will be reviewed by the 
PI to assess whether FMT appears to be safe in the subject before continuing the subject 
towards open-label use of FMT.  
 
3.2. 
Study Population 
The study will enroll 60 eligible patients with active UC (as defined by PUCAI score of >9). 
Patients from the Gastroenterology clinic at Boston Children’s Hospital and outside patients 
referred or self-referring to the clinic will be considered for participation in the study. 
 
3.2.1. Inclusion Criteria 
Male and female children and young adults, aged 5 years to 30 years, who meet the 
following inclusion criteria, will be enrolled in the study. 
 
An initial subset of 10 subjects will be limited to patients with mild to moderate ulcerative 
colitis (i.e., PUCAI < 65) and to individuals > 12 years of age.  If FMT appears to be safe in 
this subset of patients after 8 weeks in the study (to be assessed by a Data Safety Monitoring 
Board), expanded enrollment as is described above will occur. 
 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
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All patients must satisfy below criteria: 
1. Have UC (PUCAI >9) and have failed, are intolerant to, or have refused first-line 
maintenance therapy. 
2. Have had visual or histologic evidence of inflammation confirmed through 
colonoscopy ideally within 90 days but no more than 105 days prior to randomization. 
3. Have negative test results for Hepatitis B (HBV), Hepatitis C (HCV), and Human 
Immunodeficiency Virus (HIV). 
4. Have a negative urine hCG test if female of childbearing potential. 
5. Able to swallow antibiotic, FMT or placebo capsules. 
6. Able to give informed consent and/or assent as appropriate (patients 12-17 will be 
asked to provide written assent, patients 5-11 will be observed for assent or dissent 
behaviorally, or with verbal/written communication) 
7. Willing and able to participate in the study requirements, including serial stool 
collection, survey completion and clinic visits. 
8. Willing to undergo telephone follow-up to assess for safety and adverse events. 
9.  Must be free of any known food allergy. 
10. Agrees and willing to have an enema for purposes of induction therapy. 
 
Patients who have disease that has required other medications (including steroids, 
immunosuppressives, and biologics) will be included.  
 
3.2.2. Exclusion Criteria 
Subjects who fall into any of the following exclusion criteria at the time of screening are not 
eligible for enrollment into the study. 
 
1. Patients in a clinical remission (PUCAI < 9). 
2. Patients with recent (within 4 weeks) dose change of biologics, 5-ASA, steroids or 
immunomodulators 
3. Patients considered to have toxic megacolon. 
4. Patients with a known drug allergy to vancomycin, metronidazole or polymyxin. 
5. Patients with a history of aspiration, gastroparesis, surgery involving the upper 
gastrointestinal tract (that might affect upper gastrointestinal motility) or unable to 
swallow pills. 
6. Patients with esophageal dysmotility or swallowing dysfunction. 
7. Patients with known food allergies.  
8. Patients with positive test results for HBV, HCV, or HIV. 
9. Female patients with a positive test result on a urine hCG test. 
10. Patients unwilling or unable to give consent or participate in all study requirements. 
11. Patients unable or unwilling to receive a retention enema for purposes of induction 
therapy. 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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12. Patients with recent (within 6 weeks) systemic antibiotic use. 
13. Patients who have testing consistent with active clostridium difficile.  
14. Patients with known prior experience with donor FMT.  
Research personnel and care providers will be educated about inclusion/exclusion criteria so 
that only appropriate patients are approached for informed consent. This will reduce the 
burden of worry for families and patients as to whether they are suitable candidates for the 
study. Subjects who are found to have no evidence of active disease by colonoscopy will be 
excluded from the study. 
 
3.2.3. Subject withdrawal criteria 
All subjects are free to withdraw from participation in the study at any time, for any reason, 
specified or unspecified. A subject may be withdrawn from the study under any of the 
following circumstances: 
 
 Withdrawal of informed consent or assent when applicable. 
 If, in the opinion of the investigator, IRB or DSMB, it is no longer in the subject’s 
best interest to continue in the study. 
 The subject no longer meets the inclusion criteria or meets any of the exclusion 
criteria. 
 Lack of compliance with study procedures or study treatment, as determined by the 
investigator. 
 
3.2.4   Screen failure 
 
A subject who consented to participate in the study but who was disqualified during 
screening procedures and never began Antibiotic/Placebo conditioning will enter Passive 
follow-up, which means the subject may reach out to the study team for a second opinion for 
follow-up care or any other medically related reason.  These subjects will not be included in 
the per protocol analysis.  

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
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Initial Sponsor-Investigator IND 
 
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4. 
STUDY TREATMENT 
4.1. Investigational Agent 
4.1.1. Fecal Microbiota Transplant (FMT) and placebo 
The investigational agent consists of screened-donor inoculum of a biologically active 
human substance (FMT). FMT will be administered using either frozen screened-donor 
liquid stool (the investigational agent) in the form of retention enema (60 mL total for ages 
5-10 and up to 120 mL total for ages greater than 10) or frozen capsules. Placebo will be 
administered using either placebo liquid or placebo capsules (both consisting of cocoa 
butter, glycerol, and brown food coloring). Donor material and placebo material will be 
obtained from Microbiome Health Research Institute (OpenBiome), a stool bank affiliated 
with the MIT-Broad Institute. All donors will be thoroughly screened for health and 
infectious status. (Cross ref. BB-MF 15543). 
 
