Fecal Microbial Transplantation in Patients With Medication Refractory Clostridium Difficile and/or Ulcerative Colitis or Indeterminate Colitis
Phase: EARLY_PHASE1
Conditions: Clostridium Difficile Infection, Ulcerative Colitis, Indeterminate Colitis
Sponsor: Stony Brook University

- Stony Brook Medicine
August 30, 2019 
Title: Fecal Microbial Transplantation for C. Difficile and/or Ulcerative Colitis or Indeterminate Colitis (FMT) 
. 
. 
ClinicalTrials.Gov NCT03268213 
Please find enclosed the following documents: 
1. IRB approved protocol
2. Recipient permission-consent form UC
3. Recipient permission-consent form CDI
4. Recipient assent form UC
5. Recipient assent form CDI
6. Donor permission consent form
7. Donor assent form
Anupama Chawla, MD 
Professor of Pediatrics/ Division of Gastroenterology 
Stony Brook Medicine 
07/25/2019 
07/03/2019 
07/03/2019 
07/03/2019 
07/03/2019 
07/03/2019 
07/03/2019 
Stony Brook University Hospital 
Department of Pediatrics, Division of Gastroenterology 
Health Science Tower 
101 Nicolls Road 
Level 11 Room 080 
Stony Brook, New York 1179498111 
P: 631-444-7269 F: 631-444-6045 

July 2019
1
Protocol 
TITLE:  Fecal microbial transplantation in patients with medication-refractory Clostridium difficile and/or 
Ulcerative colitis or indeterminate colitis. 
ClinicalTrials.gov ID:NCT03268213, 479696, IND 15642
INVESTIGATORS:  
Anupama Chawla M.D. (Principal Investigator)
Professor of Pediatric Gastroenterology
Ellen Li M.D., PhD (co-PI)
Professor of Medicine/Gastroenterology
Jeffrey Morganstern M.D.
Associate Professor of Pediatric Gastroenterology
Grace Gathungu M.D.
Assistant Professor of Pediatric Gastroenterology
Lesley Small-Harary M.D.
Assistant Professor of Pediatric Gastroenterology
Michelle Tobin M.D.
Assistant Professor of Pediatric Gastroenterology
Jonathan Buscaglia M.D.
Associate Professor of Medicine/Gastroenterology
Ramona Rajapakse M.D.
Associate Professor of Medicine/Gastroenterology
Juan Carlos Bucobo, M.D.
Assistant Professor of Medicine/Gastroenterology
Tyson Collazo, M.D.
Assistant Professor of Medicine/Gastroenterology
Lionel D’Souza, M.D.
Assistant Professor of Medicine/Gastroenterology
Alexandra Guillaume, M.D.
Assistant Professor of Medicine/Gastroenterology
Bradley Morganstern, M.D.
Assistant Professor of Medicine/Gastroenterology
Farah Monzur, M.D.
Assistant Professor of Medicine/Gastroenterology
A. SPECIFIC AIMS: 
The following hypothesis will be tested in this study:
1. Fecal microbiota transplantation is a safe, tolerable and efficacious procedure.
2. The fecal microbial diversity, composition and function in stool recipients after fecal transplantation will change 
to a similar microbial diversity, composition and functionality as found in donor stool.
Primary objectives: 
1.
To determine the short term safety, tolerability and efficacy of fecal microbiota transplantation up to 12 
weeks post-transplant in patients with
a.
Recurrent or refractory Clostridium difficile infection (CDI) not responsive to standard therapy in 
subjects without inflammatory bowel diseases 
b.
Recurrent or refractory CDI not responsive to standard therapy in subjects with inflammatory bowel 
disease.
c.   Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone 
Secondary objectives:
1.
To determine the long term safety, tolerability and efficacy of fecal microbiota transplantation (FMT) up to 
one year post transplant in patients with
a.
Recurrent or refractory CDI not responsive to standard therapy in subjects without inflammatory 
bowel diseases 
b.
Recurrent or refractory CDI not responsive to standard therapy in subjects with inflammatory bowel 
disease.
c.   Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone
 
2.
To compare microbial diversity, composition and function in healthy donor stools compared to pre-FMT 
recipient stools collected from patients (recipients) with 
a.
Recurrent or refractory CDI not responsive to standard therapy in subjects without inflammatory 
bowel diseases 
b.
 Recurrent or refractory CDI not responsive to standard therapy in subjects with inflammatory bowel 
disease.
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c. Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone 
3.
To compare microbial diversity, composition and function in healthy donor stools and pre-FMT recipient 
stools with 1 week post transplant recipient stool samples collected from patients (recipients) with
a.
Recurrent or refractory CDI not responsive to standard therapy in subjects without inflammatory 
bowel diseases 
b.
Recurrent or refractory CDI not responsive to standard therapy in subjects with inflammatory bowel 
disease.
c.   Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone 
4.
To compare microbial diversity, composition and function in healthy donor stools and pre-FMT recipient 
stools with 12 week post transplant recipient stool samples collected from patients (recipients) with
a.
Recurrent or refractory CDI not responsive to standard therapy in subjects without inflammatory 
bowel diseases 
b.
Recurrent or refractory CDI not responsive to standard therapy in subjects with inflammatory bowel 
disease.
c.  Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone
5.
Stool calprotectin levels will be measured in the recipient at baseline pre-FMT, 1 week and 12 weeks post 
FMT to determine if FMT causes a statistically significant change.
B. BACKGROUND AND SIGNIFICANCE
Clostridium difficile is the leading cause of antibiotic-associated diarrhea with increasing infection rates and 
economic burden in developed countries. 1-4 According to the United States Healthcare Cost and Utilization 
Project Kids’ Inpatient Database (HCUP-KID), there has been an increase in pediatric Clostridium difficile from 
a rate of 7.24/10000 hospitalizations in 1997 to 12.80/10000 hospitalizations in 2006.5 As the C. difficile epidemic 
worsens, the numbers of failed treatments and patients who experience relapses or recurrences also continues 
to grow. Patients being treated with usual first-line treatments such as metronidazole and vancomycin are 
encountering “hypervirulent” and resistant strains of C. difficile such as North American Pulsed Field type 1 
(NAP1), restriction-endonuclease analysis (REA) type BI, or polymerase-chain reaction ribotype 027 (referred to 
collectively as the NAP1/B1/027 strain).6 The NAP1/B1/027 strain of C. difficile has been deemed “hypervirulent” 
for its ability to produce binary toxin C. difficile 126 adenosine diphosphate-ribosyltransferase not typically found 
in other strains of C. difficile. This, in combination with its ability to produce excessive quantities of enteroxins A 
and B, compared with other strains of C. difficile, makes it hypervirulent7 Even the newer agent, fidaxomicin, 
which was approved by the FDA in 2011, has a similar effectiveness to vancomycin with respect to the clinical 
resolution of acute diarrheal disease due to C. difficile.6 The problem is that after completing antibiotic treatment 
20-35% of CDI patients experience a recurrence of CDI.  Vancomycin tapers or fidaxomicin may be associated 
with a lower rate of recurrence.  Once recurrent CDI occurs, 45-65% of patients will continue to experience 
recurrent infections over several years and have a higher mortality.7-11 
Fecal microbial transplantation (FMT) of healthy donor stool into the patient’s gut has emerged as one of 
the most effective treatments of recurrent CDI.12-14  Patients with inflammatory bowel diseases (IBD), particularly 
ulcerative colitis (UC) and indeterminate colitis (IC) but also Crohn’s disease (CD), are at increased risk of 
developing CDI.15-20 FMT is also highly effective in treatment of recurrent CDI with IBD patients, although the 
effectiveness may be reduced compared to patients with recurrent CDI without IBD.21-23  While some patients 
with recurrent CDI and IBD appear to benefit overall from the FMT, there have been reports of exacerbation of 
IBD after eradication of CDI, although it remains to be determined whether FMT contributed to the 
exacerbation.24,25  
Thus far studies on the effectiveness of FMT in the treatment of IBD without CDI, have utilized different 
protocols and have yielded mixed results.26-38  Performing FMT in patients with IBD without CDI appears to be 
safe.  As noted above, a review of FMT trials conducted on IBD patients with and without CDI noted that post-
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FMT exacerbation of IBD patients without recurrent CDI appeared to occur less often than in IBD patients with 
recurrent CDI.25 
Colonoscopic instillation into the right side of the colon of ~50 g stool is associated with the highest rates 
of preventing further CDI (~90%).  The effectiveness of the oral capsule route, may be related to the total amount 
of stool ingested and ranges from 68 to greater than 90%.39-41  In a very recent randomized trial of oral capsule 
vs. colonic instillation of 150g of stool, ingestion of oral capsules was not inferior to colonoscopic administration 
(96% in both arms).41 
FMT is believed to restore the normal microbiological balance in the recipient primarily by transferring 
microbial components of the donor stool, although there is some evidence that non-microbial molecular 
components, such as short-chain fatty acids and bile acids may also play a role.42,43  The normal microbiological 
balance may be perturbed in patients with C. difficile infection and or IBD.44
The overall goal of this study protocol registered as ClinicalTrials.gov ID:NCT03268213, 479696, is to 
better define the microbial and non-microbial components in donor stool that contribute to post-FMT changes in 
the microbiome in the following three groups of recipients:
a.
Recurrent or refractory CDI not responding to standard medical treatment without IBD, 
b.
Recurrent or refractory CDI not responding to standard medical therapy with IBD 
c.
Ulcerative colitis or indeterminate colitis without CDI who have required therapy beyond 5-ASA or 
mesalamine therapy alone 
D. RESEARCH DESIGN AND METHODS
 
1.
Rationale/overview:
It is important to emphasize that this study is not designed to investigate clinical efficacy. FMT clinical 
efficacy for preventing further recurrence of CDI is now well established in the literature for recipients with 
recurrent or refractory CDI not responding to standard medical treatment, with and without IBD.  However 
it remains to be determined what the key microbial or nonmicrobial components of the donor stool 
contribute to clinical efficacy.  Consequently this study is designed to:
a.
Measure baseline microbial imbalances in these three groups of recipients (i. recurrent or refractory 
CDI not responding to standard medical treatment without IBD, ii. recurrent or refractory CDI not 
responding to standard medical therapy with IBD iii. UC and IC without CDI.) compared to healthy 
donors.
b.
Measure whether FMT will alter recipient microbial imbalances one week and 12 weeks after the 
procedure.
c.
Measure short (12 weeks) and long term (one year) safety, tolerability and efficacy of FMT in these 
three groups of recipients.
2.
FDA statement on requirement for IND for FMT.
The March 2016 Enforcement Policy Regarding Investigational New Drug Requirements for Use of 
Fecal Microbiota for Transplantation to Treat Clostridium difficile Infection Not Responsive to Standard 
Therapies Draft Guidance for Industry45 states: “We, FDA or Agency, are informing members of the 
medical and scientific community and other interested persons that we intend to exercise enforcement 
discretion under limited conditions, regarding the investigational new drug (IND) requirements for the use 
of fecal microbiota for transplantation (FMT) to treat Clostridium difficile (C. difficile) infection not 
responding to standard therapies. FDA intends to exercise this discretion, provided that: 1) the licensed 
health care provider treating the patient obtains adequate consent from the patient or his or her legally 
authorized representative for the use of FMT products. The consent should include, at a minimum, a 
statement that the use of FMT products to treat C. difficile is investigational and a discussion of its 
reasonably foreseeable risks; 2) the FMT product is not obtained from a stool bank; and 3) the stool 
donor and stool are qualified by screening and testing performed under the direction of the licensed 
health care provider for the purpose of providing the FMT product for treatment of the patient. A stool 
bank is defined, for the purpose of this guidance, as an establishment that collects, prepares, and stores 
FMT product for distribution to other establishments, health care providers, or other entities for use in 
patient therapy or clinical research. An establishment that collects or prepares FMT products solely under 
the direction of licensed health care providers for the purpose of treating their patients (e.g., a hospital 
laboratory) is not considered to be a stool bank under this guidance. FDA does not intend to extend 
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enforcement discretion for the IND requirements applicable to stool banks distributing FMT products. 
Such distributions are subject to the requirements that a sponsor, typically the stool bank, have an IND 
in effect before distributing the FMT product to investigators for administration to subjects in accordance 
with the investigational plan under the Public Health Service (PHS) Act (42 U.S.C. 262(a)(3)) and 21 CFR 
Part 312. However, as described in this guidance, an IND sponsor may request a waiver of certain IND 
regulations applicable to investigators for those licensed health care providers receiving FMT product to 
treat patients with C. difficile infection not responsive to standard therapies. (See 21 CFR 312.10). FDA 
has developed this policy to assure that patients with C. difficile infection not responding to standard 
therapies may have access to this treatment, while addressing and controlling the risks that centralized 
manufacturing in stool banks presents to subjects. FDA intends for this to be an interim policy, while the 
Agency develops a comprehensive approach for the study and use of FMT products under IND.” At this 
time, since administration of FMT products from stool bank(s) has not been approved by SBUH regulatory 
committees in the Endoscopy suite in Stony Brook University Hospital, administration of FMT products 
from stool banks cannot be offered to recipients with recurrent CDI.  
An IND (IND 15642) was obtained from the FDA for performing FMT on UC and IC recipients without 
recurrent or refractory CDI not responsive to standard medical treatment.
3.
Research Site(s):
The following research sites are all located within Stony Brook University Medical Center (SBUMC).
a.
Patient and donor recruitment and screening. This will take place at Stony Brook University Medical 
Center (SBUMC) in both the hospital and outpatient Pediatric and Adult Gastroenterology Clinic 
setting.  The Pediatric Gastroenterology Clinic is located at 4 Technology Drive, Suites 250 and 
270, across the street from the Adult Gastroenterology Clinic, which is located at 3 Technology 
Drive, Suite 300. 
b.
Preparation of donor stool for FMT. The donor stool will be prepared for colonoscopic instillation 
following standard operating procedure, as described below, in a biosafety cabinet located within 
Dr. Li’s laboratory within the Department of Medicine/Division of Gastroenterology research space 
located in in the Health Sciences Center Building (room HSC T17-080).  The research laboratory 
in the HSC Building is connected by a bridge to Stony Brook University Hospital, allowing for rapid 
transport of the stool instillate to the Endoscopy unit on the 14th floor.
c.
Colonoscopic instillation of donor stool. Colonoscopic administration of the FMT will be performed 
in the Stony Brook University Endoscopy Unit located 
d.
Processing of stool samples for microbiome analysis.  The research stools samples obtained from 
the donor (at the time of transplant), and the recipient (pre-FMT, 1 week post-FMT, and 12 weeks 
post-FMT) will be processed in Dr. Li’s laboratory within the Department of Medicine/Division of 
Gastroenterology research space
4.
Participants
Each FMT will involve two participants, the recipient of the FMT, and a healthy known donor selected 
by the recipient or recipient’s parents (pediatric recipient age <18).  The inclusion and exclusion criteria 
for recipients with CDI with or without IBD are identical see D4.a).  The inclusion and exclusion of the 
UC and IC only without recurrent CDI recipients are described separately under D4.b. The inclusion 
and exclusion criteria for the healthy donors are identical for all three recipient groups under D4.c.
a.
Inclusion and exclusion criteria for recipients with recurrent or refractory CDI with or without 
IBD not responsive to standard medication:
Inclusion: (see Appendix A) 
i.
Recipient age ≥ 7 years of age.46 
ii.
Recurrent of refractory CDI with or without IBD not responding to standard medication therapy 
as one of the following criteria:

The recipient has had at least three episodes or two recurrences of mild to moderate 
CDI  (diarrheal stool ≤ 6 a day) diagnosed via positive polymerase chain reaction 
(PCR) or enzyme immunoabsorbant assay (EIA) for toxin after two courses of 
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standard antibiotic treatment (including at least one course of either vancomycin or 
fidaxomicin).

The recipient has had at least two episodes of severe CDI (diarrhea stool > 6 a day) 
within 6 months resulting in hospitalization and associated with significant morbidity

The recipient has had moderate CDI (3-6 diarrheal stool not responding to 
successive standard therapy (e.g. metronidazole, vancomycin and/or fidaxomicin) 
lasting at least 28 days.