If randomized to FMT Arm, subjects will be matched with a specific stool donor and will 
then receive FMT induction enemas and FMT capsules containing this stool for the 8 week 
randomized portion of the trial. From each donor, sufficient stool to complete the study will 
be secured by OpenBiome and stored at their facility under appropriate storage conditions. 
The 8 week supply of the donor’s inoculum will be maintained on-site at BCH and stored in 
accordance with supplier specifications and investigational agent guidelines. If subjects are 
eligible for open-label FMT and have previously been randomized to FMT, every effort will 
be made to use the same donor if possible.  It is conceivable that enough stool to continue 
through open-label FMT treatment period(donors move or may become ineligible for stool 
donation) will not be practicably available and another appropriate donor may be selected 
for open-label FMT use if necessary.  
 
4.1.2. Storage and Accountability 
The Boston Children’s Hospital (BCH) research pharmacy will be responsible for the receipt 
and accountability of study agent. The pharmacy will maintain accountability logs with 
quantities received and dispensed, specifying the corresponding dates, and the identification 
code of the study subject. 
 
Bottles (containing the FMT and placebo enema preparations) and FMT and placebo 
capsules will be delivered in temperature controlled packaging on dry ice with a time-
temperature indicator. The bottles and capsules will be stored at -80C in an access 
controlled freezer in accordance with the manufacturer’s and BCH Infection Control 
specifications until dispensed for administration in a clinical research unit (CTSU).  
 
In order to maintain the integrity of the FMT inoculum during storage, the study team will 
use temperature-controlled, limited access freezers. Each freezer is equipped with a 
temperature monitoring system that alerts members of the lab and study team if the freezer 
fails (e.g. power failure or abnormal temperature fluctuations). In the event that a failure 
does occur and the study drug becomes unusable, the affected items will be voided and 
discarded.   

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
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Initial Sponsor-Investigator IND 
 
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4.1.3. Administration and Dispensing 
The first FMT or placebo dose will be administered as an enema 48 hours after completing 
antibiotic therapy (Week 1, Day 1). An un-blinded, independent pharmacy technologist will 
prepare the retention enemas or placebo which will be provided by OpenBiome. An un-
blinded research study nurse will then dispense FMT or placebo (study treatment) retention 
enema according to the treatment arm to which the patient is assigned. The enema containers 
will be fully color-tinted from the tip to the bottom of the container. The container will be 
placed inside a paper bag, to prevent any odor detection. Both the patient and the study 
nurse will be required to wear a tightly fitted mask at all times during the infusion and 
retention of the enema. 
 
Subjects will be put in left lateral decubitus position with elevated hips in a designated 
private study visit exam room for 60 minutes for FMT induction (or placebo) by retention 
enema. Each subject will receive FMT (or placebo) as either one or two retention enema(s)  
over 15-30 minutes.  Each 60 mL enema will be infused over 5 minutes. Subjects will be 
asked to rotate 180° (from left lateral to right lateral position and then return to left lateral 
position) slowly over a 10 minute period. While 120 mL of fecal solution (or placebo) will 
be prepared for induction retention enema for patients over the age of 10, the final 
administered dose will be dependent on subject’s comfort and willingness to proceed with 
the next enema which will be assessed after the first 60 mL enema infusion. Subjects will 
be monitored by a blinded study nurse for 60 minutes after enema administration for any 
immediate adverse events and discharged. 
 
For the next 7 weeks of study treatment, an unblinded research pharmacist will dispense 
FMT (study treatment) or placebo capsules to be administered under observation in the 
CTSU. 15 capsules of study treatment (the equivalent of 7.5 grams of human stool) will be 
administered within 90 minutes of thawing once weekly for a total of 7 weeks. After the 
initial 8 weeks, participants who responded to FMT during the blinded portion of the study 
or participants who did not respond to placebo will have the option to continue treatment 
with weekly open-label FMT. 
 
4.1.4. Blinding and Randomization 
The first ten eligible subjects will be randomized in a 1:1 ratio according to a pre-determined 
block randomization procedure to receive either FMT or placebo. If safety allows, the 
remaining cohort of 50 eligible subjects will be randomized in a 1:1 ratio according to a pre-
determined block randomization procedure to receive either FMT or placebo. An unblinded 
pharmacist or delegate will maintain the randomization list ensuring subjects are randomized 
appropriately and dispensed the correct treatment. The investigator, research personnel and 
study subjects will be blinded to treatment assignments. 
  
4.1.5. Drug Related Risks 
Theoretically, there is a small potential of transmission of an unknown pathogen when 
delivering human donor fecal material to a recipient.  Additionally, there is potential concern 
that the recipient might have an allergic reaction to a food component in donor stool that 
they might not be aware of and the donor has not avoided.  There is also a potential that 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
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certain disease states might be inherently related to the gut microbial environment and a 
donor’s risk for disease might be transmitted to a recipient.   These risks will be mitigated by 
carefully screening donors for health status as well as relevant (known) infectious 
pathogens.    
 
The literature to date comprises 100’s of cases of FMT for CDI as well as for IBD.  To date, 
no serious adverse events have been reported. Both Vermeire and Vandenplas reported 
systemic symptoms of fevers and abdominal pain in refractory IBD patients after FMT that 
resolved within 24-48 hours without intervention. (10,14) Pierog at Columbia University 
reported the development of  granulomatous appendicitis two weeks after FMT for the 
indication of recurrent CDI  in a  pediatric patient with underlying ileocecal granulomatous 
Crohn’s disease, but there is no clear reason to assume FMT is responsible for this otherwise 
Crohn’s related outcome. (23)  Quera reported a repeated sepsis episode with multi-drug 
resistant E. coli in a 61 year old male ill Crohn’s patient treated by FMT for recurrent CDI 
who had had several episodes of similar bacteremia previous to FMT. (24)  Dr. Hohmann 
reported a case of a 37 year old man who self-administered FMT at home for his ulcerative 
colitis who subsequently developed CMV colitis. (25)  Additionally, De Leon reported a 
case of a patient who experienced a transient flare of ulcerative colitis that had been 
quiescent for twenty years after FMT for recurrent CDI. (26) 
 