The recipient has severe and/or fulminant CDI with no response to standard therapy 
after 48 h.
iii.
A negative pregnancy test on day of FMT (female of childbearing age)
iv.
Recipient agrees to share medical records for FMT consultation at SBUMC
Exclusion (see Appendix A):
i.
Recipient age < 7 years of age.
ii.
Scheduled for abdominal surgery within the next 12 weeks
iii.
Pregnancy
iv.
Grade 4 anemia (Hemoglobin < 6 g/dL)
v.
Grade 1 neutropenia (Absolute Neutrophil Count <1500)
vi.
Known diagnosis of Graft vs. host disease
vii.
Major abdominal surgery within the past 3 months
viii.
Administration of any investigational drug within the past 2 months
ix.
Use of a TNF-α antagonist within 2 weeks of the proposed date of transplantation
x.
Bacteremia within past 4 weeks (28 days)
xi.
Recipients > 18 years of age unable or unwilling to give informed consent. The consent form will 
outline that although fecal microbiota transplantation appears safe based on past studies, a 
theoretical risk of transmission of an unrecognized infectious agent or substance exists and could 
result in an unexpected disease. For recipients with CDI and IBD, the consent form will outline that 
post FMT exacerbation of IBD has been reported in these patients.
b. Inclusion and exclusion criteria for recipients with Ulcerative colitis (UC) or indeterminate 
colitis (IC) without CDI who have required therapy beyond 5-ASA or mesalamine therapy alone 
         Inclusion: (see Appendix B) 
i.
Recipient age ≥ 7 years of age.
ii.
Recipients diagnosed with UC or IC by primary gastroenterologist as documented by 
colonoscopy, pathology and imaging findings based on review of medical records.
iii.
Recipients who have required therapy beyond 5-ASA or mesalamine therapy alone 
iv.
Recipient agrees to share medical records for FMT consultation at SBUMC
Exclusion: (see Appendix B)
i.
Recipient age < 7 years of age.
ii.
Scheduled for abdominal surgery within the next 12 weeks
iii.
Pregnancy
iv.
Grade 4 anemia (Hemoglobin < 6 g/dL)
v.
Grade 1 neutropenia (Absolute Neutrophil Count <1500)
vi.
Known diagnosis of Graft vs. host disease
vii.
Major abdominal surgery within the past 3 months
viii.
Administration of any investigational drug within the past 2 months
ix.
Use of a TNF-α antagonist within 2 weeks of the proposed date of transplantation
x.
Bacteremia within past 4 weeks (28 days)
xi.
Any previous FMT
c.
Inclusion and exclusion criteria for healthy donors for all three groups of recipients (CDI with 
and without IBD and UC and IC only without CDI).
Inclusion (see Appendix C): 
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i.
Spouses, parents, family members, friends, or associates of the stool recipient who consent to 
completing donor screening questionnaire 
ii.
Age ≥ 7 years of age 
iii.
Agree to undergo laboratory testing for known pathogens within 4 weeks of FMT procedure 
(screening tests listed below). 
Exclusion:
i.
Potential donors who answer “yes” to and one of the following donor screening 
questionnaire questions (see Appendix C):

Are you younger than 7 years of age?

Do you have known HIV, tuberculosis, Hepatitis B or Hepatitis C infections?

Have you been exposed to HIV, tuberculosis or viral hepatitis (within the past 12 months)

Do you engage in any high-risk sexual behaviors (examples: sexual contact with anyone 
with HIV/AIDS, tuberculosis or hepatitis or engage in sex for money?

Have you used illicit drugs within the past 3 months?

Have you had a tattoo or body piercing within the past 6 months?

Have you ever been incarcerated?

Have you been to an area with Mad Cow disease (risk factor for Creutzfeld-Jakob disease?)

Have you traveled within the past 3 months to developing countries?

Do you have a history of inflammatory bowel disease or chronic diarrhea (i.e. > 3 loose 
stools daily for the past 3 months?

Do you have a history of gastrointestinal malignancy or known polyposis?

Have you used systemic antibiotics within the preceding 3 months?

Are you currently using any major immunosuppressive medications (e.g. calcineurin 
inhibitors, systemic anti-neoplastic, exogenous glucocorticoids, biologic agents?)

Do you have eczema, allergies, or asthma requiring steroids or immunomodulating therapy?

Do you have autoimmune disease, metabolic syndrome, chronic pain syndrome, neurologic 
or developmental disorder?

Do you have contact with hospital patients?

Have you been hospitalized or in a long term care facility in the past 6 months?

Do you attend outpatient medical or surgical clinics more than once a month?

Have you engaged in medical tourism in the past 6 months?
ii.
Potential Donors who have positive laboratory testing for any one of the following tests :

C. difficile toxin B

Salmonella

Shigella

Campylobacter

Shiga toxin (screen for Sorbitol negative E. coli or E. coli O157-H7)

Vancomycin resistant enterococci (VRE)

Extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL)

Carbapenem-resistant Enterobacteriaceae (CRE)

Methicillin-resistant Staphylococcus aureus (MRSA)

Giardia antigen

Modified acid fast stain for Cryptosporidia, Cyclospora, Isospora

Ova and parasite (including trichrome)

HIV, type I and type II screen

Hepatitis A IgM

Hepatitis B (HepBs Ag, anti-HepB Core IgM)

Hepatitis C Ab

Syphilis RPR

Syphilis Fluorescent treponemal antibody FTA-ABS

Tuberculosis (QuantiFERON®-TB Gold)
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iii.
Donor reports having fever (T > 100.4 oF) within two weeks of FMT.
iv.
Donor reports of having a runny nose and cough within two weeks of FMT
v.
Donor reports ingesting foods that the recipient has an allergy to within one week of FMT
vi.
Donor reports having diarrhea within two weeks of FMT.
vii.
Donor stool appears grossly abnormal (e.g. presence of blood, etc) prior to processing for 
colonoscopic instillation. 
5.
Protocol for Recipient Involvement (CDI without IBD, CDI with IBD, UC or IC without CDI). (see 
Appendix D for flow sheet)
Pre-FMT events for recipient.
a.
Initial pre clinic visit screening of recipient eligibility. Recipients, families and referring physicians learn 
about the study through the ClinicalTrials.gov registry and have contacted by e-mail either the research 
coordinator, Dr. Chawla or Dr. Li for further information on ClinicalTrials.gov ID:NCT03268213, 
479696.  The research coordinator (or Drs. Li and Chawla) reply to the inquiry using a template e-mail 
that provides further information on the trial (see Appendix E).  Pre-screening of recipients is carried 
out by Drs. Chawla (recipients age <18 y) and Li (recipients age ≥18 y) after they have reviewed the 
recipients’ medical records to determine eligibility.  For recipients in the UC only without CDI group, 
Dr. Chawla or Dr. Li will contact the primary gastroenterologist to discuss whether the patient’s 
gastroenterologist feels that FMT is an appropriate intervention in this patient, discuss the 
possibility that the patient could flare post-FMT and to discuss whether the primary 
gastroenterologist agrees to clinically manage the patient’s IBD after FMT.  
If the recipient is deemed eligible for the study based on pre-screening, he/she or the guardians 
of the patient will be given the donor screening criteria (Appendix C) and asked to identify a potential 
donor. The donor is deemed eligible if he/she answers no to each question on the checklist. .The 
recipient and donor will then be scheduled to be seen for formal screening, including a physical exam 
in Adult or Pediatric GI clinic by either Dr. Li or Dr. Chawla, respectively.
b.
Screening and recruitment of recipient in clinic. The recipient will be evaluated and recruited in a face 
to face encounter with either Dr. Chawla or Dr. Li.  At this screening and recruitment clinic visit, 
additional baseline clinical data will be collected to confirm recipient eligibility (see Appendix F1/F2).  
The information will include past medical history in terms of previous episodes of C. difficile associated 
disease and/or inflammatory bowel diseases (age of diagnosis, duration, medications) and standard 
clinical information such as age, sex, race, disease phenotype, medications, and smoking history.  The 
recipient and family members will be instructed on how to prepare for the colonoscopy procedure. If 
they consent to provide research samples and dietary information, they will be instructed on how to 
collect the research stool samples, complete the daily food diary one week prior to the FMT samples, 
reminded to stop antibiotics 48 h before the procedure.  The colonoscopic FMT procedure will be 
scheduled with colonoscopists on the study team, so as to allow for donor screening results to be sent 
to the study team for review prior to the procedure.
c.
7 days before FMT- initiate recipient daily food diary: The recipients in all three groups will be asked to 
record their diet using a diary provided by the investigators, during the week that they provide stool 
samples (Appendix G). The purpose of this is to ensure that the donor does not ingest any foods that 
may be potentially allergenic to the recipient. The ingested foods may also impact the microbial load of 
the donor stool
d.
2-5 days before FMT-recipient instruction: The recipients will be contacted by phone to review study 
instructions. CDI recipients will be reminded again to stop antibiotics used to suppress CDI at least 48h 
before transplant (Appendix H).
e.
1 day before FMT - Collection of recipient pre-FMT research stool sample: The kits given to the recipient 
will include gloves, a commode specimen collection system, two specimen containers, biohazard bag 
and refrigerator packs to keep the stools cold during transport to the endoscopy suite.  One of the 
specimen containers will be empty and the second will be filled with 10 ml RNAlater (Qiagen), an RNA 
stabilization solution, to better improve recovery of bacterial and human nucleic acids during the 
transport period.  
f.
1 day before FMT- Recipient bowel prep for colonoscopy:  The stool recipient will be reminded about 
instructions for a bowel prep based on the patient’s weight. Participants and/or guardians will be told 
that in order to properly visualize their intestines, they must be “prepped” or flushed of their contents.  
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These medications will cause diarrhea which is the desired effect.  The recipient should be in an area 
with easy access to the bathroom when the medication is given.  The goal is to be passing clear fluid 
without any formed stool.  The recipients will be told to call the study coordinator if this does not occur, 
so that it can be determined whether any additional medications are necessary for preparation.  Once 
the prep has begun, the recipient will be told to be on a diet consisting of clear liquids only.  
Clear liquids are those that they can see through and they will be told to avoid red, orange or 
purple liquids.  Acceptable liquids include water, ginger ale, chicken broth (no chicken or noodles), 
apple juice, Pedialyte, or jello.  For the last 7 hours prior to the procedure, the recipient should 
have nothing to eat or drink.  Medications may be taken with a very small amount of water. The colon 
cleanout prep will be determined by the patient’s gastroenterologist. The recipient should be passing 
clear stools by 5 PM day before FMT. If the recipient is not passing loose to watery clear stools by this 
time, they will be told to call the study coordinator or principal investigator.
Day of colonoscopic FMT for recipient.
g.
Day of FMT, undergoing colonoscopic FMT and having research blood sample drawn in SBUMC 
Endoscopy unit.  
Pre-procedure. The recipient is consented for colonoscopy by the colonoscopist performing the 
procedure in the pre-procedure area of the Endoscopy Suite.  Female recipients of child bearing age 
will undergo poc urine pregnancy test, and if positive the procedure will be aborted. Research blood 
samples (total 20 ml) will be collected either during insertion of the IV in the pre-procedure area, or 
drawn separately shortly after the procedure, while the patient is still sedated.  
Procedure. The colonoscopist will record the appearance of the colon to the terminal ileum. In recipients 
with UC (with or without CDI), the colonoscopist will assign a Mayo endoscopic subscore (0-3, see 
Appendix I) based on the appearance of the worst affected mucosa in the rectosigmoid area. Upon 
reaching the ileum or the cecum, the donor stool (50-100 g in 250 to 300 ml of sterile saline, see below 
for standard operative procedure for preparing stool infusate), will be infused into the ileum and/or the 
cecum.   No other colonoscopic intervention (e.g. biopsy or polypectomy) will performed during the 
procedure.  If there is a colonoscopic finding that the colonoscopist feels needs to be immediately 
addressed for clinical care by a therapeutic intervention including biopsy, then the FMT will be aborted 
and the stool infusate will not be administered.  
h.
Post procedure. The recipient will be placed in the right lateral decubitus position and monitored for at 
least an hour in the post procedure area of the Endoscopy suite, prior to discharge.  The recipient will 
be instructed on collection of the 1 wk and 12 wk post-FMT research stool samples, and be given the 
stool collection kits to bring home after discharge from the Endoscopy suite. Each recipient will receive 
a diary card (Appendix J) where he/she or the recipient’s guardian will note when the stool recipient 
experiences a new symptom or exacerbation of current symptoms. This diary card will be reviewed 
during the followed up phone calls.
Post-FMT events for recipient.
i.
1 day post-FMT. The recipient and/or guardian are contacted by phone by the study team in order to 
complete the Day after Transplant Case Report Form (see Appendix K).   
1st week post-FMT collection of recipient food diary and 1 wk post-FMT research stool sample. The 
recipient/family will complete a one week daily food diary during the week post-transplant and collect 
the 1 wk-post FMT research stool sample which will be shipped overnight in refrigerator packs to Dr. 
Li’s research lab.  
j.
1 week to 12 weeks post FMT. - weekly phone follow up of recipient. The recipient and/or recipient’s 
(pediatric recipient) guardian are contacted by phone by the study team weekly during the first 12 weeks 
post-FMT to complete the Follow up Phone Call/Adverse Event Form (Appendix L1 for CDI recipient 
without IBD, Appendix L2 for UC or IC recipient with or without CDI).  The forms contain a prompt to 
inform the Principal Investigator of any adverse events. Patients will be triaged to either the Emergency 
Department or to Adult or Pediatric Gastroenterology Clinic if any concerning adverse events occur. 
Any serious adverse events (Grades 3,4,5) will be documented (Appendix L), evaluated by the Principal 
Investigator and reported immediately to IRB as well as Safety Monitoring Committee.
k.
12 week post-FMT - collection of recipient food diary and 12 week post-FMT research stool sample.  . 
The recipient/family will complete a one week daily food diary during the week post-transplant and 
collect the 12 wk-post FMT research stool sample which will be shipped overnight in refrigerator packs 
to Dr. Li’s research lab.  
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l.
3-4 mo post FMT flexible sigmoidoscopy.  If the primary gastroenterologist caring for the patient, 
schedules the patient for a follow up flexible sigmoidoscopy, we will request that the colonoscopist 
obtain a Mayo endoscopic subscore during the procedure.
m. 4 mo to 12 mo post-FMT – monthly phone call follow up of recipient. The recipient and/or recipient’s 
(pediatric recipient) guardian are contacted by phone by the study team monthly between 4 and 12 
months post-FMT to complete the Follow up Phone Call/Adverse Event Form (Appendix L1 for CDI 
recipient without IBD  Appendix L2 for UC or IC recipient with or without CDI). Any serious adverse 
events (Grades 3,4,5) will be documented (Appendix M), evaluated by the Principal Investigator and 
reported immediately to IRB as well as Safety Monitoring Committee.
6.
Protocol for Donor Involvement. (See Appendix D for flow sheet)
Pre-FMT events for donor.
a.
Screening and recruitment of potential donor in clinic.  Once the recipient has been entered into the 
study, the recipient will identify the donor. If the donor is age > 18 y will be screened and evaluated 
by Dr. Li in the Adult Gastroenterology Clinic (see Research Site, section D.3) with a complete history 
and physical to ascertain eligibility. If the donor is age ≥7 y and ≤18 y, the donor will be screened and 
evaluated by Dr. Chawla in the Pediatric Gastroenterology Clinic (see Research Site, section D.3) 
with a complete history and physical to ascertain eligibility.  The donor will be consented to participate 
in the study, which requires undergoing stool and serological testing to assess for infectious 
pathogens that may theoretically be passed from the donor to the recipient. The donor (as well as the 
recipient) will sign an acknowledgement form that if medical insurance does not cover the costs of 
these tests, the costs of the donor screening tests will be borne by the recipient or donor (Appendix 
N).  (The study team is in the process of applying for research grant funding that will cover the costs 
of donor screening for pathogens, but currently there are no research funds available to cover these 
costs). Once the donor has consented to the study, the donor will be instructed on collecting the stool 
to be used for the transplant, completing the one week food diary prior to providing the sample.  Dr. 
Li or Dr. Chawla will order the following laboratory tests for the donor to complete before the 
colonoscopic FMT is performed:
Stool tests:

C. difficile toxin PCR (CPT 87493) 

Routine stool culture screen (CPT 87046) - includes Salmonella, Shigella, Campylobacter, 
Sorbitol negative E. coli or E. coli O157-H7 (Shiga toxin)

Giardia Ag EIA (CPT 87328)

Modified acid fast stain of stool (CPT 87015/87207) Cryptosporidia, Cyclospora, 

Ova and parasite with trichrome (CPT 87177) includes Isospora

Vancomycin-resistant enterococci (VRE), (CPT 87081)

Extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL), (CPT 87184)

Carbapenem-resistant Enterobacteriaceae (CRE) ,(CPT 87081)

Methicillin-resistant Staphylococcus aureus (MRSA), (CPT 87081)
Blood tests:

HIV type 1 and type 2 screen (CPT 86701/86702)

Acute Viral Hepatitis Panel: Hepatitis A IgM, Hepatitis Bs Ag, Hepatitis Bc IgM, Hepatitis C Ab 
(CPT 80074)

Syphilis Rapid Plasma Reagin or RPR (CPT 86592) 

Fluorescence Treponemal Ab or FTA-Abs (CPT 86781)

Tuberculosis (QuantiFERON®-TB Gold) (CPT 86480)
The laboratory test results must be dated within 4 weeks of the day the colonoscopic FMT is 
performed.  The investigators are in the process of applying for grant support in order to cover the 
costs of donor screening, since this is not universally covered by medical insurance.
If the donor tests positive for a potential pathogen, Dr. Li or Dr. Chawla will inform the donor of 
the test results and will ask for the contact information for the donor’s PCP to forward the test results 
to.  The donor will be counseled to follow up with PCP to discuss the test results and the need for any 
further testing or treatment.
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b.
7 days before FMT - initiate donor daily food diary. The donor will initiate recording daily food diary 
and avoid ingesting any foods the recipient is allergic to.
c.
2-5 days before FMT – donor instructions.  The study team will contact the donor by phone to check 
that the donor has initiated the daily food diary, has not been febrile T > 100.4o F within 2 weeks of 
the procedure, and has avoided ingesting any of the recipient’s food allergens during the week prior 
to the transplant (see Appendix O).
d.
1-day before FMT – initiate collection of donor stool.  The donor will have been given two stool 
collection kits at the initial clinic visit.  The donor is instructed to collect one stool within 24 h before 
the procedure and to keep the stool refrigerated with the refrigerator packs.  If possible, the donor is 
instructed to collect a stool within 6 h before the procedure and kept the second stool refrigerated 
with the refrigerator packs.  The donor will also have been instructed to aliquot research stool samples 
at both time points into specimen jars, one plain and the other filled with 10 ml of RNAlater as 
described for the recipient in section D.5.e.  The donor is instructed to bring, or have the recipient 
bring both stool samples to the Endoscopy Suite for the research team to pick up 2 h before the FMT 
procedure is scheduled.
e.
Day of FMT. – Collection and evaluation of donor stool
Preprocedure. The donor (or the recipient on behalf of the donor) will deliver the stools to the 
Endoscopy Suite for the research study team to pick up and process 2 h before the FMT procedure.  
The study team will complete Day of Transplant Donor Checklist Form (Appendix P) either face to 
face or by phone contact with the donor, to make sure no donor exclusions apply, prior to processing 
the stool to prepare the stool infusate, as described in the next section. 
ii.
Protocol for preparation of donor stool infusate for colonoscopic infusion. 
The donor stool (refrigerated not frozen) is transported by the study team to Dr. Li’s laboratory and 
processed for infusion via colonoscopy following standard operating procedures as previously 
described:44