Retention enema is likely low-risk but may be less effective in some patients with inability 
to retain the FMT inoculum or placebo rectally. Mild discomfort and distress with anal 
manipulation are possible, though enemas are routinely used in our clinical practice to treat 
distal IBD colitis as well as constipation. Indeed in adult populations with advanced age, 
multiple comorbidities or limited life expectancy, this delivery mode is preferable. (27)  
 
 
 
 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
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5. 
STUDY SCHEDULE AND PROCEDURES 
Potential subjects will be assigned a unique identifier or study ID which will be used to 
identify the subject throughout the study period. Subjects who meet eligibility criteria will 
be consented and randomized to the FMT or placebo arm. 
 
During the study period, no changes to the previous medical therapy of patients will be 
made unless clinically indicated. At all times during the study, progression of standard 
medical therapy will be advised and available if necessary regardless of study drug 
assignment. Weaning of steroids will be allowed of a patient by PI discretion 

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5.1. Schedule of Events 
SCREENING 
BLINDED TREATMENT 
UNBLINDING 
 
OPEN-LABEL FMT 
 
FOLLOW UP12 
Early 
Termination 
 
Day 
 
Day 
Visit Week 
(± 2 days) 
Day 
Visit Week 
(± 2 days) 
Month 
 
Procedures 
-90 
to -9 
-8 
-1 
0 
(Wk 1, D1) 
2-3 
4 
5-7 
8 
-8 
-1 
0 
(Wk 9, D1) 
Weekly 
Every 4 
weeks 
1,2,4,5 
3 
EOS 
6 
 
Informed Consent 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Eligibility 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
MD visit 
x 
 
 
x 
 
x 
 
x 
 
 
x 
 
x 
 
x 
x 
 
HBV, HCV, HIV3 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Lavage 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Colonoscopy (up to 105 days) 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Randomization 
 
x 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Antibiotics1/placebo 
 
X 
 
 
 
 
 
 
X11 
 
 
 
 
 
 
 
 
hCG3 
x 
X8 
 
 
 
x 
 
x 
X8 
 
 
 
x 
 
 
 
 
Labs2 
x 
 
 
x 
 
x 
 
x 
 
 
x 
 
x 
 
x 
x 
x 
Disease activity surveys 5 
x 
x 
x 
x 
x 
x 
x 
x 
 
x 
x 
x 
x 
 
 
x 
x 
x 
x 
Stool sample7,9 
 
x 
 
x 
x 
x 
x 
x 
 
x 
 
x 
x 
 
 
 
x 
x 
x 
AE assessment by RN/MD 
 
x 
x 
x 
x 
x 
x 
x 
 
x 
x 
x 
x 
x 
x 6 
x 
x 
x 
Telephone contact by 
RN/MD 
 
 
x 
 
 
 
 
 
 
 
x 
 
 
 
x 
 
 
 
FMT/placebo dosing 
 
 
 
X4 
x 
x 
x 
x 
 
 
X4,10 
X10 
 
 
 
 
 
17-day induction regimen of 3 antibiotics (vancomycin 125 mg, polymixin 62.5 mg, and metronidazole) 
BSA for vancomycin 125 mg, polymixin 62.5 mg = SQRT [(cm*kg)/3600] 
<0.5 m²: PO 1 capsule, TID 
0.5 – 1 m²: PO 2 capsules, TID 
1 – 1.5 m²: PO 3 capsules, TID 
1.5 –2 m²: PO 4 capsules, TID 
 
Metronidazole weight-based dosing parameters 
12.5 kg > Patient Weight > 25.0 kg: 125 mg PO BID 
25.0 kg > Patient Weight > 37.5 kg: 250 mg PO BID 
37.5 kg > Patient Weight > 50.0 kg: 375 mg PO BID 
Patient Weight > 50 kg: 500 mg PO BID
2 “Screening labs” are considered for research purposes only, and will be covered by the study. Routine laboratory assessments are per routine clinical care, and if you are a patient at BCH, these will be 
covered by the subject’s insurance company. If the patient is not seen at BCH, then these are considered for research purposes and will be covered by the study.  
 
3 HBV, HCV, HIV, and hCG testing are research-only labs and are required to be obtained no earlier than 2 weeks prior to the 1st FMT dose. 
4 Initial FMT/placebo dose (Week 1 of blinded therapy will be administered as a retention enema).  Week 1 of open label therapy will be a selective FMT induction enema or FMT weekly capsule. 
5 Disease activity surveys include the Patient Reported Outcomes Diary and Pediatric Ulcerative Colitis Activity Index 

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6 Weekly telephone AE Assessments will also be conducted on a weekly basis for the 1st month of follow-up. 
7 IBD Biomarkers (quantitative fecal calprotectin) will be done after study completion from frozen samples taken from every study stool sample. 
8 A urine pregnancy test should only be obtained on day -8 if one has not been done in the past 30 days. 
9 The “X” location of stool samples indicates when the stool will be collected from the participant.  I.e. stool will be collected from the subject on day -8 and Week 1, Day1 however collection kits will 
have been provided to the subject beforehand.  Lack of stool sample collection will not constitute a protocol deviation.  
10Subjects in the OL treatment will receive FMT (not placebo) 
11 If eligible, subjects in OL treatment will receive selective Antibiotics (no placebo). 
12 If a subject received at least 1 dose of FMP IP. 

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5.2. Study treatment and procedures 
5.2.1. Screening and Enrollment 
Patients with active UC that are part of the Boston Children’s Hospital Gastroenterology and 
Nutrition clinic as well as referrals from outside of BCH will be pre-screened for study 
participation. Potential subjects who agree to participate in the study will have a medical 
exam with labs to assess eligibility. Participants will also undergo a baseline serologic 
assessment of HIV, HBV and HCV status within 2 weeks prior to the first FMT dose. 
Females who have achieved menses will undergo urine hCG testing. These four lab tests are 
considered for research purposes only. 
 
It is expected that study participants will receive ongoing clinical care at BCH for the 
duration of the study. Study participants, who self-refer or are referred by a GI provider not 
at BCH,  will have their primary GI provider notified of their participation in the FMT study 
and follow up clinical care at BCH during the course of the study at planned intervals. The 
study PI will provide the primary GI provider with contact information to relay any 
questions and concerns during the study period. At the completion of the subject’s 
involvement in the study, the PI will provide a final written and/or verbal report to the 
primary GI provider for continuity of care. 
 
Presence of active mucosal inflammatory bowel disease (active colitis) is an eligibility 
requirement for this study. Subjects with evidence of inflammation in a prior staging 
colonoscopy completed no more than 105 days will not be required to repeat a standard 
staging colonoscopy solely for the purposes of research. Subjects who have no evidence of 
active disease by endoscopic scoring of disease at the time of staging colonoscopy will not 
be randomized and will be excluded from the study.  
 
An initial subset of 10 subjects will be limited to patients with mild to moderate Ulcerative 
colitis (i.e., PUCAI < 65) and to individuals > 12 years of age. 
 
Upon confirmation of eligibility and completion of randomization, subjects will receive an 
induction antibiotic regimen (or corresponding placebo if in placebo arm) for one week to 
decrease levels of indigenous microflora (Study Day -8 until Day -1). 
 
The antibiotic regimen will include: 
1) A double antibiotic capsule containing vancomycin 125 mg  and polymixin 62.5 mg 
to be administered orally (PO) according to the following body surface area (BSA) 
parameters: 
 
BSA* (m2) 
Capsule 
Frequency 
<0.5 
1 
3 times a day 
0.5-1 
2 
3 times a day 
1-1.5 
3 
3 times a day 
1.5-2 
4 
3 times a day 
 

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*BSA will be calculated as BSA = SQRT [(cm*kg)/3600] 
2) A third antibiotic metronidazole administered orally (PO) as a separate capsule 
according to the following weight-based dosing parameters: 
 
Patient Wt (kg) 
Dose (mg) 
Frequency 
12.5 - 25.0  
125  
2 times a day 
25.0 - 37.5 
250 
2 times a day 
37.5 – 50.0 
375 
2 times a day 
>50.0  
500 
2 times a day 
 
Corresponding placebo for each antibiotic will be supplied and distributed by the BCH 
Research Pharmacy. 
 
Clinical data including symptom logs, medications and disease activity and stool samples 
will be collected at the time of study entry and after completion of the antibiotic regimen. 
Routine laboratory analysis will be done at the time of enrollment and before commencing 
study treatment. 
 
Subjects who meet all eligibility criteria will be randomized to receive either FMT or 
placebo. 
 
5.2.2. Fecal microbiota or placebo transplantation (8 weeks) 
Approximately 48 hours after stopping antibiotics or placebo antibiotics, subjects will return 
for a clinic visit in the Clinical and Translational Study Unit (CTSU) for administration of 
either FMT or placebo. At the visit, they will undergo a medical exam by the investigator 
and laboratory samples will be collected. Subjects will then receive an induction retention 
enema of either FMT or placebo over a 15-30 minute period and will be encouraged to 
retain the inoculum for as long as possible. Subjects will be observed for 60 minutes after 
last enema and before discharge. 
 
Subjects will return to the CTSU weekly, for a total of 7 weeks, for administration of 
blinded study treatment (FMT from the same donor or placebo). Prior to each weekly visit, 
subjects will provide stool and complete a survey (PUCAI) to monitor symptoms, 
medications and disease activity. At week 4 and week 8, subjects will also have routine 
laboratory assessments and a medical examination by the investigator. Adverse events will 
be assessed at each visit. 
 
5.2.3. Open-label FMT or Follow-up 
After completing 8 weeks of blinded study treatment, study subjects will be given the option 
to receive open-label maintenance FMT weekly for the remainder of the study if they 
initially received placebo and did not improve OR if they received FMT, improved, and 
wish to continue treatment. Subjects will be considered to have improved if their PUCAI 
score shows improvement of at least 10 points compared to baseline or a score of 10 points 
or less.  

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After a subject receives the last dose of blinded study treatment at week 8, the subject’s 
treatment assignment will be unblinded to determine the appropriate course of action.  Those 
subjects, who 1) are found to have improved after receiving 8 weeks of placebo or 2) are 
found not to have improved after receiving 8 weeks of FMT, will not be eligible to receive 
open-label FMT. Those subjects will be considered in follow up and will have disease status 
assessments conducted weekly for the 1st month and then monthly for the following month 
or 5 months. Subjects will also collect a stool sample and have medical examinations done 
at 3 and 6 months after their last dose of FMT. 
 