Stool preparation will occur in the biological safety hood

Universal precautions will be adhered to. Those involved with mixing and/or handling the fecal 
transfusion material will wear a fluid-resistant gown, gloves, and mask with goggles, or eye shield 

Donor stool will be transferred to a single-use disposable container

Preservative-free normal saline (250-500 mL) at room temperature will be used to dilute the stool 
sample until it reaches a liquid slurry consistency

The stool slurry will then be filtered to remove as much particulate matter as possible. This will be 
accomplished using gauze pads lining the inside portion of a plastic disposable funnel

The filtered stool slurry will be divided into aliquots of 50 mL and will be used within an hour of 
preparation
iii.
Protocol for Processing and Analysis of Recipient and Donor Samples: As noted in sections 4 
and 5, blood and stool samples may be collected from the recipient and from the donor for further 
analysis.  Those recipients and donors who have agreed to provide clinical data, blood and stool 
samples are consented under a separate consent under a separate IRB ((IRB net ID: 163184-15) for 
collection and storage of samples within the Stony Brook GI satellite Biobank, which operates as a 
module under the Stony Brook Biobank New York State License for Biobanking.  The clinical data, 
stripped of patient health identifiers, will be assigned a patient ID and a visit ID and will be stored in 
the Stony Brook University Digestive Diseases Research Tissue Procurement Facility clinical 
database.  The patient samples will also be stripped of patient health identifiers and assigned a 
patient ID, visit ID and sample ID and will be archived within the Stony Brook University GI Biobank.  
The analysis of the samples and downstream products will including the following:
a.
Genotyping for IBD risk alleles.  DNA will be extracted from peripheral mononuclear blood cells 
(in blood) as previously described in Dr. Li’s laboratory.43  The DNA will be assigned the same 
patient ID, visit ID and sample ID from the original sample.  We have used Taqman PCR assays, 
Sequenom, and array methods for analyzing genotypes thus far, but the technology is rapidly 
evolving.22 We will seek the most cost effective means of obtaining accurate genotyping of 
established IBD risk alleles. If we submit the samples for genotyping at another facility, each of 
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these samples will be assigned another sample ID, to further protect the privacy of the subjects, 
prior to shipping these samples to an outside facility.
b.
16S rRNA sequencing. 16S rRNA sequencing will provide a first tier of microbiome surveillance 
and will measure taxa based microbial diversity and composition.43 This may involve shipping 
stool DNA to outside facilities for library construction and sequencing (University of Colorado).  If 
we submit these DNA samples to outside institutions for analysis, each of these samples will be 
assigned another sample ID, to further protect the privacy of the subjects, prior to submission of 
these samples to an outside facility.  For all rRNA sequence datasets, we routinely screen for 
and remove contaminating human DNA/RNA sequences by use of bowtie2 read-mapping 
software; thus, no human sequences will be analyzed beyond this step or will be included in 
public repositories.  We propose to measure the alterations in microbial diversity and composition 
before and after fecal microbial transplantation.  
c.
Targeted qPCR sequencing. To detect targeted microbial taxa and functions we will utilize 
targeted qPCR and reverse transcriptase qPCR. These analyses will be carried out in Dr. Li’s 
and Dr. Gathungu’s laboratory.46  
d.
Fecal calprotectin. Fecal calprotectin is a marker of intestinal inflammation that will complement 
the colonoscopic scores and patient questionnaires.  We propose to measure fecal calprotectin 
in each of the collected stools using the PhiCal commercial ELISA kit (CALPRO, Oslo, Norway) 
according to the manufacturer’s instructions within Dr. Li’s laboratory. Frozen stools archived at
 -80oC will be batch extracted and analyzed along with the manufacturer’s control to avoid 
interassay variability.
e.
Shotgun metagenomics, bacterial metatranscriptomics, fecal metabolomics, fecal proteomic.  We 
propose to conduct multiple omic studies on microbial function using the collected stool samples 
if we are successful in obtaining outside funding to support these studies.  This may require 
sending aliquots of samples or their downstream products to other institutions for analysis.  If so, 
the samples will be assigned another sample ID to further protect the privacy of the subjects 
before shipping these samples out to other institutions.  For all meta-omic sequence datasets, 
we routinely screen for and remove contaminating human DNA/RNA sequences by use of 
bowtie2 read-mapping software; thus, no human sequences will be analyzed beyond this step or 
will be included in public repositories.
E.  STATISTICS:
The number of patients enrolled will not be limited since a primary goal of this study is to establish safety, 
tolerability and efficacy of FMT.  It is anticipated that data from 80 FMTs with a balanced design of 20 FMTs 
performed on each of the following four groups of recipients (CDI without IBD, CDI with UC, CDI with CD, and 
UC without CDI) associated with this IRB protocol (ClinicalTrials.gov ID:NCT03268213, 479696, IND for UC only 
15642), in combination with data from 20 FMTs performed on CD without CDI recipients recruited through a 
sister protocol (IRB 973349-5, ClinicalTrials.Gov ID NCT03267238, IND16795) will be needed to generate a 
power analysis on the multi-omic datasets.  A linear mixed model will used to compare alpha-diversity 
(ShannonH) and beta-diversity (Bray-Curtis and Jaccard distance) between each time point (donor, pre-FMT, 1 
week and 3 month post-FMT) and each disease group as previously described.46  The two-way interaction term, 
Group*FMT, will be used to estimate the differences between any two time points within a specific disease group. 
Covariance structure to model correlation among measurements from the same patient and his/her 
corresponding donor will be selected based on Akaike Information Criteria (AIC).  Possible covariance structures 
to model correlation among longitudinal measurement from the same patient and measurement in the 
corresponding donor included unstructured (UN), compound symmetry (CS), Toeplitz (TOEP), Heterogeneous 
CS (CSH) and Heterogeneous TOEP (HTOEP). Using the two-way interaction term between Group and FMT, 
generalized linear mixed models (GLMMIX) will be used to examine the possible change in individual OTU 
relative abundance after FMT in recipients and such difference between recipient and donor over time. The 
actual counts of each OTU will be assumed to follow a negative binomial distribution.47 The log-transformed 
overall sequence count for each individual at each time point will be considered as an offset. In case that there 
is model converging issue GLMMIX, generalized estimating equation (GEE) will be used. In GEE, the 
dependence structure was chosen based on Quasi Information Criteria (QIC). The p-values from comparison 
analysis of all OTUs will adjusted for multiple comparisons by the Bonferroni correction or by the Benjamin-
Hochberg method (FDR < 0.05). Principal coordinate analyses will be carried out using the R package vegan. 
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Similar models will be used to examine the difference in the expression level of a specific gene or protein 
based on metatranscriptomic data and metabolomic data between recipient and donor and the change in such 
difference over time.  Beyond analysis of individual data-types integr-omic analyses that combine all data types 
(i.e. metabolomics, microbiome, and clinical) will rely on the use of Similarity Network Fusion,47 which performs 
unsupervised clustering of patients based on each datatype and then fuses the obtained networks, strengthening 
links in complementary networks. These analyses will reveal the relationships among taxonomic composition, 
microbiome diversity and function and metabolomics which implies the mechanism how FMT works. All analysis 
will be performed in SAS 9.4 (SAS institute Inc., Cary, NC) and R 3.4.0 (R Foundation for Statistical Computing, 
Vienna, Austria).
F. FUNDING STATUS, DETAILS:
There is currently no funding for the procedure or evaluation of the recipient and donors in clinic, or the laboratory 
screening of the donor.  The Simons Foundation Award is currently used to cover the costs of processing, 
sequencing and analysis of stool and blood samples.  
G.  HUMAN SUBJECTS RESEARCH PROTECTION FROM RISK
1.
Risk to Subjects: 
The risks to the recipient and the donor are described separately.
a.
Risk to recipient.
i.
Risk of recipient undergoing colonoscopy. The risks associated with the colonoscopy are infection, 
bleeding, and < 0.1% chance of perforation, which may require surgery. Additionally, there are risks 
associated with receiving anesthesia during colonoscopy including anaphylaxis, aspiration and 
respiratory distress.
ii.
Risk of undergoing FMT in recipient with recurrent CDI without IBD.    
Risks to FMT include 
bloating/flatulence, abdominal pain/cramping, diarrhea, blood in the stool, fatigue, and fever.  
iii.
Risk of undergoing FMT in recipient with recurrent CDI with IBD. Risks to FMT include 
bloating/flatulence, abdominal pain/cramping, diarrhea, blood in the stool, fatigue, and fever.  In 
addition, there is a risk that even if the C. difficile is treated that there may be exacerbation of the 
underlying IBD.25
iv.
Risk of undergoing FMT in recipient with UC or IC without CDI. Risks to FMT include 
bloating/flatulence, abdominal pain/cramping, diarrhea, blood in the stool, fatigue, and fever.  In 
addition, there is a risk that there may be continued progression or exacerbation of the underlying 
IBD.25
v.
Collection of stool and blood from recipient. These are minimally invasive procedures.  The risks of 
collecting blood are infection at the site of needle stick and bruising.
vi.
Risk of collecting recipient clinical data.  There is an extremely rare possibility that the patient data 
can be shared in a way that identifies the recipient. Great lengths will be made to restrict access to 
patient and sample codes.
b.
Risk to donor
i.
Collection of stool from recipient. This is minimally invasive procedure.  
ii.
Risk of collecting recipient clinical data.  There is an extremely rare possibility that the clinical data 
can be shared in a way that identifies the donor. Great lengths will be made to restrict access to 
patient and sample codes.
2.
Adequacy of Protection Against Risks:
The clinical data and stool samples will be stripped of patient health identifiers and assigned a patient code 
and sample code.  The subject’s participation will end after the collection of stool and clinical data is completed 
1 year after enrollment in the study. We are only requesting that we be able to collect clinical metadata by 
prospective questionnaires and reviewing the medical records, and to collect recipient fecal and blood samples 
before FMT and after FMT.  The consents will be obtained by the physicians or research staff, who have been 
trained in good clinical practices and are highly experienced in providing and obtaining informed consent in this 
patient population.
Additionally, all recipients will have adverse event monitoring as outlined below:
Day of fecal microbiota transplantation:
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a. During the colonoscopy procedure: an anesthesiologist will be assigned to the recipient and the 
endoscopy unit will have full-code preparedness
b. Post colonoscopy procedure: the recipient will be monitored in the post-operative area of the 
endoscopy suite for one hour by continuous monitoring
Post fecal microbial transplantation
The study team will closely monitor the recipient by phone call and an algorithm will be attached to the 
checklist to refer patients to either clinic or the Emergency Department if necessary.
a. 1 day post-transplant: The transplant recipient will receive a phone call the day after the procedure 
and questions will be asked from a standardized checklist containing the following items:
i. General well being
ii. Presence of abdominal pain
iii. Presence of temperature greater than 100.4 degrees Fahrenheit 
iv. Presence of diarrhea (loose, watery stools) or blood in the stool
v. Presence of new rash
b. Weekly monitoring 1-12 weeks post transplant: All recipients will have weekly monitoring via telephone 
call for 12 weeks. This will include the following additional questions:
i. Has diarrhea stopped or improved?
ii. If the diarrhea had stopped, is there a recurrence of diarrhea?
iii. If the diarrhea has not improved, have you tried other treatments?
iv. Has there been any need of antibiotics since the transplant?
v. Did any medical condition you had before your fecal transplant go away after your fecal transplant?   
(for example, arthritis and chronic skin rash)
vi. Has abdominal pain if present prior to fecal microbiota transplant resolved?
vii. Have you developed any new medical conditions since the fecal transplant?
c.
Monthly monitoring 4-12 months post transplant: All recipients will have monthly monitoring via 
telephone call between 4 and 12 months after the first twelve weeks.
d.
Recipients and/or their guardians will be advised to call either the Pediatric Gastroenterology or Adult 
Gastroenterology offices for any questions or health related concerns for up to 1 year post-transplant.
e.
The study team will meet with Drs. Chawla and Li on a monthly basis (last Wednesday of every 
month) to review follow up phone calls.
3.
Potential Benefits of Proposed Research to the Subjects and Others:
The potential benefits of having the fecal transplantation for treatment of recurrent or refractory CDI not 
responsive to standard medical therapy is prevention of recurrent CDI.  
The potential benefits of having the fecal transplantation for treatment of recurrent or refractory CDI not 
responsive to standard medical therapy, in addition to prevention of recurrent CDI is improvement in their IBD 
symptoms.
The potential benefits of having the fecal transplantation for treatment of UC or IC without CDI is 
improvement in their IBD symptoms.
Conducting research on these samples, including the research proposed in this application may create new 
tests, treatments, or cures. If it does the subjects (recipients or donors) who have donated samples will not 
receive any money from those products.
4.
Importance of the Knowledge to be Gained:
This study will enable us to contribute to the literature regarding the safety, efficacy, and tolerability of fecal 
microbiota transplantation. Additionally, by collecting well phenotyped linked samples, future integrations of the 
microbiome data not only with phenotype but also with genetic data and metabolomics data will be possible. 
This will enable further studies investigating the mechanism(s) by which gut bacteria can affect susceptibility to 
medication refractory Clostridium difficile and/or ulcerative colitis or indeterminate colitis.
H.   SAFETY MONITORING COMMITTEE (for more than minimal risk studies):
A safety monitoring committee (SMC) has been established and is composed of the three following experts:
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a) Sharon Nachman, M.D., Chair of Safety Monitoring Committee, Professor of Pediatrics, Chief, Division 
of Infectious Diseases, Stony Brook University School of Medicine. Expertise in clinical trials.
b) Roy Steigbigel, M.D., Professor of Medicine, Pathology, Pharmacology and Microbiology, Division of 
Infectious Diseases, Stony Brook University School of Medicine. Expertise in infectious diseases. 
c)
Matthew Ciorba, M.D., Associate Professor of Medicine, Director of Research in the IBD Program 
Division of Gastroenterology and Hepatology, Washington University School of Medicine. Clinical and 
research expertise in the microbiome in inflammatory bowel diseases and colon cancer.
The committee will be asked to perform an interim assessment of safety 4 weeks after every ten subjects are 
enrolled in the study and undergo fecal transplant. This will help in determining whether or not this study protocol 
should continue to be implemented or requires modifications.
Adverse events (AE) will be recorded by follow up phone calls as per the following grading (Division of 
AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events:50
 