Study subjects who are eligible and interested in continuing on to open-label FMT can be 
enrolled within 14 days (+ 7 days) following blinded treatment completion. For the open 
label phase, subjects who received active treatment (FMT) will proceed directly to open 
label treatment weekly capsules.  However, subjects randomized to placebo (aka no 
antibiotics, no FMT) will undergo a 7-day antibiotic conditioning and a 2-day rest period 
prior to commencing open-label FMT treatment that will begin with a retention enema. 
Thereafter, all subjects will return weekly for observed FMT administration as previously 
described, AE assessment and survey and stool collection. Routine laboratory assessments 
and medical exams will be conducted monthly. At all times during this study, standard of 
care progression of medical/surgical therapy will be offered if clinical course dictates it is 
necessary for both FMT and placebo arms of the study. 
 
5.2.4. Post-treatment follow up 
All study subjects who received at least one dose of FMP will be followed by telephone to 
assess adverse events and disease status for a total of 6 months after their last FMT dose. 
Subjects will be contacted by phone weekly for the 1st month and then monthly for the 
following 5 months and will have stool sample collection and medical examination at 3 
months and 6 months after their last dose.  
 
5.2.5. End of Study or Early Termination Visit 
If withdrawing early from the study for any reason, subjects will be invited to come in for a 
final visit to provide a stool sample and routine labs (if indicated). 
Follow-up for subjects who signed the consent form, but did not complete the study (does 
not include screen failures) is as followed:   
 
Active (full follow-up schedule) if subject received at least one dose of FMP IP.  
 
Active-abbreviated (Subjects will be called weekly for one month and then once at 
the second month for a total of two months), for subjects that received at least one 
dose of antibiotics and/or placebo IP but did not complete blinded treatment period 
or receive any FMP. 
 
 

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5.3. Assessments 
5.3.1. Stool analysis 
Subjects will collect a maximum of 29 stool samples over the course of the study and 
complete a maximum of 36 disease activity surveys. All fecal samples will be stored at 
−80°C. DNA will be extracted, and the V4 region of the 16S gene will be sequenced using 
an Illumina MiSeq (Illumina, San Diego, California) as described previously. (28) The 
Shannon Diversity Index will be computed for each sample and a custom python script will 
be used to create summary plots illustrating the relationship between clinically relevant 
groupings and the diversity observed in the microbiome. We will use the Shannon diversity 
index as our primary measure of diversity because it takes into account both abundance and 
evenness of species present in the community and has been shown to most robustly 
accommodate the variation in sampling depth. (29) 
 
5.3.2. Microbial analysis 
A long-time collaborator, Eric Alm, PhD (MIT) and his group have pioneered novel 
approaches to analyzing complex microbial environments already leading to fruitful work 
together on IBD and the microbiome.(29) The Alm lab has a robust pipeline for processing, 
sequencing and analyzing this complex data and has already partnered with a leading 
biotechnology firm to study adult FMT for CDI. Our rich, patient-reported metadata 
collection technique will allow for numerous clinical correlations to be parsed out using the 
random forest machine learning capabilities of synthetic learning in microbial ecology 
(SLiME) to identify taxonomic features associated with important clinical parameters. These 
approaches are at the cutting edge of microbial ecology but are especially novel to the field 
of fecal transplantation, which has not yet been subjected to quantitative ecological analysis 
of any kind.  
 
 

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5.3.3. Clinical Outcomes 
Primary Outcome Measures 
1. Presence of FMT-related adverse events grade 2 or above. 
2. Proportion of subjects with any FMT-related adverse events of grade 2 or above at 8 
weeks post-FMT.  Patient related outcomes of rectal bleeding and number of bowel 
movements. Rectal bleeding will be assessed using common language from PUCAI 
scoring. (See Figure 1) 
 
Figure 1.   
 
Rectal Bleeding 
None 
Small amount only, in less than 50% of stools 
Small amount with most stools 
Large amount (> 50% of stool content) 
 
 
Secondary Outcome Measures 
1. Remission as defined by PUCAI of < 9 
2. Improvement in inflammatory biomarkers (stool calprotectin, serum ESR/CRP, 
albumin, Hematocrit). 
3. Changes in gut microbial composition. 
4. Improvement of PUCAI of ≥ 20 points. (30)  
5. Assessment of engraftment of donor microbes into recipients. 
 

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6. 
SAFETY ASSESSMENT 
6.1. Adverse Event Assessment and Reporting 
Comprehensive assessments of any apparent adverse event(s) (AE) experienced by the study 
subject will be performed throughout the course of the study.  
 
The PI will submit reports of unexpected Serious adverse events (SAEs) and other 
unanticipated problems to the Institutional Review Board (IRB) at Boston Children's 
Hospital and to OpenBiome according to their policies.  
 
The PI will report events that are both serious and unexpected and that are associated with 
FMT/study intervention to the FDA and other applicable health authorities within the 
required timelines as specified in 21 CFR 312.32 (IND Safety Reports). 
 
The following unexpected AEs will be assessed, recorded and reported to the Data Safety 
Monitoring Board (DSMB) on an expedited basis: all SAEs, AEs grade 3 (according to 
CTCAE 5.0 (31) if applicable) or above, and any unexpected AEs grade 2 or above that is 
possibly or probably related to FMT (as determined by a blinded investigator). Only an AE 
that meets the above criteria will be recorded and reported.  Each reported AE will be 
described by its duration (i.e., start and end dates), regulatory seriousness criteria if 
applicable, expectedness, suspected relationship to the study treatment, and actions taken (a 
blinded investigator will determine expectedness, severity and relationship to study 
treatment). 
 
Individual subject participation will be temporarily halted until the DSMB determines 
appropriateness of re-initiation of therapy in any subject experiencing an adverse event 
resulting in: an Emergency Department visit that is possibly or probably related to FMT, 
significant worsening of their disease, or experiences 1 SAE Grade > 3. 
 
Individual subject participation in the study will be permanently stopped if a SAE Grade >3 
is deemed possibly or probably related to FMT, including any hospital admission. 
 
If 2 or more subjects experience 1 SAE grade >4, all study activities will be halted until the 
DSMB determines appropriateness of re-initiation of therapy in any subject.  
 
 
 
 

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6.2. Safety and Data Monitoring 
A data and safety monitoring board consisting of three physicians and a biostatistician 
independent of the principal investigator will monitor this study.  The DSMB will review all 
adverse events as previously described and will convene at least every four months or when 
needed to review initial limited cohort safety data as described previously. Additionally, the 
DSMB will be convened to evaluate subject data if the subject has been temporarily halted 
from participating in the trial in order to assess appropriateness of resuming participation in 
the trial.  
 
If an SAE is thought to have been caused by the fecal transfer, the DSMB and IRB 
recommendation as to whether the protocol should be suspended or not will be followed. 
 
6.3. Clinical Monitoring 
Monitoring will be conducted according to a written monitoring plan to ensure the 
protection of the rights and safety of all participating human subjects, as well as to ensure 
the quality and integrity of data resulting from this investigation.  Monitoring services will 
be performed by qualified monitors provided by Boston Children’s Hospital. 

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7. 
STATISTICAL CONSIDERATIONS 
7.1. Power Calculation 
The primary aim of this phase I/II study is to establish whether or not FMT is a safe 
treatment for children and young adults with UC. Based on clinical experience, adverse 
events (AEs) in IBD patients are common and include abdominal pain, cramping, diarrhea, 
fever, bloody stool, vomiting, frequent defecation, joint pain, and eye pain.  It’s estimated 
that 70% of patients in any given year will experience a flare of their disease and have some 
or a combination of these symptoms.  Safety, therefore, needs to be assessed relative to the 
high prevalence of AEs in this population. For the primary outcome, we will take any new 
reported SAEs or worsening of the existing AEs during the study period following 
enrollment into account. 
 
The study will be powered for equivalence in the proportion of new SAEs or worsening of 
the existing AEs, assuming null (Ho) and alternative (Ha) hypotheses defined as follows: 
 
      Ho: p1 – p2 ≤ -δL  or  p1 – p2 ≥ δU. 
      Ha: δL ≤ p1 – p2 ≤ δU 
 
where p1 is the proportion of new SAEs or worsening of the existing AEs in the placebo 
group, p2 is the proportion in the FMT group, δL is the lower margin and δU is the upper 
margin. We expect to enroll a total of 60 patients into this study for a total of 30 FMT and 
30 placebo patients. Assuming the rate of new incident SAEs or worsening of existing AEs 
in the placebo group is 10%, there will be 82% power to reject Ho that the difference in 
proportions is 0.20 or greater from zero in the same direction. Similarly, we will have an 
85% power to reject a difference of 0.25 or greater if the rate of new incident SAEs or 
worsening of existing AEs increases to 15%. 
 
7.2. Simon’s two stage design 
We will follow stopping rule in Simon’s two-stage design if high incidence of new SAEs 
occurred in study participants. In the first stage, a subset of 5 patients will be enrolled. If all 
the 5 patients develop new SAE in the study period, we will declare the study is not safe for 
patients and will stop the trial immediately to check if FMT is related to these SAEs. If less 
than 5 patients develop SAEs in the first stage, we will proceed to second stage to enroll 
another 5 patients. If 7 out of the total 10 patients enrolled develop at least one SAE, we will 
stop again and check if FMT is related to these SAEs.  Otherwise the enrollment will be 
continued until the sample size for the primary outcome analysis is met.     
 
Assuming the probability of the new SAE is 76% among study participants, following the 
5/5 and 7/10 two-stage stopping rule, we will have 25% chance to stop in the first stage, and 
80% chance to stop in the second stage. If probability of new SAE increases to 0.96, we will 
have 82% chance to stop in the first stage, and 100% chance to stop in the second stage. 
 
 

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Table. The probability of stop following 5/5 and 7/10 stopping rule in two-stage design. 
True probability of SAE 
0.76 
0.80 
0.90 
0.96 
0.98 
Probability to stop in the 
first stage 
0.25 
0.33 
0.59 
0.82 
0.90 
Probability to stop in the 
second stage 
0.80 
0.88 
0.99 
1.00 
1.00 
 
 
7.3. Data Analysis 
All patients who are eligible, randomized, and have received at least one-dose of the study 
medication including antibiotics/placebo in the first week will be included into the analysis 
for primary outcomes to assess the safety and tolerability of FMT, as this will be a per 
protocol (and not intent-to-treat) analysis . Continuous variables will be presented as mean 
and standard deviation (SD) or median and interquartile range (IQR), depending on the 
distribution of the data. Categorical variables will be presented as number and percentage. 
Disease severity (PUCAI) and patient characteristics at baseline will be compared between 
the treatment groups to determine whether or not randomization resulted in balanced groups. 
Methods of 2-group comparison will include Student’s t-test, the Mann-Whitney test, 
Pearson chi-square test, and Fisher exact test, depending on the distribution of the variable 
under consideration. The primary outcome of safety will be assessed via a 2 × 2 cross-
tabulation, where the proportion of patients with new incident SAEs or upgrade of existing 
AEs in the FMT group will be compared to the proportion in the placebo group. Two one-
sided tests for equivalence (32) will be constructed and the overall P value taken to be the 
larger of the lower and upper tests. Statistical significance will be assessed at P<0.05. 
 