Grade 1 Mild; asymptomatic or mild symptoms; clinical or diagnostic observations only; intervention not 
indicated.
Grade 2 Moderate; minimal, local or noninvasive intervention indicated; limiting age-appropriate 
instrumental Activities of Daily Living (ADL). 
Grade 3 Severe or medically significant but not immediately life-threatening; hospitalization or 
prolongation of hospitalization indicated; disabling; limiting self-care ADL. 
Grade 4 Life-threatening consequences; urgent intervention indicated. 
Grade 5 Death related to AE.
Grades 3, 4 and Grade 5 adverse events will trigger the team to request a safety monitoring committee 
review of the data and pause further enrollment.
Adverse events will be recorded when follow-up phone calls are made. Intensity and relationship of adverse 
events with FMT will be described using Common Terminology Criteria for Adverse Events (CTCAE version 4.0) 
and Toxicity Grading Guidance from Vaccine Clinical Trials (U.S. Food and Drug Administration, September 
2008). 
Four weeks after every 10th subject’s enrollment and completion of fecal transplant a cumulative report will be 
submitted to SMC for formal review. SMC will have 1 week to respond. During this period there will be a safety 
hold for the Ulcerative colitis subjects. If no issues are identified, the study will be reopened and further enrollment 
will be allowed. 
After the data on the next 10 subjects have been reviewed by SMC and no concerns are raised, the hold period 
will no longer be necessary.
Principal investigator may request an ad hoc SMC review if needed at any time point.
There will be no safety hold on enrollment of Clostridium difficile subjects for FMT procedure as this procedure 
has been widely accepted in the medical field and comparable to standard of care procedures for refractory 
Clostridium difficile. FDA does not require an IND status for FMT treatment of refractory C. Difficile.  The 
committee may also require changes to the protocol to ameliorate the safety concerns that pose significant risk 
to stool recipients. In the absence of protocol changes, the SMC must follow the protocol-specified stopping 
rules.
I.  LITERATURE CITED:
1.
Hopkins MJ, MacFarlane GT. Changes in predominant bacterial populations in human faeces with age 
and with Clostridium difficile infection. J Med Microbiol 2001; 51:448-454. 
2.
Chang JY, Antonopoulos DA, Kalra A, et al. Decreased diversity of the fecal microbiome in recurrent 
Clostridium difficile-associated diarrhea. J Infect Dis 2008; 197:435-438.
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3.
Bouza E. Consequences of Clostridium difficile infection: understanding the healthcare burden. Clin 
Microbiol Infect. Suppl 2012; 6:5-12.
4.
Kassam Z, Lee CH, Yuan Y, et al. Fecal microbiota transplantation for Clostridium difficile infection: 
systematic review and meta-analysis. Am J Gastroenterol 2013; 108:500-508.
5.
Pant C, Despande A, Altaf M, et al. Clostridium difficile infection in children: a comprehensive review. 
Curr Med Res Opin. 2013; 29:967-84. 
6.
Louie TJ, Miller MA, Mullane KM, et al. Fidaxomicin versus vancomycin for Clostridium difficile infection. 
N Eng J Med 2011; 364:422-431.
7.
Lancaster JW, Matthews SJ. Fidaxomicin: The newest addition to the armamentarium against Clostridium 
difficile infections. Clin Ther 2012; 34:1-13.
8.
Garey KW, Sethi S, Yadav Y, DuPont HL. Meta-analysis to assess risk factors for recurrent Clostridium 
difficile infection. J Hosp Infect. 2008;70:298-304. 
9.
Johnson S. Recurrent Clostridium difficile infection: a review of risk factors, treatments, and outcomes. 
The Journal of infection. 2009;58:403-10.
10. McFarland LV, Elmer GW, Surawicz CM. Breaking the cycle: treatment strategies for 163 cases of 
recurrent Clostridium difficile disease. Am J Gastroenterol. 2002;97:1769-75.
11. Olsen MA, Yan Y, Reske KA, Zilberberg MD, Dubberke ER. Recurrent Clostridium difficile infection is 
associated with increased mortality. Clin Microbiol Infect. 2015;21:164-70. 
12. Kelly CR, Khoruts A, Staley C, et al. Effect of Fecal Microbiota Transplantation on Recurrence in Multiply 
Recurrent Clostridium difficile Infection: A Randomized Trial. Ann Intern Med. 2016;165:609-616. 
13. Mattila E, Uusitalo-Seppala R, et al. Fecal transplantation, through colonoscopy, is effective therapy for 
recurrent Clostridium difficile infection. Gastroenterology. 2012;14:490-6
14. Cammarota G, Ianiro G, Tilg H, et al. European consensus conference on faecal microbiota transplantation 
in clinical practice. Gut. 2017;66(4):569-80. 
15.
Rodemann JF, Dubberke ER, Reske KA, Seo DH, Stone CD. Incidence of Clostridium difficile infection 
in inflammatory bowel disease. Clin Gastroenterol Hepatol. 2007;5:339-44.
16. Issa M, Vijayapal A, Graham MB, et al. Impact of Clostridium difficile on inflammatory bowel disease. Clin 
Gastroenterol Hepatol. 2007;5:345-51.
17. Ananthakrishnan AN, Binion DG. Impact of Clostridium difficile on inflammatory bowel disease. Expert Rev 
Gastroenterol Hepatol. 2010;4:589-600. 
18.
Pascarella F, Martinelli M, Miele E, et al.  Impact of Clostridium difficile infection on pediatric inflammatory 
bowel disease. J Pediatr. 2009;154:854-8. 
19. Martinelli M, Strisciuglio C, Veres G, et al. Clostridium difficile and pediatric inflammatory bowel disease: a 
prospective, comparative, multicenter, ESPGHAN study. Inflamm Bowel Dis. 2014;20:2219-25. 
20. Saffouri G, Gupta A, Loftus EV, Jr., et al. The incidence and outcomes from Clostridium difficile infection 
in hospitalized adults with inflammatory bowel disease. Scand J Gastroenterol. 2017;52:1240-1247. 
21. Hourigan SK, Chen LA, Grigoryan Z, et al. Microbiome changes associated with sustained eradication of 
Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory 
bowel disease. Aliment Pharmacol Ther. 2015;42:741-52. 
22. Fischer M, Kao D, Kelly C, et al. Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or 
Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis. 
2016;22:2402-9. 
23. Khoruts A, Rank KM, Newman KM, et al. Inflammatory Bowel Disease Affects the Outcome of Fecal 
Microbiota Transplantation for Recurrent Clostridium difficile Infection. Clin Gastroenterol Hepatol. 
2016;14:1433-8. 
24. Newman KM, Rank KM, Vaughn BP, et al. Treatment of recurrent Clostridium difficile infection using fecal 
microbiota transplantation in patients with inflammatory bowel disease. Gut Microbes. 2017;8:303-309.
25. Qazi T, Amaratunga T, Barnes EL, et al. The risk of inflammatory bowel disease flares after fecal 
microbiota transplantation: Systematic review and meta-analysis. Gut Microbes. 2017;8:574-588.
26. Jacob V, Crawford C, Cohen-Mekelburg S, et al. Single Delivery of High-Diversity Fecal Microbiota 
Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative 
Colitis. Inflamm Bowel Dis. 2017;23:903-11. 
27. Kump PK, Grochenig HP, 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;19:2155-65. 
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
16
28. Kump P, Wurm P, Grochenig HP, et al. The taxonomic composition of the donor intestinal microbiota is a 
major factor influencing the efficacy of faecal microbiota transplantation in therapy refractory ulcerative 
colitis. Aliment Pharmacol Ther. 2018;47:67-77. 
29. Kunde S, Pham A, Bonczyk S, et al. Safety, tolerability, and clinical response after fecal transplantation in 
children and young adults with ulcerative colitis. J Pediatr Gastroenterol Nutr. 2013;56:597-601. 
30. Michail S. Fecal Microbial Transplant In Children With Ulcerative Colitis: A Randomized, Double-Blinded, 
Placebo-Controlled Pilot Study. J Pediatr Gastroenterol Nutr. 2017. 
31. Mizuno S, Nanki K, Matsuoka K, et al. Single fecal microbiota transplantation failed to change intestinal 
microbiota and had limited effectiveness against ulcerative colitis in Japanese patients. Intest Res. 
2017;15:68-74. 
32. Moayyedi P, Surette MG, Kim PT, et al. Fecal Microbiota Transplantation Induces Remission in Patients 
With Active Ulcerative Colitis in a Randomized Controlled Trial. Gastroenterology. 2015;149:102-9 
33. Nishida A, Imaeda H, Ohno M, et al. Efficacy and safety of single fecal microbiota transplantation for 
Japanese patients with mild to moderately active ulcerative colitis. J Gastroenterol. 2017;52(4):476-82. 
34. Paramsothy S, Kamm MA, Kaakoush NO, et al. Multidonor intensive faecal microbiota transplantation for 
active ulcerative colitis: a randomised placebo-controlled trial. Lancet. 2017;389:1218-28. 
35. Rossen NG, Fuentes S, van der Spek MJ, et al. Findings From a Randomized Controlled Trial of Fecal 
Transplantation for Patients With Ulcerative Colitis. Gastroenterology. 2015;149:110-8 
36. Suskind DL, Singh N, Nielson H, Wahbeh G. Fecal microbial transplant via nasogastric tube for active 
pediatric ulcerative colitis. J Pediatr Gastroenterol Nutr. 2015;60:27-9. 
37. Uygun A, Ozturk K, Demirci H, et al. Fecal microbiota transplantation is a rescue treatment modality for 
refractory ulcerative colitis. Medicine (Baltimore). 2017;96:e6479. 
38. Vermeire S, Joossens M, Verbeke K, et al. Donor Species Richness Determines Faecal Microbiota 
Transplantation Success in Inflammatory Bowel Disease. J Crohns Colitis. 2016;10:387-94. 
39. Hirsch BE, Saraiya N, Poeth K, et al. Effectiveness of fecal-derived microbiota transfer using orally 
administered capsules for recurrent Clostridium difficile infection. BMC Infect Dis. 2015;15:191.
40. Youngster I, Mahabamunuge J, Systrom HK, et al. Oral, frozen fecal microbiota transplant (FMT) 
capsules for recurrent Clostridium difficile infection. BMC Med. 2016;14:134.
41. Kao D, Roach B, Silva M, et al. Effect of Oral Capsule- vs Colonoscopy-Delivered Fecal Microbiota 
Transplantation on Recurrent Clostridium difficile Infection: A Randomized Clinical Trial. JAMA. 
2017;318:1985-1993.
42. Ott SJ, Waetzig GH, Rehman A, et al. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With 
Clostridium difficile Infection. Gastroenterology. 2017;152:799-811
43. Li E, Hamm CM, Gulati AS, et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 
genotype are associated with shifts in human ileum associated microbial composition. PLoS One. 
2012;7:e26284.
44. Bakken JS, Borody T, Brandt LJ, et al. Treating Clostridium difficile infection with fecal microbiota 
transplantation. Clin Gastroenterol Hepatol. 2011;9:1044-9.
45. https://www.fda.gov/downloads/biologicsbloodvaccines/guidancecomplianceregulatoryinformation/guidan
ces/vaccines/ucm488223.pdf
46. Shim JO. Clostridium difficile in Children: To Treat or Not to Treat? Pediatr Gastroenterol Hepatol Nutr. 
2014; 17: 80–84.
47. Zhang Y, Rowehl L, Krumsiek JM, et al. Identification of Candidate Adherent-Invasive E. coli Signature 
Transcripts by Genomic/Transcriptomic Analysis. PLoS One. 2015;10:e0130902.
48. Mintz M, Khair S, Grewel S, et al. Longitudinal microbiome analysis of single donor fecal microbiota 
transplantation in patients with recurrent Clostridium difficile infection and/or ulcerative colitis. PLoS ONE, 
in press.
49. Son JS, Khair S, Pettet DW 3rd, et al. Altered Interactions between the Gut Microbiome and Colonic 
Mucosa Precede Polyposis in APCMin/+ Mice. PLoS One. 2015;10:e0127985.
50. Wang B, Mezlini AM, Demir F, et al. Similarity network fusion for aggregating data types on a genomic 
scale. Nat Methods. 2014; 11: 333-7.
51. https://rsc.tech-res.com/docs/default-source/safety/daids_ae_grading_table_v2_nov2014.pdf
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

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APPENDIX A  
Stool Recipient Screening Questionnaire (C. difficile)
 with or without IBD
Recipient Name:______________________
Date:___________
Inclusion: Recipient is deemed eligible if any one of the following criteria are met:
___   Patient is 7 years of age or older with at least two recurrences (total three CDI infections) of mild 
to moderate C. difficile (<6 diarrheal stools/day) diagnosed by positive toxin PCR or EIA after 
completing standard medical therapy with metronidazole, vancomycin or fidaxomicin.
___   Patient is 7 years of age or older with at least two episodes of severe C. difficile infection
(>6 diarrheal stools/day requiring hospitalization and associated with significant morbidity).
___   Patient is 7 years of age or older with moderate C. difficile infection (3-6 diarrheal stools/day not 
responding to successive standard therapy, e.g. metronidazole, vancomycin and/or fidaxomicin) 
lasting at least 28 days.
___   Patient is 7 years of age or older with severe and/or fulminant C. difficile colitis
(> 6 diarrheal stools/day) with no response to standard therapy after 48 hours.
Exclusion: Recipient is deemed ineligible if the answer to any of the following questions is yes:
Question
Yes
No
Is the patient younger than 7 years old?
Is the patient scheduled for abdominal surgery within the next 12 weeks?
Has the patient had major abdominal surgery within the past 3 months?
Is the patient pregnant (if applicable)?
Does the patient have a Hgb < 6 g/dL?
Is the patient’s absolute neutrophil count less than 1500/mm3?
Does the patient have a known diagnosis of graft vs. host disease?
Has the patient used an investigational drug within the past 2 months?
Has the patient used a TNFα agonist within the past 2 weeks?
Has the patient been diagnosed with Bacteremia within the past 4 weeks?
_______________________________ 
__________________________________
Name of person completing this form 
Signature of person completing this form
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
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APPENDIX B
Stool Recipient Screening Questionnaire
 (Ulcerative Colitis or Indeterminate Colitis)
Recipient Name:______________________
Date:___________
Inclusion: Recipient is deemed eligible if any one of the following criteria are met.
___   Patient is 7 years of age or older and has been treated with steroid therapy for at least
 one month.
___   Patient is 7 years of age or older and has been treated with immunomodulatory therapy for 
         at least one month
___   Patient is 7 years of age or older and has been treated with biological therapy for at least
 one month.
Exclusion: Recipient is deemed ineligible if the answer to any of the following questions is yes:
Question
Yes
No
Is the patient younger than 7 years old?
Is the patient scheduled for abdominal surgery within the next 12 weeks?
Has the patient had major abdominal surgery within the past 3 months?
Is the patient pregnant (if applicable)?
Does the patient have a Hgb < 6 g/dL?
Is the patient’s absolute neutrophil count less than 1500/mm3?
Does the patient have a known diagnosis of graft vs. host disease?
Has the patient used an investigational drug within the past 2 months?
Has the patient used a TNFα agonist within the past 2 weeks?
Has the patient been diagnosed with Bacteremia within the past 4 weeks?
Has the patient had any previous FMT? 
_______________________________
 __________________________________
Name of person completing this form 
Signature of person completing this form 
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

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APPENDIX C
Stool Donor Screening Questionnaire
Donor Name:______________________
Date:___________
Question
Yes*
No
1. Are you younger than 7 years of age?
2. Do you have known HIV, tuberculosis, Hepatitis B, or C 
infections?
3. Have you been exposed to HIV, tuberculosis or viral hepatitis 
(within the previous 12 months)?
4. Do you engage in any high-risk sexual behaviors (examples: 
sexual contact with anyone with HIV/AIDS, tuberculosis or 
hepatitis, sex for drugs or money)?
5. Have you used illicit drugs within the past 3 months?
6. Have you had a tattoo or body piercing within the past 6 
months?
7. Have you ever been incarcerated?
8. Have you been to an area with Mad Cow Disease (risk factor for 
Creutzfeld-Jakob disease)?
9. Have you traveled (within the last 3 months) to developing 
countries?
10. Do you have a history of inflammatory bowel disease or 
chronic diarrhea (i.e. greater than 3 loose stools daily for the 
past 3 months)?
11. Do you have a history of gastrointestinal malignancy or known 
polyposis?
12. Have you used systemic antibiotics in the past 3 months?
13. Are you currently using any major immunosuppressive 
medications (e.g., calcineurin inhibitors, systemic anti-
neoplastic, exogenous glucocorticoids, biologic agents)?
14. Do you have eczema, allergies or asthma requiring steroids or 
immune-modulating therapy?
15. Do you have an autoimmune disease, metabolic syndrome, 
chronic pain syndrome, neurologic or developmental disorder?
16. Do you have contact with hospital patients?
17. Have you been hospitalized or in a long term care facility in the 
past 6 months?
18. Do you attend outpatient medical or surgical clinics more than 
once a month?
19. Have you engaged in medical tourism in the past 6 months?
*Answer of “yes” to any of the questions results in exclusion.
_______________________________ 
_________________________________
Name of person completing this form 
Signature of person completing this form
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
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Stool Donor Screening Questionnaire
Donor Name:______________________
Date:___________
*Answer of “yes” to any of the questions results in exclusion.
_______________________________ 
_________________________________
Name of person completing this form 
Signature of person completing this form
Did the Donor Test Positive For:
Yes
No
1. Clostridium difficile toxin A or B? 
2. Stool culture?
3. Giardia antigen?
4. Cryptosporidium antigen?
5. Ova and parasites?
6. Acid-fast stain for Cyclospora, Isospora?
7. HIV, type 1 and 2?
8. Hepatitis A (HAV IgM)?
9. Hepatitis B (HBsAg, anti-HBc, anti-HBs)?
10. Hepatitis C (HCV Ab)?
11. Syphilis (RPR and FTA-ABS)?
12. Sorbitol negative E. Coli?
13. Tuberculosis?
14.  Vancomycin resistant enterococci (VRE)
15.  Extended spectrum beta-lactamase-producing    
Enterobacteriaceae (ESBL)?
16.  Carbapenem-resistant Enterobacteriaceae (CRE)?
17.  Methicillin-resistant Staphylococcus aureus (MRSA)?
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
21
APPENDIX D:
Study Flowsheet
Protocol
Day(s)
Yes
Recruitment of stool recipient 
(Appendix F1 for recurrent CDI ±IBD)
(Appendix F2 for UC or IC without IBD)
-28
Performed?
No
Yes
Donor screening 
(Appendix C)
-28
Eligible?
No
Yes
Donor Serum and Stool Screening
-28
Eligible?
No
Diet Record completed by Recipient? 
(Appendix G)
Yes
No
Diet Record completed by Donor? 
(Appendix G)
-7 to 0
Yes
No
Pre-transplant stool collection?
-3 to -1
Yes
No
Recipient has stopped antibiotics
-3 to -2
Yes
No
Recipient undergoing bowel prep with 
resultant clear yellow stool?
-1
Yes
No
Donor stool processed?
(Appendix P)
0
Yes
No
Day of transplant stool collection?
0
Yes
No
Recipient blood obtained? 
0
Yes
No
Patient monitored?
0
Yes
No
Follow-up Phone Call? 
(Appendix L1 for recurrent CDI ±IBD )
(Appendix L2 for UC or IC)
1
Yes
No
Protocol
Week (s)
Follow-up Phone Call? 
(Appendix L1 for recurrent CDI ±IBD )
(Appendix L2 for UC or IC)
Yes
No
Post-transplant diet record?
Yes 
No
Post-transplant stool collection?
1
Yes
No
2
Yes
No
3
Yes
No
4
Yes
No
5
Yes
No
6
Yes
No
7
Yes
No
8
Yes
No
9
Yes
No
Follow-up Phone Call? 
(Appendix L1 for recurrent CDI ±IBD )
(Appendix L2 for UC or IC)
10
Yes
No
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
22
11
Yes
No
Follow-up Phone Call? 
(Appendix L1 for recurrent CDI ±IBD )
(Appendix L2 for UC or IC)
Yes
No
Post-transplant diet record?
Yes 
No
Post-transplant stool collection?
12
Yes
No
Protocol
Month (s)
4
Yes
No
5
Yes
No
6
Yes
No
7
Yes
No
8
Yes
No
9
Yes
No
10
Yes
No
11
Yes
No
Follow-up Phone Call? 
(Appendix L1 for recurrent CDI ±IBD )
(Appendix L2 for UC or IC)
12
Yes
No
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
23
APPENDIX E
TEMPLATE E-MAIL IN RESPONSE TO INQUIRY ABOUT NCT03268213, 479696, 
Dear -
Thank you for your interest. I am referring you to 
(IF ADULT RECIPIENT) Dr. Ellen Li, Professor of Medicine/Gastroenterology,Stony Brook Medicine  
(IF PEDIATRIC RECIPIENT) Dr. Chawla, Chief and Professor of Pediatrics/ Gastroenterology, Stony 
Brook Medicine.
We are currently open to enrollment and accept local and out-of-state candidates.
However, we need your gastroenterologist to be on board with this study, which is strictly observational 
and simply asking if we can change your microbiome. In addition, we need you to select a healthy donor 
who fulfills the attached screening criteria. The evaluation of both the patient (recipient of the transplant) 
and donor takes place at Stony Brook Medicine, NY.  So, this requires two trips to Stony Brook.  One for 
the initial recruitment and the second for the colonoscopic delivery of the transplant.  We do not cover 
travel costs, donor screening costs or the cost of the colonoscopy (usually covered by your health 
insurance company). However, costs of analyzing the stools for all microbiome-related studies will be 
covered by us.
We prefer no change in your medications and no biologic therapy for at least 2 weeks prior to the 
transplant.
Please contact your gastroenterologist. If they are in agreement to proceed and you wish to move ahead, 
please send us the name, e-mail and fax of your primary gastroenterologist. The last office visit note 
should be sent to us via fax 
(IF ADULT RECIPIENT) (631-444-5225) ATTN: DR. ELLEN LI or email: 
ellen.li@stonybrookmedicine.edu
(IF PEDIATRIC RECIPIENT) (631-444-6045) ATTN: DR. ANUPAMA CHAWLA or email: 
anupama.chawla@stonybrookmedicine.edu
It should also include the most recent colonoscopy, pathology and imaging reports.
Please see the attached documents, which you can share with your gastroenterologist.
1.      Recipient Permission/Consent form
2.      Recipient Screening form
3.      Donor Permission/Consent form
4.      Donor Screening form
5.      Cost Discussion form
6.      Food Diary
Regards,
Katherine Markarian
Research Coordinator
631-444-3868 
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
24
APPENDIX F1 (Clostridium difficile with or without IBD):
STUDY PATIENT CHARACTERISTICS
Within 2 weeks prior to Fecal microbial transplantation
RECIPIENT CODED No.: ___________________________   SEX: M/F
DOB: ___ ___/___ ___/___ ___
Assigned Code Number: ____
WEIGHT: ____ KGS                 BMI: ____                                      
HEIGHT: ____ CMS
1. Duration of symptoms related to C. 
difficile 
____ Month(s)
2. C. difficile PCR and/or toxin date(s)
__ __/__ __/__ __
__ __/__ __/__ __
Name
Duration 
(days)
3. Antibiotics for C. difficile the patient 
has been treated with:
Name
Duration 
(days)
4. Probiotics for C. difficile the patient has 
been treated with:
5. Diarrhea (BMs/day):
<3
3-6
>6
6. Blood in stool:
Yes
No
7. Mucous in stool:
Yes
No
8. Abdominal pain (Scale 0-10)
___/10
9. Fatigue
Yes
No
10. Weight loss during illness
___KGS
11. Previous abdominal surgery
Yes
Location:___________
No
12. Smoker?
Yes
Packs/day:__________
No
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
25
APPENDIX F2 (Ulcerative Colitis or Indeterminate Colitis with or without CDI):
STUDY PATIENT CHARACTERISTICS
Within 2 weeks prior to Fecal Transplantation
RECIPIENT CODED No.: _______________________     SEX: M/F
DOB: ___ ___/___ ___/___ ___                                          
Assigned Code Number: ____
WEIGHT: ____ KGS                  BMI: ____                                      
HEIGHT: ____ CMS
1. Duration of symptoms related to 
Ulcerative colitis or indeterminate colitis 
____ Month(s)
2. Date of IBD diagnosis
__ __/__ __/__ __
Name
3. Current medications
Name
Duration 
(days)
4. Medications for IBD the patient has 
been treated with:
Name
Duration 
(days)
5. Probiotics the patient has been treated 
with:
6. Diarrhea (BMs/day):
<3
3-6
>6
7. Blood in stool:
Yes
No
8. Mucous in stool:
Yes
No
9. Abdominal pain (Scale 0-10)
___/10
10. Fatigue
Yes
No
11. Weight loss during illness
Yes
____KGs
No
12. Previous abdominal surgery
Yes
Location___________
No
13. Smoker?
Yes
Packs/day:__________
No
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
26
APPENDIX G
Stony Brook University Medical Center Food Diary
Record all food, fluid, supplement intake including Probiotics
Record all condiments, sauces, oils, etc.
Date:
MEAL
FOOD: Brand/Description
(i.e. Whole milk, rye bread)
HOW WAS IT PREPARED
(i.e. 3 ounces fried chicken)
**Record each day on separate sheet**                                               
Coded Number: ______________
Physician: ___________________
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
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APPENDIX H
Checklist for instructing Recipient 2-5 days prior to Fecal Microbial 
Transplantation
RECIPIENT CODED No.: _________________________________
DATE/TIME OF CALL: ___ ___/___ ___/___ 
___:___AM/PM
RECIPIENT DATA:
1. Do you fully understand the colonoscopy prep procedure?
YES
NO
2. Have you completed tapering of any antibiotics (if applicable)?  
It is important that antibiotics must be stopped 48 h before the 
transplant because the antibiotics will kill the bacteria in the 
transplant*
YES
NO
3. Do you fully understand the stool collection instructions & kit?
YES
NO
4. Will you arrive to Endoscopy 1.5-2 hrs before the scheduled 
procedure?
YES
NO
5. Have you been recording your diet in the food diary?
YES
NO
*FMT will not be performed if answered “no”.
RECIPIENT NOTES:
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
28
APPENDIX I:
Mayo Score
DAY OF TRANSPLANT___
RECIPIENT CODED No.: __________________
Item
Points
1. Stool Frequency
Normal number of stools for the patient
0
1-2 stools more than normal
1
3-4 stools more than normal
2
5 or more stools more than normal
3
2. Rectal bleeding
None
0
Streaks of blood with stool less than half of the time
1
Obvious blood with stool most of the time
2
Blood alone passed
3
3. Endoscopic Findings (Rectosigmoid)
Normal or inactive disease
0
Mild disease (erythema, decreased vascular pattern, 
mild friability)
1
Moderate disease (marked erythema, absent vascular 
pattern, friability, erosions)
2
Severe disease (spontaneous bleeding, ulceration)
3
4. Physician’s Global Assessment
Normal
0
Mild disease
1
Moderate disease
2
Severe disease
3
Total Score
________
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
29
APPENDIX J:
DIARY CARD
DATE:_________________
DESCRIPTION OF SYMPTOMS THAT ARE NEW OR WORSENED:
DATE:_________________
DESCRIPTION OF SYMPTOMS THAT ARE NEW OR WORSENED:
DATE:_________________
DESCRIPTION OF SYMPTOMS THAT ARE NEW OR WORSENED:
DATE:_________________
DESCRIPTION OF SYMPTOMS THAT ARE NEW OR WORSENED:
Contact us (631-444-7225) immediately if you are seen in the emergency room 
or hospitalized for any reason.
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
30
APPENDIX K:
DAY AFTER TRANSPLANT: CASE REPORT FORM
RECIPIENT CODED No.: __________________
DATE/TIME OF CALL: ___ ___/___ ___/___ ___        ___:___AM/PM
RECIPIENT DATA:
1. How do you feel today?
WELL
UNWELL
2. Have you had a fever > 100.4 degrees 
Fahrenheit in the past 2 weeks?
YES
NO
3. Is your abdominal pain:
BETTER
WORSE
SAME
4. Is your diarrhea:
BETTER
WORSE
SAME
5. Is the blood in your stool:
BETTER
WORSE
SAME
6. Is there a presence of a new rash on your 
body?
YES
NO
DESCRIPTION OF SYMPTOMS THAT HAVE WORSENED:
NAME OF PHYSICIAN INFORMED IF PATIENT RESPONSE CORRESPONDS TO ANY 
OF THE BOLDED ITEMS ABOVE: 
_______________________MD/DO
PHYSICIAN DECISION OF FURTHER EVALUATION:
CLINIC
EMERGENCY ROOM
PHONE 
FOLLOW-UP
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
31
APPENDIX L1 (Clostridium difficile with or without IBD):
FOLLOW UP PHONE CALL/ADVERSE EVENT: CASE REPORT FORM
WEEK(S)/MONTH(S) POST-TRANSPLANT ___
RECIPIENT CODED No.: __________________
DATE/TIME OF CALL: ___ ___/___ ___/___ ___        ___:___AM/PM
1. How do you feel 
today?
WELL
UNWELL
2. Have you had a fever 
> 100.4 degrees 
Fahrenheit since the last 
phone call?
YES
NO
3. Has your abdominal 
pain:
RESOLVED
IMPROVED
WORSENED
N/A
4. Has your diarrhea:
RESOLVED
IMPROVED
WORSENED
N/A
5a. Frequency of 
stools/day:
<3
3-6
>6
5b. Has the blood in 
your stool:
RESOLVED
IMPROVED
WORSENED
N/A
YES
6. Have you been 
fatigued?
Mild
Moderate
Severe
NO
7. Have you experienced 
weight changes since the 
last phone call?
NO
YES
± ____ LBS
YES
8. Have you required 
antibiotics since the 
fecal transplant? If yes, 
what is the name of the 
antibiotic(s)?
Name of antibiotic(s):
______________
NO
YES
9. Have you taken any 
new medication(s), 
including OTC or 
probiotics since the last 
phone call?
Name of medication(s):
______________
NO
YES
10. Have you developed 
any NEW medical 
conditions since the last 
phone call?
Please specify:
______________
NO
YES
11a. Did any medical 
condition(s) you had 
before your fecal 
transplant go away after 
your fecal transplant?
Please specify:
______________
NO
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
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11b. Please list all 
medication(s) you take 
on a regular basis 
(dosage not necessary) 
including 
chemotherapeutic 
agents, if applicable
Name of medication(s):
_____________________________________
DESCRIPTION OF ADVERSE EVENT(S): 
(An adverse event will be defined as any unfavorable or unintended sign, symptoms, disease, syndrome, 
abnormal laboratory finding, or concurrent illness that emerges or worsens relative to the recipient’s pre-
transplant baseline, whether or not it is considered to be related to the fecal transplantation)
All Grade 3 – 5 adverse events will be sent to the Safety Monitoring Committee
NAME OF PHYSICIAN INFORMED IF PATIENT RESPONSE 
CORRESPONDS TO ANY OF THE BOLDED ITEMS ABOVE: 
_______________________MD/DO
PHYSICIAN DECISION OF FURTHER EVALUATION:
CLINIC
EMERGENCY 
ROOM
PHONE 
FOLLOW-UP
FOLLOW UP C. DIFFICILE TESTING
DATE OF TESTING: __ __/__ __/__ __  
POSITIVE NEGATIVE
DOCUMENTATION SENT TO SAFETY MONITORING COMMITTEE ON ___ 
___/___ ___/___ ___: 
YES
NO
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
33
APPENDIX L2 (Ulcerative Colitis or Indeterminate Colitis):
FOLLOW UP PHONE CALL/ADVERSE EVENT: CASE REPORT FORM
WEEK(S)/MONTH(S) POST-TRANSPLANT ___
RECIPIENT CODED No.: __________________
DATE/TIME OF CALL: ___ ___/___ ___/___ ___        ___:___AM/PM
1. How do you feel 
today?
WELL
UNWELL
2. Have you had a fever 
> 100.4 degrees 
Fahrenheit since the last 
phone call?
YES
NO
3. Has your abdominal 
pain:
RESOLVED
IMPROVED
WORSENED
N/A
4. Has your diarrhea:
RESOLVED
IMPROVED
WORSENED
N/A
5a. Frequency of 
stools/day:
<3
3-6
>6
5b. Has the blood in 
your stool:
RESOLVED
IMPROVED
WORSENED
N/A
YES
6. Have you been 
fatigued?
Mild
Moderate
Severe
NO
7. Have you experienced 
weight changes since the 
last phone call?
NO
YES
± ____ LBS
YES
8. Have you required 
antibiotics since the 
fecal transplant? If yes, 
what is the name of the 
antibiotic(s)?
Name of antibiotic(s):
______________
NO
YES
9. Have you taken any 
new medication(s), 
including OTC or 
probiotics since the last 
phone call?
Name of medication(s):
______________
NO
YES
10. Have you developed 
any NEW medical 
conditions since the last 
phone call?
Please specify:
______________
NO
YES
11a. Did any medical 
condition(s) you had 
before your fecal 
transplant go away after 
your fecal transplant?
Please specify:
______________
NO
Approved: 7/25/2019
Expiration Date: 7/1/2020
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July 2019
34
11b. Please list all 
medication(s) you take 
on a regular basis 
(dosage not necessary) 
including 
chemotherapeutic 
agents, if applicable
Name of medication(s):
_____________________________________
DESCRIPTION OF ADVERSE EVENT(S): 
(An adverse event will be defined as any unfavorable or unintended sign, symptoms, disea1se, syndrome, 
abnormal laboratory finding, or concurrent illness that emerges or worsens relative to the recipient’s pre-
transplant baseline, whether or not it is considered to be related to the fecal transplantation)
All Grade 3 – 5 adverse events will be sent to the Safety Monitoring Committee.
NAME OF PHYSICIAN INFORMED IF PATIENT RESPONSE 
CORRESPONDS TO ANY OF THE BOLDED ITEMS ABOVE: 
_______________________MD/DO
PHYSICIAN DECISION OF FURTHER EVALUATION:
CLINIC
EMERGENCY 
ROOM
PHONE 
FOLLOW-UP
DOCUMENTATION SENT TO SAFETY MONITORING COMMITTEE ON ___ 
___/___ ___/___ ___: 
YES
NO
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
35
APPENDIX M:
SERIOUS ADVERSE EVENT (SAE): CASE REPORT FORM
WEEK(S)/MONTH(S) POST-TRANSPLANT ___
 INITIAL REPORT/ FOLLOW-UP REPORT
RECIPIENT CODED No.: __________________
  
ONSET OF EVENT: ___ ___/___ ___/___ ___  
Severity of SAE
Grade 3
Grade 4
Grade 5
 RECOVERED WITH 
SEQUELAE
 RECOVERED WITHOUT 
SEQUELAE
RECOVERY DATE
___ ___/___ ___/___ ___
 PERSISTING
 UNKNOWN/LOST TO 
FOLLOW-UP
Outcome of SAE:
 DEATH
 DEATH*
 LIFE THREATENING
 HOSPITALIZATION 
REQUIRED#
 PROLONGED IN-PATIENT 
HOSPITALIZATION#
SAE category:
 PERSISTENT/SIGNIFICANT 
DISABILITY OR INCAPACITY
 OTHER MEDICALLY 
IMPORTANT CONDITION
*IF DEATH HAS OCCURRED: 
1. Date of death
___ ___/___ ___/___ ___
2. Primary cause of death 
(if known)
_____________________________
#IF RECIPIENT HAS REQUIRED HOSPITALIZATION: 
1. Hospital admission date
___ ___/___ ___/___ ___
2. Current duration of 
hospitalization
____________ (WEEKS/MONTHS)
DESCRIPTION OF SERIOUS ADVERSE EVENT(S): 
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
36
NAME OF PHYSICIAN INFORMED OF SAE: 
_______________________MD/DO
DOCUMENTATION SENT TO SAFETY MONITORING COMMITTEE ON ___ 
___/___ ___/___ ___: 
YES
NO
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
37
APPENDIX N
Research Study: Fecal microbial transplantation in 
patients with medication-refractory
Clostridium difficile and/or Ulcerative colitis or
indeterminate colitis (IRBNet #: 479696) 
Principal Investigator: Dr. Anupama Chawla
FMT recipient
____________________________
FMT donor
____________________________
Dr. Anupama Chawla has discussed the screening test for the 
Donor with both recipient and donor as named above and 
explained that the costs involved in these tests might not be 
covered by the insurance. The research study does not provide any 
monetary support for these donor-screening tests. 
Signature of Recipient___________________________
Signature of Donor
___________________________ 
____________________________________________
Full name of person obtaining consent
____________________________________________
Signature of person obtaining consent
Date
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
38
APPENDIX O
Checklist for instructing Donor 2-5 days prior to Fecal Microbial Transplantation
DONOR CODED No.: ____________________________________
DATE/TIME OF CALL: ___ ___/___ ___/___ 
___:___AM/PM
DONOR DATA:
1. Do you fully understand the stool collection instructions & kit?
YES
NO
2. Have you been recording your diet in the food diary?
YES
NO
3. Have you ingested any known allergy/sensitivity of the 
recipient?* If so, see notes below
YES
NO
4. Will you be present with the recipient on day of transplant? (If 
no, complete TPF questionnaire over phone and schedule a time 
to complete “Day Of Transplant Case Report” form)
YES
NO
DONOR NOTES:
*Reschedule fecal microbial transplant.
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
39
APPENDIX P:
DAY OF TRANSPLANT: DONOR CASE REPORT FORM
DATE OF STUDY: ___ ___/___ ___/___ ___             TIME OF STUDY: ___:___
DONOR CODED No.: ____________________________________
RECIPIENT CODED No.: _________________________________
DONOR DATA:
1. Do you feel unwell today?
YES
NO
2. Have you had a fever > 100.4 degrees Fahrenheit in the 
past 2 weeks?
YES
NO
3. Have you had cough or runny nose within the last 2 
weeks?
YES
NO
4. Have you ingested ________ (recipient allergen) in the 
past week?
YES
NO
If answer to any question is “yes”, discuss with attending physician.
DONOR STOOL DATA:
1. What date and time was the stool produced?
__ __/__ __/__ __  
AM/PM
2. If produced > 6 hours before time of colonoscopy, was 
the stool kept at room temperature?
YES
NO
N/A
3. Was the stool collected with any contamination with 
the toilet bowl?
YES
NO
4. Is there presence of blood in the stool?
YES
NO
5. Is there presence of mucous in the stool?
YES
NO
6. What is the consistency of stool?
Hard
Soft
Liquidy
If answer to any question from #2 to #5 is “yes”, FMT will not be performed.
Approved: 7/25/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