For the second outcome, we will use longitudinal data analysis methods  to 
investigate changes in inflammatory biomarkers including stool calprotectin, stool 
lactoferrin, serum ESR/CRP, albumin, and hematocrit over the study period. Generalized 
Estimating Equations will be performed to examine the association between FMT and 
changes in these biomarkers.   

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8. 
DATA CAPTURE AND RECORD KEEPING 
All study data will be captured in a 21CFR Part 11 compliant INFORMTM database. Data 
and source documents will be maintained in compliance with ICH-GCP and local and 
national regulatory requirements. 
 
By conducting this study, the investigator affirms that all study results and information 
furnished will be maintained in strict confidence.  Such information will be communicated 
to the investigator’s review committee under an appropriate understanding of 
confidentiality.  A published summary of the results of this study is not inconsistent with the 
preceding affirmation of confidentiality. 
 
All subjects will be actively followed by an investigator at Boston Children’s Hospital 
within the Division of Gastroenterology & Nutrition/ Inflammatory Bowel Disease Center 
for the duration of the study.  The patients will undergo routine visits with clinical staff as is 
described and a running log of symptoms, medication(s)/medication change(s), and adverse 
events will be maintained.  This information will be collected by case report forms for entry 
in the INFORMTM database and will be signed-off by the Principal Investigator. The 
subjects’ progress in the study and any changes to their treatment plans will be reviewed 
with the study team at regularly scheduled weekly study team meetings while the patient 
remains on the study protocol.  Others providing care to the patients will be included to the 
extent needed to provide appropriate medical care to the patients with patient permission.  
 
 

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9. 
PROTECTION OF HUMAN STUDY SUBJECTS 
9.1. Declaration of Helsinki and Ethical Review 
The study will be conducted in accordance with the protocol, applicable ICH Guidelines, 
Good Clinical Practice and the World Medical Association (WMA) Declaration of Helsinki 
and its amendments concerning medical research in humans. 
 
In accordance with guidelines and U.S. Code of Federal Regulations applicable to clinical 
studies, the protocol and informed consent/assent forms will be reviewed and approved by 
the Boston Children’s Hospital Institutional Review Board (IRB). The investigator will 
inform the IRB and FDA of subsequent protocol amendments and reportable events as 
defined by IRB policy and FDA regulation. 
 
9.2. Informed Consent 
In accordance with applicable guidelines, informed consent/assent will be documented by 
the use of a written informed consent approved by the IRB and signed by the subject and/or 
subject’s parent or guardian before any screening and protocol specific procedures are 
performed. 
 
The investigator (or designee) will explain to the subject and/or the subject’s parent or 
guardian the nature of the study, the action of the study treatment, and any risks and 
benefits. The subject and/or subject’s parent or guardian will be informed that participation 
is voluntary and that the subject can be withdrawn from the study at any time without 
prejudice to their subsequent care. 
 
The subject and/or the subject’s parent or legal guardian will be given a copy of the fully 
executed consent/assent and the original will be maintained with the subject’s records. 
9.3. Inclusion of Women, Minorities, and Children (Special Populations) 
Eligible male and female subjects who are members of minority groups and their 
subpopulations will not be excluded from the study.  Children 5 years of age or older will be 
included in the study.  
 

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10. REFERENCES 
1. Eiseman B, Silen W, Bascom GS, Kauvar AJ. Fecal enema as an adjunct in the 
treatment of pseudomembranous enterocolitis. Surgery [Internet]. 1958/11/01 ed. 
1958;44(5):854–9.  
2. Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota 
transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. 
Clin Infect Dis [Internet]. 2011/10/18 ed. 2011;53(10):994–1002.  
3. Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, De Vos WM, et al. 
Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile. N Engl J Med. 
2013; 368 (5): 407-15. 
4. Hamilton MJ, Weingarden AR, Sadowsky MJ, Khoruts A. Standardized frozen 
preparation for transplantation of fecal microbiota for recurrent Clostridium difficile 
infection. The American Journal of Gastroenterology [Internet]. Nature Publishing 
Group; 2012 May [cited 2013 Mar 1];107(5):761–7.  
5. Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. High-throughput 
DNA sequence analysis reveals stable engraftment of gut microbiota following 
transplantation of previously frozen fecal bacteria. Gut microbes [Internet]. 2013 Jan 
18 [cited 2013 Feb 23];4(2).  
6. Youngster I, Sauk J, Pindar C, Wilson R, Kaplan J, Smith M, Alm E, Gevers D, 
Russell G  and  Hohmann E. Fecal Microbiota Transplant for Relapsing Clostridium 
difficile Infection Using a Frozen Inoculum from Unrelated Donors – a Randomized, 
Open Label, Controlled Pilot Study. Clinical Infectious Disease. 2014: 58(11): 1515-
1522. 
7. Borody TJ, Warren EF, Leis S, Surace R, Ashman O. Treatment of ulcerative colitis 
using fecal bacteriotherapy. J Clin Gastroenterol [Internet]. 2003/06/18 ed. 
2003;37(1):42–7.  
8. Anderson JL, Edney RJ, Whelan K. Systematic review: faecal microbiota 
transplantation in the management of inflammatory bowel disease. Aliment Pharmacol 
Ther [Internet]. 2012/07/26 ed. 2012;36(6):503–16.  
9. Kunde S, Pham A, Bonczyck S, et al. Safety, Tolerability, and Clinical Response after 
Fecal Transplantation in Children and Young Adults with Ulcerative Colitis. Journal of 
Pediatric Gastroenterology and Nutrition. 2013; 56(6): 597-601. 
10. Vermeire S, Joosens M, Verbeke K, et al. Pilot Study on the Safety and Efficacy of 
Faecal Microbiota Transplant in Refractory Crohn's Disease. Gastroenterology. 2012; 
142(5): s360. 
11. Kump P, Grocehnig H, Lackner S, et al. Alteration of Intestinal Dysbiosis by Fecal 
Microbiota Transplantation Does Not Induce Remission in Patients with Chronic 
Active Ulcerative Colitis. Inflamm Bowel Dis, 2013; 0:1-11. 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
Confidential 
30 
 