July 2019
40
APPENDIX Q:
Pediatric Ulcerative Colitis Activity Index 
WEEK(S)/MONTH(S) POST-TRANSPLANT ___
RECIPIENT CODED No.: __________________
Item
Points
1. Abdominal pain
No pain
0
Pain can be ignored
5
Pain cannot be ignored
10
2. Rectal bleeding
None
0
Small amount only, in <50% of stools
10
Small amount with most stools
20
Large amount (>50% of stool content)
30
3. Stool consistency of most stools
Formed
0
Partially formed
5
Completely formed
10
4. Number of stools per 24 hours
0-2
0
3-5
5
6-8
10
>8
15
5. Nocturnal stools (any episode causing 
wakening)
No
0
Yes
10
6. Activity level
No limitation of activity
0
Occasional limitation of activity
5
Severe restricted activity
10
Total Score
________
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 1 of 9
 RECIPIENT RESEARCH PERMISSION/CONSENT FORM   (UC/IC)
Project Title: Fecal microbial transplantation in patients with medication-refractory Clostridium 
difficile and/or Ulcerative colitis or indeterminate colitis 
Principal Investigator: Anupama Chawla, MD
Co-Investigators: 
 Ellen Li, MD PhD
Departments: 
 Pediatric Gastroenterology & Nutrition and Medicine/Gastroenterology
When we say “you” in this consent form, we mean you or your child; “we” means the doctors and 
other staff. If you are a parent or legal guardian of a child who may take part in this study, 
permission from you is required and the assent (agreement) of your child may be required.
You are being asked to be a volunteer in a research study. You are encouraged to take your time 
in making your decision. You may want to discuss this study with your friends and family. 
PURPOSE 
The purpose of this study is:
•
To determine the safety and tolerability of fecal (stool) transplantation to treat Ulcerative 
colitis or indeterminate colitis. 
•
Ulcerative colitis (UC) is a chronic disease affecting the colon without a medical cure. The 
precise cause of having inflammatory bowel disease (IBD) such as UC, Crohn’s disease, or 
indeterminate colitis is unclear, however, genetics and the environment are thought to play 
a role. Studies have found that patients with UC have a decreased prevalence of protective 
bacteria and an increase in harmful bacteria in the colon. Inflammation in the colon in these 
patients is thought to be due to this imbalance between helpful and harmful bacteria. 
Currently, the treatment of IBD includes steroids, anti-inflammatory medications and 
biological therapy, each with its own side effects. Given the role of the gastrointestinal 
bacteria in driving inflammation in patients with IBD, treatments that manipulate these 
bacteria have been investigated, including the use of medications containing beneficial 
bacteria (probiotics), with some benefit. Fecal transplantation (FMT), the transfer of 
gastrointestinal bacteria (microbiota) from a healthy donor via infusion of a liquid stool 
suspension, is proving to be an effective alternative treatment for medication-resistant UC 
or indeterminate colitis. The goal of this method is to remove the harmful bacteria in the 
colon and replace them with normal bacteria.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 2 of 9
Since you have Ulcerative colitis or indeterminate colitis and your symptoms have not improved 
with the medications you are currently on, fecal transplantation is a treatment option for you. As 
mentioned before, several studies have found that this transplantation is helpful in improving the 
symptoms associated with IBD such as abdominal pain and diarrhea. This study hopes to document 
fecal transplant’s safety, tolerability and effectiveness and improve or even eliminate your 
symptoms by performing the transplantation and then following-up routinely with you for one 
year. We will perform stool and genetic studies on you to see if the bacteria in your colon really did 
change after the transplantation and if any of your genes influence the composition of your colon 
bacteria. 
We expect to enroll a minimum of 100 patients in this study at Stony Brook University Hospital.
PROCEDURES 
If you decide to be in this study, your part will involve: 
•
You will first have to choose somebody who will donate the stool which will be 
transplanted. The donor can be anyone who we will consent separately and who meets 
eligibility criteria to donate stool. He/she will be asked questions and screened by 
performing blood work and stool studies to make sure he/she is a healthy candidate for 
stool transplantation. We will not share the lab results of your donor specimen with you 
even if they fail the inclusion criteria. 
•
After the donor is chosen and he/she meets criteria to donate stool, we will give you a date 
for the fecal transplantation which will be done during a colonoscopy.
•
If you are of child-bearing age, a pregnancy test will be given to you as a clinic standard of 
care before the colonoscopy procedure. If the test result is positive for pregnancy then we 
will not perform the fecal transplantation colonoscopy.
•
During the week before fecal transplantation, we will ask you to record everything you have 
eaten on a diet record which we will provide to you. Stool for research will be collected 1-3 
days before your day of fecal transplantation.
•
On the day before your transplant, you will be given instructions for a bowel prep to clean 
out your colon completely so it can be visualized well when we perform the fecal 
transplantation and make the procedure more effective. For the last 7 hours before your 
scheduled fecal transplantation, you will have nothing to eat or drink.
•
On the day of the transplantation, you will arrive at Stony Brook University Hospital and go 
to the Endoscopy Suite, located on the 14th Floor. There you will change into a hospital 
gown and an intravenous line (IV) will be placed to provide you with fluids and sedation 
during the colonoscopy. Four teaspoons of blood will be taken for research, to perform 
genetic studies.
•
Your donor’s stool will be prepared and while you are properly sedated the stool will be 
instilled into your colon.
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 3 of 9
•
At the time of scope and transplant, if the scope reveals anything clinically suspect that 
might require a biopsy, or the physician decides that the colon is healthy enough, then the 
transplant will not be done.
•
You will stay in the Endoscopy Suite, lying on your right side, for at least one hour. This is to 
maximize contact between the transplanted stool and your colon. If you are not cleared to 
depart after one hour, you will stay until the anesthesiologist (doctor who administered 
sedation during colonoscopy) does clear you to depart. You will be able to eat and drink 
right after you wake up and can resume normal activities as soon as the anesthesia wears 
off and you feel well.
•
You will receive a phone call the day after the procedure, and be asked various questions to 
determine your general well-being.
•
You will then receive weekly phone calls for 12 weeks at a convenient time for you, to ask 
you further general well-being questions.
•
You will keep another diet record during the first week post-transplant. 1 week after your 
fecal transplantation, you will collect stool for research, similar to how you collected stool 
prior to your stool transplantation.
•
You will keep another diet record during the 12th week post-transplant. 12 weeks after your 
fecal transplantation, you will collect stool for research, similar to how you collected stool 
prior to your stool transplantation. 
•
After your 12-week stool collection and testing you will receive monthly phone calls until 
one year after the transplant to determine your general well-being.
•
If you are diagnosed with bacteria in your blood within past 4 weeks (28 days) of intended 
FMT, you will be excluded from the study.
When you are first recruited for the study, you will be assigned a coded number. Stool and blood 
samples collected from you and follow-up questionnaires will all have your coded number so your 
information will not be directly linked to your samples and medical or diet diary information.
RISKS / DISCOMFORTS 
The following risks/discomforts may occur as a result of you being in this study: 
•
Although donor stool is vigorously screened for infectious agents, there is a still a rare risk 
of an infection with harmful bacteria and multidrug resistant organisms (MDRO) being 
passed from the donor’s stool to you. MDRO are common bacteria that have developed 
resistance to multiple types of antibiotics. These bacteria are present on the bodies of some 
people and they can co-exist with normal bacteria and cause no symptoms (“commensal”) 
or lead to serious infection spreading to the blood and other organs (“invasive”). Invasive 
infection is more common in patients with compromised immunity. Infections caused by 
MDRO are correlated with increased illness, death and prolonged hospitalization. Measures 
have been implemented for donor screening (exclude donors at higher risk of MDRO 
infection) and donor stool testing (exclude stool that tests positive for MDRO)
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 4 of 9
•
Uncommon risks associated with fecal transplantation that have been documented in the 
literature include cramping, fullness, passing gas, bloating, vomiting, diarrhea, fever, and 
blood in the stool. Since this is a research study, not all risks associated with fecal 
transplantation are known at this time; there may be unforeseen risks associated with study 
participation. 
•
There are risks associated with colonoscopy: infection, bleeding, and less than a 1% chance 
of a perforation or hole being created (A separate consent form for colonoscopy will be 
given on the day of fecal transplantation). 
•
Your colitis may progress or get worse after the transplantation.
•
When your blood is drawn, temporary pain and bruising where the needle enters the skin, 
and sometimes, fainting and/or infection. 
•
There is a rare possibility that confidential information about you may be accidentally 
disclosed. 
•
Some of the research that will be done on your blood are genetic studies. The genetic 
studies are only for research, and will not be used in making decisions about your care. We 
will not contact you about any results of these genetic studies. 
BENEFITS 
The following benefits may occur as a result of being in this study: 
The potential direct benefit of performing fecal microbiota transplantation for the treatment of 
ulcerative colitis or indeterminate colitis is improvement or resolution of symptoms associated with 
having inflammatory bowel disease such as diarrhea, abdominal pain, fatigue, poor appetite and 
minimizing the need for stronger medications that have their own associated side effects. 
The indirect benefits include contributions to our knowledge regarding the safety and tolerability
of fecal microbiota transplantation. Additionally, by performing research studies examining the 
bacteria in your stool, as well as performing genetic studies, we hope to see if there is a link 
between genetics and colonic bacteria as well as determine the relative abundance of each 
bacterium. This will also enable us to see if performing the stool transplant changed the 
composition of your stool and may one day lead to creating medications that increase healthy 
bacteria in the colon or target harmful bacteria.
PAYMENT TO YOU
You will not be paid for your participation in this study. This research might create new tests, 
treatment, or cures. If it does, you will not get any money from those products.
Approved: 7/3/2019
Expiration Date: 7/1/2020
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Page 5 of 9
CONFIDENTIALITY 
We will take steps to help make sure that all the information we get about you is kept confidential. 
Your name will not be used wherever possible. We will use a code instead. All the study data that 
we get from you will be kept locked up. The code will be locked up too. If any papers and talks are 
given about this research, your name will not be used. 
We want to make sure that this study is being done correctly and that your rights and welfare are 
being protected. For this reason, we will share the data we get from you in this study with the 
study team, Stony Brook University's Committee on Research Involving Human Subjects, applicable 
Institutional officials, and certain federal offices. However, if you tell us you are going to hurt 
yourself, hurt someone else, or if we believe the safety of a child is at risk, we will have to report 
this. 
This study requires that we collect very private information about you. Therefore, we had the 
National Institutes of Health give us a Certificate of Confidentiality (COC). This piece of paper says 
that nobody can force the researchers to give out your information, even if a court of law asks for 
it. This will give you more protection. The only time information about you can be given out is: 
If you are going to hurt yourself. 
If you are going to hurt someone else. 
If we believe the safety of a child is at risk. 
If data about the fecal transplantation needs to be reported to the Food and Drug Administration. 
If the data are required by other federal, state or local laws, such as for reporting of communicable 
diseases.
You should know that the Certificate of Confidentiality does not apply to information about your 
participation in research, including a consent form that is placed in your medical record (though 
HIPAA protection does apply). This information may be disclosed to individuals requesting your 
medical record.
This Certificate doesn’t mean you can’t talk about this study. If you give written permission, your 
insurance company, your boss, or your private doctor can be given the research information too. 
While you are in this study we will get data about your health from your medical record. We will 
also get health data from the results of the tests you will have done in this study. You have a right 
to privacy but the data we get about your health in this study can be shared with the people 
referenced above (the study team, Stony Brook University's Committee on Research Involving 
Human Subjects, applicable institutional officials, and certain federal offices) as well as (as 
applicable):
•
Your private doctor 
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Page 6 of 9
•
A board that reviews the safety of the study on an on-going basis. 
Your health data are shared to make sure the study is being done correctly, costs are charged 
correctly, and to make sure your rights and safety are protected. Not all of these people are 
required by law to protect your health data. They might share it with others without your 
permission. 
You have the right to stop allowing us to use or give out your health data. You can do this at any 
time by writing to Anupama Chawla, M.D. If you do this, we will stop collecting any new health data 
from you, except if we need to keep an eye on a bad side effect you were having in the study. We 
will use any data we collected before you wrote your letter. When you sign the consent form at the 
end, it means: 
•
That you have read this section. 
•
That you will allow the use and reporting of your health data as described above. 
•
You have received a form from the University Hospital. It is called the Notice of Privacy 
Practices form. 
The Genetic Information Nondiscrimination Act (GINA)
You should know that a federal law called the Genetic Information Nondiscrimination Act (GINA) 
generally makes it illegal for health insurance companies, group health plans, and most employers 
to discriminate against you based on your genetic information. This law will generally protect you 
in the following ways:
§ Health insurance companies and group health plans may not request your genetic information 
from this research.
§ If health insurance companies and group health plans do somehow receive your genetic 
information from this research, they may not use it to make decisions about your eligibility or 
premiums.
§ Employers with 15 or more employees may not use your genetic information from this research 
when making a decision to hire, promote, or fire you when setting the terms of your employment.
Be aware that this new law does not protect you against genetic discrimination by companies that 
sell life insurance, disability insurance, or long-term care insurance.
COSTS TO YOU 
•
If a colonoscopy is scheduled to perform the fecal transplant, we will obtain a prior 
authorization for colonoscopy to perform the transplant from your insurance company if 
needed. You may have to pay for a portion of the colonoscopy depending on your insurance 
plan. We encourage you to contact your insurance company to discuss this potential cost 
prior to consenting to be in the study.
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Stony Brook University Human Subjects Committee (IRB)

Page 7 of 9
•
All stool tests and bloodwork for research purposes will be performed without any cost to 
you for participating in this study.
ALTERNATIVES
•
An alternative to having the fecal microbiota transplantation is stepping up the medications 
you are currently on for your inflammatory bowel disease to immunomodulators and 
possibly biological agents such as Tumor Necrosis Factor - alpha antagonists which carry 
their own risks.
•
The other alternative to performing the fecal microbiota transplantation is living with 
symptoms of ulcerative colitis or indeterminate colitis, such as bloody diarrhea, abdominal 
pain, fatigue, rashes, joint pains and other manifestations of inflammatory bowel disease.
IN CASE OF INJURY
If you are injured as a result of being in this study, please contact Dr. Anupama Chawla at 
telephone # 631-444-8115. The services of Stony Brook University Hospital will be open to you in 
case of such injury. However, you and/or your insurance company will be responsible for payment 
of any resulting treatment and/or hospital stay.
CONSEQUENCES OF WITHDRAWING
You may withdraw your consent at any time by contacting Dr. Anupama Chawla. If you do this, we will 
stop collecting any new health data from you for research purposes but will continue to use the data 
we collected prior to your withdrawal. Your choice will not at any time affect the commitment of your 
health care providers to administer care. There will be no penalty or loss of benefits to which you are 
otherwise entitled.
YOUR RIGHTS AS A RESEARCH SUBJECT
•
Your participation in this study is voluntary. You do not have to be in this study if you don't 
want to be.
•
You have the right to change your mind and leave the study at any time without giving any 
reason, and without penalty.
•
Any new information that may make you change your mind about being in this study will be 
given to you.
•
You will get a signed and dated copy of this consent form to keep.
•
You do not lose any of your legal rights by signing this consent form.
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Page 8 of 9
QUESTIONS ABOUT THE STUDY OR YOUR RIGHTS AS A RESEARCH SUBJECT
•
If you have any questions, concerns, or complaints about the study, you may contact
Dr. Anupama Chawla, at telephone # (631-444-8115).
•
If you have any questions about your rights as a research subject or if you would like to 
obtain information or offer input, you may contact Stony Brook University Research Subject 
Advocate, Ms. Lu-Ann Kozlowski, BSN, RN, (631) 632-9036, OR by e-mail,
lu-ann.kozlowski@stonybrook.edu.
•
Visit Stony Brook University’s Community Outreach page, 
http://research.stonybrook.edu/orc/community.shtml#overview-of-volunteering-in-
research for more information about participating in research, frequently asked questions, 
and an opportunity to provide feedback, comments, or ask questions related to your 
experience as a research subject.
If you sign below, it means that you have read (or have had read to you) the information given in 
this consent form, and you would like to be a volunteer in this study.
Please initial your response to each statement below.________________________________
1. I have been told about the risks, benefits, and alternatives to fecal microbiota transplantation, 
and I wish to undergo the procedure.
Yes_____ No _____
2. I agree to follow-up via telephone so that the study investigators can evaluate my general well-
being for one year post-transplant.
Yes_____ No _____
3. I agree to give a stool specimen 1-3 days prior to the fecal microbiota transplantation, 1 week 
post-transplant, and 3 months post-transplant for research.
Yes_____ No _____
4. I agree to have my blood drawn on the day of fecal microbiota transplantation for research.
Yes_____ No _____
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

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_________________________________     _________________________________________
Subject Name (Printed) 
           Subject Signature 
Date
_________________________________    _________________________________________
Name of Person Obtaining Consent            Signature of Person Obtaining Consent    
Date
(Printed)
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

                                                                                                                 Page 1 of 9
 RECIPIENT RESEARCH PERMISSION/CONSENT FORM (CDIFF)
Project Title: Fecal microbial transplantation in patients with medication-refractory Clostridium 
difficile and/or Ulcerative colitis or indeterminate colitis
Principal Investigator: Anupama Chawla, MD
Co-Investigator: 
 Ellen Li, MD PhD
Departments: 
 Pediatric Gastroenterology & Nutrition and Medicine/Gastroenterology
When we say “you” in this consent form, we mean you or your child; “we” means the doctors and 
other staff. If you are a parent or legal guardian of a child who may take part in this study, 
permission from you is required and the assent (agreement) of your child may be required.
You are being asked to be a volunteer in a research study. You are encouraged to take your time 
in making your decision. You may want to discuss this study with your friends and family. 
PURPOSE 
The purpose of this study is:

To determine the safety, tolerability, and effectiveness of fecal (stool) transplantation to 
treat Clostridium difficile infection. 