12. Russell GH, Kaplan JL, Winter HS. Fecal Microbiota Transplant to treat Recurrent C. 
difficile Infection in Children with and without Inflammatory Bowel Disease. Journal 
of Pediatric Gastroenterology & Nutrition. 2014; 58(5): 588-592. 
13. Kao D, Hotte N, Gillevet P, et al. Fecal Microbiota Transplant Inducing Remission in 
Crohn's Colitis and Associated Changes in Fecal Microbial Profile. J Clin 
Gastroenterol. 2014; 48(7): 625-8. 
14. Vandenplas Y, Veereman G , van der Weerf ten Bosch J, et al. Fecal microbial 
transplantation in a one-year old girl with early onset colitis - caution advised.  JPGN. 
Published Ahead of Print. 2014. 10.1097/MPG.0000000000000281. 
15. Moayeddi P, Surrette M, Wolfe M, et al. A randomized, placebo controlled trial of 
fecal microbiota therapy in active ulcerative colitis. Gastroenterology. 2014; 146 (5): 
s-159. 
16. Brandt LJ, Borody TJ, Campbell J. Endoscopic fecal microbiota transplantation: “first-
line” treatment for severe clostridium difficile infection? J Clin Gastroenterol 
[Internet]. 2011/07/01 ed. 2011;45(8):655–7.  
17. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A 
core gut microbiome in obese and lean twins. Nature [Internet]. 2008/12/02 ed. 
2009;457(7228):480–4.  
18. Costello EK, Stagaman K, Dethlefsen L, Bohannan BJM, Relman DA. The application 
of ecological theory toward an understanding of the human microbiome. Science (New 
York, N.Y.) [Internet]. American Association for the Advancement of Science; 2012 
Jun 8 [cited 2013 Feb 28];336(6086):1255–62.  
19. Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. 
Nat Rev Gastroenterol Hepatol [Internet]. 2011/12/21 ed. 2012;9(2):88–96.  
20. Kostic A, Xavier R, Gevers D. The Microbiome in Inflammatory Bowel Disease: 
Current Status and the Future Ahead.  Gastroenterology  2014; 146:1489-1499 
21. Turner D, Levine A, Kolho, Kaija-Leena, et al. Combination of oral antibiotics might 
be effective in severe pediatric ulcerative colitis: a preliminary report. Journal of 
Crohn’s and Colitis. 2014; Jun 20. pii: S1873-9946(14)00183-4. doi: 
10.1016/j.crohns.2014.05.010. [Epub ahead of print] 
22. Caporaso JG, Lauber CL,WaltersWA, et al. Ultra-high-throughput microbial 
community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 2012; 
6:1621–4. 
23. Pierog A, Mencin A, Reilly N, et al. Fecal Microbial Transplantation for Children with 
Recurrent Clostrodium difficile Infection. The Pediatric Infectious Disease Journal. 
Published Ahead of Print.  2014; 33 (11): 1198-200. 

FMT transplant in Ulcerative Colitis 
Protocol version: 11MAY2018 
Sponsor: Stacy Kahn, MD 
Initial Sponsor-Investigator IND 
 
Confidential 
31 
 
24. Quera R. Letter to the Editor – Bacteremia as an adverse event of fecal microbiota 
transplantion in a patient with Crohn’s disease and recurrent Clostridium difficile infection. 
Journal of Crohn’s and Colitis. 2014; 8 : 252-3. 
25. Hohmann EL, Ananthakrishan AN, Deshpande V. Case 25-2014: Case records of the 
Massachusetts General Hospital. New England Journal of Medicine. 2014; 371(7): 668-675. 
26. De Leon LM, Watson JB, Kelly CR.  Transient flare of ulcerative colitis after fecal 
microbiota transplantation for recurrent Clostridium difficile infection.  Clinical 
Gastroenterology & Hepatology. 2013; 11(8): 1036-8. 
 
27.  Kassam Z, Hundal R, Marshall J, Lee C. Fecal Transplant via Retention Enema for 
Refractory or Recurrent Clostridium difficile Infection. Arch Intern Med 2012; 
172(2):2012-14) 
 
28. Preheim SP, Perrotta AR, Friedman J, et al. Computational methods for high-
throughput comparative analyses of natural microbial communities. Methods 
Enzymol 2013; 531:353–70. 
29. Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, et al. Non-invasive 
mapping of the gastrointestinal microbiota identifies children with inflammatory 
bowel disease. Ravel J, editor. PLoS ONE [Internet]. Public Library of Science; 
2012;7(6):e39242.  
 
30. Turner D, Otler A, Mack D, et al. Development, Validation, and Evaluation of a 
Pediatric Ulcerative Colitis Activitis Index: A Prospective Multi-center Study. 
Gastroenterology.  2007; 133: 422-432. 
 
31. National Cancer Intitute’s Common Terminalogy Criterial for Adverse Events 
(CTCAE version 5.0 [cited 2017 Nov 27];0:0–135.  
 
32. Schuirmann, D. J. (1987), "A Comparison of the Two One-Sided Tests Procedure 
and the Power Approach for Assessing the Equivalence of Average Bioavailability," 
Journal of Pharmacokinetics and Biopharmaceutics, 15, 657–680.