Clostridium difficile is a bacteria that can cause abdominal pain and diarrhea which is often 
bloody. This can lead to not absorbing nutrients from food properly, becoming anemic, and 
feeling tired. In severe cases, patients have to be hospitalized to provide them with 
intravenous fluids, antibiotics, or to treat their pain. Patients may even require colon 
surgery if the bacteria causes intractable pain and diarrhea or leads to a hole being created 
in the colon. It is also the leading cause of antibiotic-associated diarrhea with increasing 
infection rates. The bacteria is usually treated with antibiotics such as metronidazole 
(Flagyl) or vancomycin, however these antibiotics do not work all the time due to resistant 
strains of Clostridium difficile. When a person is infected with these bacteria, he/she has a 
high percentage of this bacteria compared to all the other normal bacteria which are usually 
found in their colon. Fecal transplantation (FMT), the transfer of gastrointestinal bacteria 
(microbiota) from a healthy donor via infusion of a liquid stool suspension, is proving to be 
an effective alternative treatment for antibiotic-resistant Clostridium difficile. The goal of 
this method is to remove the harmful bacteria such as Clostridium difficile in the colon and 
Approved: 7/3/2019
Expiration Date: 7/1/2020
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                                                                                                                 Page 2 of 9
replace them with normal bacteria.
 
Since you have a Clostridium difficile infection that has not been cured by antibiotic therapy, fecal 
transplantation is a treatment option for you. As mentioned before, several studies have found 
that this transplantation is helpful in eliminating the Clostridium difficile bacteria. This study hopes 
to document fecal transplantation’s safety, tolerability and effectiveness for eliminating the 
bacteria and improving your symptoms by performing the transplantation and then following-up 
routinely with you for one year. We will perform stool and genetic studies on you to see if the 
bacteria in your colon really did change after the transplantation and if any of your genes influence 
the composition of your colon bacteria. 
We expect to enroll a minimum of 100 patients in this study at Stony Brook University Hospital.
PROCEDURES 
If you decide to be in this study, your part will involve: 

You will first have to choose somebody who will donate the stool which will be 
transplanted. The donor can be anyone who we will consent separately and who meets 
eligibility criteria to donate stool. He/she will be asked questions and screened by 
performing blood work and stool studies to make sure he/she is a healthy candidate for 
stool transplantation. We will not share the lab results of your donor specimen with you 
even if they fail the inclusion criteria. 

After the donor is chosen and he/she meets criteria to donate stool, we will give you a date 
for the fecal transplantation which will be done during a colonoscopy.

If you are of child-bearing age, a pregnancy test will be given to you as a clinic standard of 
care before the colonoscopy procedure. If the test result is positive for pregnancy then we 
will not perform the fecal transplantation colonoscopy.

During the week before fecal transplantation, we will ask you to record everything you have 
eaten on a diet record which we will provide to you. Stool for research will be collected 1-3 
days before your day of fecal transplantation.

On the day before your transplant, you will be given instructions for a bowel prep to clean 
out your colon completely so it can be visualized well when we perform the fecal 
transplantation and make the procedure more effective. For the last 7 hours before your 
scheduled fecal transplantation, you will have nothing to eat or drink.

On the day of the transplantation, you will arrive at Stony Brook University Hospital and go 
to the Endoscopy Suite, located on the 14th Floor. There you will change into a hospital 
gown and an intravenous line (IV) will be placed to provide you with fluids and sedation 
during the colonoscopy. Four teaspoons of blood will be taken for research, to perform 
genetic studies.
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                                                                                                                 Page 3 of 9

Your donor’s stool will be prepared and while you are properly sedated the stool will be 
instilled into your colon.

At the time of scope and transplant, if the scope reveals anything clinically suspect that 
might require a biopsy, or the physician decides that the colon is healthy enough, then the 
transplant will not be done.

You will stay in the Endoscopy Suite, lying on your right side, for at least one hour. This is to 
maximize contact between the transplanted stool and your colon. If you are not cleared to 
depart after one hour, you will stay until the anesthesiologist (doctor who administered 
sedation during colonoscopy) does clear you to depart. You will be able to eat and drink 
right after you wake up and can resume normal activities as soon as the anesthesia wears 
off and you feel well.

You will receive a phone call the day after the procedure, and be asked various questions to 
determine your general well-being.

You will then receive weekly phone calls for 12 weeks at a convenient time for you, to ask 
you further general well-being questions.

You will keep another diet record during the first week post-transplant. 1 week after your 
fecal transplantation, you will collect stool for research, similar to how you collected stool 
prior to your stool transplantation.

If symptoms of Clostridium difficile infection reappear after your stool transplant, you will 
be asked to provide a stool sample to a laboratory to check for Clostridium difficile bacteria.

You will keep another diet record during the 12th week post-transplant. 12 weeks after your 
fecal transplantation, you will collect stool for research, similar to how you collected stool 
prior to your stool transplantation. 

After your 12-week stool collection and testing you will receive monthly phone calls until 
one year after the transplant to determine your general well-being.

If your doctor feels it would benefit you, s/he may recommend performing an additional 
transplant at some point during this study.

If you are diagnosed with bacteria in your blood within past 4 weeks (28 days) of intended 
FMT, you will be excluded from the study.
When you are first recruited for the study, you will be assigned a coded number. Stool and blood 
samples collected from you and follow-up questionnaires will all have your coded number so your 
information will not be directly linked to your samples and medical or diet diary information.
RISKS / DISCOMFORTS 
The following risks/discomforts may occur as a result of you being in this study: 

Although donor stool is vigorously screened for infectious agents, there is a still a rare risk 
of an infection with harmful bacteria and multidrug resistant organisms (MDRO) being 
passed from the donor’s stool to you. MDRO are common bacteria that have developed 
resistance to multiple types of antibiotics. These bacteria are present on the bodies of some 
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                                                                                                                 Page 4 of 9
people and they can co-exist with normal bacteria and cause no symptoms (“commensal”) 
or lead to serious infection spreading to the blood and other organs (“invasive”). Invasive 
infection is more common in patients with compromised immunity. Infections caused by 
MDRO are correlated with increased illness, death and prolonged hospitalization. Measures 
have been implemented for donor screening (exclude donors at higher risk of MDRO 
infection) and donor stool testing (exclude stool that tests positive for MDRO)

Uncommon risks associated with fecal transplantation that have been documented in the 
literature include cramping, fullness, passing gas, bloating, vomiting, diarrhea, fever, and 
blood in the stool. Since this is a research study, not all risks associated with fecal 
transplantation are known at this time; there may be unforeseen risks associated with study 
participation. 

There are risks associated with colonoscopy: infection, bleeding, and less than a 1% chance 
of a perforation or hole being created (A separate consent form for colonoscopy will be 
given on the day of fecal transplantation). 

If you have Inflammatory Bowel Disease, it may progress or get worse after the 
transplantation. 

When your blood is drawn, temporary pain and bruising where the needle enters the skin, 
and sometimes, fainting and/or infection. 

There is a rare possibility that confidential information about you may be accidentally 
disclosed. 

Some of the research that will be done on your blood are genetic studies. The genetic 
studies are only for research, and will not be used in making decisions about your care. We 
will not contact you about any results of these genetic studies. 

If you have an additional fecal transplant, the same risks (as above) will again apply. 
BENEFITS 
The following benefits may occur as a result of being in this study: 
The potential direct benefits to you of having the fecal transplantation for treatment of Clostridium 
difficile is improvement in your diarrhea, abdominal pain, and eradication of the Clostridium 
difficile bacteria. The indirect benefits include contributions to our knowledge regarding the safety, 
efficacy and tolerability of fecal microbiota transplantation. Additionally, by performing research 
studies examining the bacteria in your stool, as well as performing genetic studies, we hope to see 
if there is a link between genetics and colonic bacteria, as well as determine the relative abundance 
of each bacterium. This will also enable us to see if performing the stool transplant changed the 
composition of your stool and may one day lead to creating medications that increase healthy 
bacteria in the colon or target harmful bacteria. 
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PAYMENT TO YOU
You will not be paid for your participation in this study. This research might create new tests, 
treatment, or cures. If it does, you will not get any money from those products. 
CONFIDENTIALITY 
We will take steps to help make sure that all the information we get about you is kept confidential. 
Your name will not be used wherever possible. We will use a code instead. All the study data that 
we get from you will be kept locked up. The code will be locked up too. If any papers and talks are 
given about this research, your name will not be used. 
We want to make sure that this study is being done correctly and that your rights and welfare are 
being protected. For this reason, we will share the data we get from you in this study with the 
study team, Stony Brook University's Committee on Research Involving Human Subjects, applicable 
Institutional officials, and certain federal offices. However, if you tell us you are going to hurt 
yourself, hurt someone else, or if we believe the safety of a child is at risk, we will have to report 
this. 
This study requires that we collect very private information about you. Therefore, we had the 
National Institutes of Health give us a Certificate of Confidentiality (COC). This piece of paper says 
that nobody can force the researchers to give out your information, even if a court of law asks for 
it. This will give you more protection. The only time information about you can be given out is: 
If you are going to hurt yourself. 
If you are going to hurt someone else. 
If we believe the safety of a child is at risk. 
If data about the fecal transplantation needs to be reported to the Food and Drug Administration. 
If the data are required by other federal, state or local laws, such as for reporting of communicable 
diseases.
You should know that the Certificate of Confidentiality does not apply to information about your 
participation in research, including a consent form that is placed in your medical record (though 
HIPAA protection does apply). This information may be disclosed to individuals requesting your 
medical record.
This Certificate doesn’t mean you can’t talk about this study. If you give written permission, your 
insurance company, your boss, or your private doctor can be given the research information too. 
While you are in this study we will get data about your health from your medical record. We will 
also get health data from the results of the tests you will have done in this study. You have a right 
to privacy but the data we get about your health in this study can be shared with the people 
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referenced above (the study team, Stony Brook University's Committee on Research Involving 
Human Subjects, applicable institutional officials, and certain federal offices) as well as (as 
applicable):

Your private doctor 

A board that reviews the safety of the study on an on-going basis. 
Your health data are shared to make sure the study is being done correctly, costs are charged 
correctly, and to make sure your rights and safety are protected. Not all of these people are 
required by law to protect your health data. They might share it with others without your 
permission. 
You have the right to stop allowing us to use or give out your health data. You can do this at any 
time by writing to Anupama Chawla, MD. If you do this, we will stop collecting any new health data 
from you, except if we need to keep an eye on a bad side effect you were having in the study. We 
will use any data we collected before you wrote your letter. When you sign the consent form at the 
end, it means: 

That you have read this section. 

That you will allow the use and reporting of your health data as described above. 

You have received a form from the University Hospital. It is called the Notice of Privacy 
Practices form. 
The Genetic Information Nondiscrimination Act (GINA)
You should know that a federal law called the Genetic Information Nondiscrimination Act (GINA) 
generally makes it illegal for health insurance companies, group health plans, and most employers 
to discriminate against you based on your genetic information. This law will generally protect you 
in the following ways:
§ Health insurance companies and group health plans may not request your genetic information 
from this research.
§ If health insurance companies and group health plans do somehow receive your genetic 
information from this research, they may not use it to make decisions about your eligibility or 
premiums.
§ Employers with 15 or more employees may not use your genetic information from this research 
when making a decision to hire, promote, or fire you when setting the terms of your employment.
Be aware that this new law does not protect you against genetic discrimination by companies that 
sell life insurance, disability insurance, or long-term care insurance.
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COSTS TO YOU 

As fecal transplant for the treatment of Clostridium difficile is now considered standard of 
care, we will obtain a prior authorization for colonoscopy to perform the transplant from 
your insurance company if needed. You may have to pay for a portion of the colonoscopy 
depending on your insurance plan. We encourage you to contact your insurance company 
to discuss this potential cost prior to consenting to be in the study.

All stool tests and bloodwork for research purposes will be performed without any cost to 
you for participating in this study. 
ALTERNATIVES

An alternative to performing the fecal microbiota transplantation is administration of 
additional antibiotics, some of which may have already been ineffective or trying 
combinations of different antibiotics that may or may not work in eradicating the disease.

The other alternative to performing the fecal microbiota transplantation for Clostridium 
difficile is living with abdominal pain and diarrhea associated with this disease, which can 
eventually lead to malabsorption problems, anemia and potential for bowel perforation and 
need for surgery.

The fecal microbial transplantation is approved as a treatment option by the FDA for 
Clostridium difficile infection. You can get this treatment at any other facility in the USA that 
offers this option without taking part in the study. Stony Brook Hospital does not offer this 
treatment without the study protocol.
IN CASE OF INJURY
If you are injured as a result of being in this study, please contact Dr. Anupama Chawla at 
telephone # 631-444-8115. The services of Stony Brook University Hospital will be open to you in 
case of such injury. However, you and/or your insurance company will be responsible for payment 
of any resulting treatment and/or hospital stay.
CONSEQUENCES OF WITHDRAWING
You may withdraw your consent at any time by contacting Dr. Anupama Chawla. If you do this, we 
will stop collecting any new health data from you for research purposes but will continue to use the 
data we collected prior to your withdrawal. Your choice will not at any time affect the commitment 
of your health care providers to administer care. There will be no penalty or loss of benefits to 
which you are otherwise entitled.
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                                                                                                                 Page 8 of 9
YOUR RIGHTS AS A RESEARCH SUBJECT

Your participation in this study is voluntary. You do not have to be in this study if you don't 
want to be.

You have the right to change your mind and leave the study at any time without giving any 
reason, and without penalty.

Any new information that may make you change your mind about being in this study will be 
given to you.

You will get a signed and dated copy of this consent form to keep.

You do not lose any of your legal rights by signing this consent form.
QUESTIONS ABOUT THE STUDY OR YOUR RIGHTS AS A RESEARCH SUBJECT

If you have any questions, concerns, or complaints about the study, you may contact Dr. 
Anupama Chawla, at telephone # (631-444-8115).

If you have any questions about your rights as a research subject or if you would like to 
obtain information or offer input, you may contact Stony Brook University Research Subject 
Advocate, Ms. Lu-Ann Kozlowski, BSN, RN, (631) 632-9036, OR by e-mail,
lu-ann.kozlowski@stonybrook.edu.

Visit Stony Brook University’s Community Outreach page, 
http://research.stonybrook.edu/orc/community.shtml#overview-of-volunteering-in-
research for more information about participating in research, frequently asked questions, 
and an opportunity to provide feedback, comments, or ask questions related to your 
experience as a research subject.
If you sign below, it means that you have read (or have had read to you) the information given in 
this consent form, and you would like to be a volunteer in this study.
Please initial your response to each statement below.___________________________________ 
1. I have been told about the risks, benefits, and alternatives to fecal microbiota transplantation, 
and I wish to undergo the procedure.
Yes_____ No _____
2. I agree to follow-up via telephone so that the study investigators can evaluate my general well-
being for one year post-transplant.
Yes_____ No _____
3. I agree to give a stool specimen 1-3 days prior to the fecal microbiota transplantation, 1 week 
post-transplant, and 3 months post-transplant.
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                                                                                                                 Page 9 of 9
Yes_____ No _____
4. I agree to have my blood drawn on the day of fecal microbiota transplantation for research.
Yes_____ No _____
_________________________________      ___________________________________________
Subject Name (Printed) 
Subject Signature 
Date
_________________________________      ____________________________________________
Name of Person Obtaining Consent 
Signature of Person Obtaining Consent 
Date
(Printed)
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 1 of 4
RECIPIENT RESEARCH ASSENT FORM  (UC/IC)
Project Title: Fecal microbial transplantation in patients with medication-refractory                        
Clostridium difficile and/or Ulcerative colitis or indeterminate colitis 
Principal Investigator: Anupama Chawla, MD 
You are being asked to be in a research study. 
Purpose: To determine the safety and tolerability of fecal (stool) transplantation to treat Ulcerative 
colitis or indeterminate colitis. 
What Will Be Done: If you decide to be in this study, your part will involve: 

You will first have to choose somebody who will donate the stool which will be 
transplanted. The donor can be anyone who we will consent separately and meets eligibility 
criteria to donate stool. He/she will be asked questions and screened by performing blood 
work and stool studies to make sure he/she is a healthy candidate for stool transplantation. 

After the donor is chosen and he/she meets criteria to donate stool, we will give you a date 
for the fecal transplantation. During the week before fecal transplantation, we will ask you 
to write down everything you have eaten on a diet record which we will provide to you. 
Stool will be collected 1-3 days before your day of fecal transplantation for research. 

On the day before your transplant, you will be given instructions for a bowel prep to clean 
out your colon completely so it can be examined when we perform the fecal 
transplantation. For the last 7 hours before your scheduled fecal transplantation, you will 
have nothing to eat or drink. 

On the day of the transplantation, you will arrive at Stony Brook University Hospital and go 
to the Endoscopy Suite, located on the 14th Floor. There you will change into a hospital 
gown and an intravenous line (IV) will be placed to provide you with fluids and sedation 
during the colonoscopy. Four teaspoons of blood will be taken for research, to perform 
genetic studies. 

Your donor’s stool will be prepared and while you are properly sedated, the stool will be 
instilled into your colon. You will stay in the Endoscopy Suite, lying on your right side, for at 
least one hour. This is to maximize contact between the transplanted stool and your colon.   
If you are not cleared to depart after one hour, you will stay until the anesthesiologist 
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 2 of 4
(doctor who administered sedation during colonoscopy) does clear you to depart. You will 
be able to eat and drink right after you wake up and can resume normal activities as soon as 
the anesthesia wears off and you feel well.

You will receive a phone call the day after the procedure and be asked various questions to 
determine your general well-being.

You will then receive weekly phone calls for 12 weeks at a convenient time for you, to ask 
you further general well-being questions.

You will keep another diet record during the first week after the transplant. 1 week after 
your fecal transplantation you will collect stool for research, similar to how you collected 
stool prior to your stool transplantation. 

You will keep another diet record during the 12th week after the transplant. 12 weeks after 
your fecal transplantation you will collect stool for research, similar to how you collected 
stool prior to your stool transplantation.

After 12 weeks, you will receive monthly phone calls until one year after the transplant to 
determine your general well-being. 
Costs to You:

You may have to pay for a portion of the colonoscopy, depending on your insurance 
plan. We encourage you to contact your insurance company to discuss this potential 
cost prior to consenting to be in the study. 

Stool tests and bloodwork for research purposes will be performed without any cost to 
you for participating in this study.
Payments to you: You will not be paid for your participation in this study.
Risks/Discomforts:

Although donor stool is checked for bad germs, there is a still a small chance of an 
infection being passed from the donor’s stool to you.

Uncommon risks associated with fecal transplantation include cramping, fullness, gas, 
bloating, diarrhea, fever, and blood in the stool. Since this is a research study, not all 
risks associated with fecal transplantation are known at this time; there may be 
unknown risks associated with being in this study.

There are risks associated with colonoscopy: infection, bleeding, and less than a 1% 
chance of a perforation or hole being created (A separate consent form for colonoscopy 
will be given on day of fecal transplantation).

Your colitis may get worse after the transplantation.

When your blood is drawn, temporary pain and bruising where the needle enters the 
skin, and sometimes, fainting and/or infection.

There is a rare possibility that confidential information about you may be accidentally 
disclosed.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 3 of 4
Benefits: The potential direct benefits to you of having the fecal transplantation for treatment of 
Ulcerative colitis or indeterminate colitis is improvement in your diarrhea, abdominal pain, and 
symptoms associated with your colitis.
The indirect benefits include increased knowledge regarding the safety of fecal transplantation. 
Additionally, by performing research studies examining the bacteria in your stool as well as 
performing genetic studies we hope to see if there is a link between genetics and colonic bacteria 
as well as determine the relative abundance of each bacteria. This will also help us see if 
performing the stool transplant changed the bacteria in your stool and may one day lead to 
creating medications that increase healthy bacteria in the colon or target harmful bacteria.
In Case of Injury: If you are injured as a result of being in this study, please contact Dr. Anupama 
Chawla at telephone # 631-444-8115. The services of Stony Brook University Hospital will be open 
to you in case of such injury. However, you and/or your insurance company will be responsible for 
payment of any resulting treatment and/or hospital stay. 
Your Rights:

You do not have to be in this study if you don't want to be. 

You have the right to change your mind and leave the study at any time without giving 
any reason, and without penalty. 

Any new information that may make you change your mind about being in this study 
will be given to you. 

You will get a signed and dated copy of this assent form to keep. 

You do not lose any of your legal rights by signing this consent form. 
Questions: 
If you have any questions about this study, you can ask your parents, or talk to the study doctor, 
Dr. Anupama Chawla at 631-444-8115. 
If you want to talk to someone about whether or not you have to be in this study, or about other 
things about this study that you don’t want to talk over with your parents or the study doctor, you 
can call Ms. Lu-Ann Kozlowski, 631-632-9036, or e-mail her at lu-ann.kozlowski@stonybrook.edu.
You can visit this webpage, http://research.stonybrook.edu/orc/community.shtml#overview-of-
volunteering-in-research for information about being in research studies. You can also ask 
questions or leave comments about how you feel about being a research subject in this study.
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Page 4 of 4
If you sign below, it means that you have read this form and you would like to be in this study.
Please initial your response to each statement below.__________________________________ 
1. I have been told about the risks, benefits, and alternatives to fecal transplantation, and I wish to 
undergo the procedure. 
Yes_____ No _____ 
2. I agree to follow-up telephone calls for one year after the transplant so that the study 
investigators can evaluate my health. 
Yes_____ No _____ 
3. I agree to give a stool specimen 1-3 days before the fecal transplantation, 1 week after the 
transplant, and 3 months after the transplant for research. 
Yes_____ No _____ 
4. I agree to have my blood drawn on the day of fecal transplantation for research. 
Yes_____ No _____ 
____________________________________        _____________________________    _______
Subject Name (Printed) 
                     Subject Signature 
                         Date 
____________________________________        _____________________________    _______
Name of Person Obtaining Assent
       Signature of Person Obtaining Assent    Date
(Printed)
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 1 of 4
RECIPIENT RESEARCH ASSENT FORM (CDIFF)
Project Title: Fecal microbial transplantation in patients with medication-refractory
Clostridium difficile and/or Ulcerative colitis or indeterminate colitis 
Principal Investigator: Anupama Chawla, MD 
You are being asked to be in a research study. 
Purpose: To determine the safety, tolerability and effectiveness of fecal (stool) transplantation to 
treat Clostridium difficile infection. 
What Will Be Done: If you decide to be in this study, your part will involve: 

You will first have to choose somebody who will donate the stool which will be 
transplanted. The donor can be anyone who we will consent separately and meets eligibility 
criteria to donate stool. He/she will be asked questions and screened by performing blood 
work and stool studies to make sure he/she is a healthy candidate for stool transplantation. 

After the donor is chosen and he/she meets criteria to donate stool, we will give you a date 
for the fecal transplantation. During the week before fecal transplantation, we will ask you 
to write down everything you have eaten on a diet record which we will provide to you. 
Stool will be collected 1-3 days before your day of fecal transplantation for research. 

On the day before your transplant, you will be given instructions for a bowel prep to clean 
out your colon completely so it can be examined when we perform the fecal 
transplantation. For the last 7 hours before your scheduled fecal transplantation, you will 
have nothing to eat or drink. 

On the day of the transplantation, you will arrive at Stony Brook University Hospital and go 
to the Endoscopy Suite, located on the 14th Floor. There you will change into a hospital 
gown and an intravenous line (IV) will be placed to provide you with fluids and sedation 
during the colonoscopy. Four teaspoons of blood will be taken for research, to perform 
genetic studies. 

Your donor’s stool will be prepared and while you are properly sedated, the stool will be 
instilled into your colon. You will stay in the Endoscopy Suite, lying on your right side, for at 
least one hour. This is to maximize contact between the transplanted stool and your colon.   
If you are not cleared to depart after one hour, you will stay until the anesthesiologist 
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 2 of 4
(doctor who administered sedation during colonoscopy) does clear you to depart. You will 
be able to eat and drink right after you wake up and can resume normal activities as soon as 
the anesthesia wears off and you feel well. 

You will receive a phone call the day after the procedure, and be asked various questions to 
determine your general well-being.

You will then receive weekly phone calls for 12 weeks at a convenient time for you, to ask 
you further general well-being questions.

You will keep another diet record during the first week after the transplant. 1 week after 
your fecal transplantation you will collect stool for research, similar to how you collected 
stool prior to your stool transplantation. 

If symptoms of Clostridium difficile infection reappear after your stool transplant, you will 
be asked to provide a stool sample to a laboratory to check for Clostridium difficile bacteria.

You will keep another diet record during the 12th week after the transplant. 12 weeks after 
your fecal transplantation you will collect stool for research, similar to how you collected 
stool prior to your stool transplantation.

After 12 weeks, you will receive monthly phone calls until one year after the transplant to 
determine your general well-being. 
Costs to You:

As fecal transplant for the treatment of Clostridium difficile is now considered standard 
of care, we will obtain a prior authorization for colonoscopy to perform the transplant 
from your insurance company if needed. You may have to pay for a portion of the 
colonoscopy depending on your insurance plan. We encourage you to contact your 
insurance company to discuss this potential cost prior to consenting to be in the study.

Stool tests and bloodwork for research purposes will be performed without any cost to 
you for participating in this study.
Payments to you:  You will not be paid for your participation in this study.
Risks/Discomforts:

Although donor stool is checked for bad germs, there is a still a small chance of an 
infection being passed from the donor’s stool to you.

Uncommon risks associated with fecal transplantation include cramping, fullness, gas, 
bloating, diarrhea, fever and blood in the stool. Since this is a research study, not all 
risks associated with fecal transplantation are known at this time; there may be 
unknown risks associated with being in this study.

There are risks associated with colonoscopy: infection, bleeding, and less than a 1% 
chance of a perforation or hole being created (A separate consent form for colonoscopy 
will be given on day of fecal transplantation).

If you have Inflammatory Bowel Disease, it may get worse after the transplantation. 
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 3 of 4

When your blood is drawn, temporary pain and bruising where the needle enters the 
skin, and sometimes, fainting and/or infection.

There is a rare possibility that confidential information about you may be accidentally 
disclosed.
Benefits:  The potential direct benefits to you of having the fecal transplantation for treatment of 
Clostridium difficile is improvement in your diarrhea, abdominal pain, and eradication of the 
bacteria. 
The indirect benefits include increased knowledge about the safety and effectiveness of fecal 
transplantation. Additionally, by performing research studies examining the bacteria in your stool, 
as well as performing genetic studies, we hope to see if there is a link between genetics and colonic 
bacteria as well as determine the relative abundance of each bacteria. This will also help us see if 
performing the stool transplant changed the bacteria in your stool and may one day lead to 
creating medications that increase healthy bacteria in the colon or target harmful bacteria. 
In Case of Injury: If you are injured as a result of being in this study, please contact Dr. Anupama 
Chawla at telephone # 631-444-8115. The services of Stony Brook University Hospital will be open 
to you in case of such injury. However, you and/or your insurance company will be responsible for 
payment of any resulting treatment and/or hospital stay. 
Your Rights:

You do not have to be in this study if you don't want to be. 

You have the right to change your mind and leave the study at any time without giving 
any reason, and without penalty. 

Any new information that may make you change your mind about being in this study 
will be given to you. 

You will get a signed and dated copy of this assent form to keep. 

You do not lose any of your legal rights by signing this consent form. 
Questions: 
If you have any questions about this study, you can ask your parents, or talk to the study doctor, 
Dr. Anupama Chawla at 631-444-8115. 
If you want to talk to someone about whether or not you have to be in this study, or about other 
things about this study that you don’t want to talk over with your parents or the study doctor, you 
can call Ms. Lu-Ann Kozlowski, 631-632-9036, or e-mail her at lu-ann.kozlowski@stonybrook.edu
You can visit this webpage, http://research.stonybrook.edu/orc/community.shtml#overview-of-
volunteering-in-research for information about being in research studies. You can also ask 
questions or leave comments about how you feel about being a research subject in this study.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 4 of 4
If you sign below, it means that you have read this form and you would like to be in this study.
Please initial your response to each statement below._________________________________ 
1. I have been told about the risks, benefits, and alternatives to fecal transplantation, and I wish to 
undergo the procedure. 
Yes_____ No _____ 
2. I agree to follow-up telephone calls for one year after the transplant so that the study 
investigators can evaluate my health.
Yes_____ No _____ 
3. I agree to give a stool specimen 1-3 days before the fecal transplantation, 1 week after the 
transplant, and 3 months after the transplant for research. 
Yes_____ No _____ 
4. I agree to give permission to have my blood drawn on the day of fecal transplantation
 for research. 
Yes_____ No _____ 
____________________________________        ____________________________     ________
Subject Name (Printed) 
        Subject Signature 
                         Date 
____________________________________        _____________________________   ________
Name of Person Obtaining Assent
       Signature of Person Obtaining Assent    Date
(Printed)
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 1 of 7
 DONOR RESEARCH PERMISSION/CONSENT FORM  (CDIFF/UC/IC)
Project Title: Fecal microbial transplantation in patients with medication-refractory Clostridium 
difficile and/or Ulcerative colitis or indeterminate colitis
Principal Investigator: Anupama Chawla, MD
Co-Investigator: 
 Ellen Li, MD PhD
Departments: 
 Pediatric Gastroenterology & Nutrition and Medicine/Gastroenterology
When we say “you” in this consent form, we mean you or your child; “we” means the doctors and 
other staff. If you are a parent or legal guardian of a child who may take part in this study, 
permission from you is required and the assent (agreement) of your child may be required.
You are being asked to be a volunteer in a research study. You are encouraged to take your time 
in making your decision. You may want to discuss this study with your friends and family. 
PURPOSE 
The purpose of this study is: 

To determine the safety and tolerability of fecal (stool) transplantation to treat Clostridium 
difficile and/or Ulcerative colitis or indeterminate colitis.

Ulcerative colitis (UC) is a chronic disease affecting the colon, without a medical cure. The 
precise cause of having inflammatory bowel disease (IBD) such as UC, Crohn’s disease, or 
indeterminate colitis is unclear. However, genetics and the environment are thought to play 
a role. Studies have found that patients with UC have a decreased prevalence of protective 
bacteria and an increase in harmful bacteria in the colon. Inflammation in the colon in these 
patients is thought to be due to this imbalance between helpful and harmful bacteria. 
Currently, the treatment of IBD includes steroids, anti-inflammatory medications and 
biological therapy, each with its own side effects. Given the role of the gastrointestinal 
bacteria in driving inflammation in patients with IBD, treatments that manipulate these 
bacteria have been investigated, including the use of medications containing beneficial 
bacteria (probiotics), with some benefit. Fecal transplantation (FMT), the transfer of 
gastrointestinal bacteria (microbiota) from a healthy donor via infusion of a liquid stool 
suspension, is proving to be an effective alternative treatment for medication-resistant UC 
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Page 2 of 7
or indeterminate colitis. The goal of this method is to remove the harmful bacteria in the 
colon and replace them with normal bacteria.

Clostridium difficile is a bacteria that can cause abdominal pain and diarrhea which is often 
bloody. This can lead to not absorbing nutrients from food properly, becoming anemic, and 
feeling tired. In severe cases, patients have to be hospitalized to provide them with 
intravenous fluids, antibiotics, or to treat their pain. Patients may even require colon 
surgery if the bacteria causes intractable pain and diarrhea or leads to a hole being created 
in the colon. It is also the leading cause of antibiotic-associated diarrhea, with increasing 
infection rates. The bacteria is usually treated with antibiotics such as metronidazole 
(Flagyl) or vancomycin. However, these antibiotics do not work all the time, due to resistant 
strains of Clostridium difficile. When a person is infected with these bacteria, he/she has a 
high percentage of these bacteria compared to all the other normal bacteria which are 
usually found in their colon. Fecal transplantation is proving to be an effective alternative 
treatment for medication-resistant Clostridium difficile. The goal of this method is to 
remove the harmful bacteria such as Clostridium difficile in the colon and replace them with 
normal bacteria.

_______________________________(recipient’s name) has one of these conditions and 
has named you as a potential stool donor so that the fecal transplantation can be 
performed. This study, hopes to document fecal transplant’s safety, tolerability and 
effectiveness and improve or even eliminate ___________________’s symptoms by 
performing the transplantation and then follow-up up routinely with him/her for one year.

We will perform stool studies on you to see if the bacteria in your colon really did change 
the composition of ___________________’s colonic bacteria. 
We expect to enroll a minimum of 100 patients in this study at Stony Brook University Hospital.
PROCEDURES 
If you decide to be in this study, your part will involve: 

Answering a questionnaire to determine your eligibility to donate stool to the transplant 
recipient. 

If you are eligible, you will be asked to have stool testing and blood work done in a 
laboratory to evaluate for infectious agents that may theoretically be transferred to the 
recipient by your stool. 

If all this testing is negative, then you and the stool recipient will be given a date for the 
stool transplant and you will be told to avoid ____________________________ (recipient 
allergen) for up to one week before the transplant. 

During the week before fecal transplantation, we will ask you to record everything you have 
eaten on a diet record which we will provide to you. 
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 3 of 7

On the night before or morning of fecal transplantation, you will be told to collect the stool 
using SaranTM Wrap, plastic hat, or a collection container. The stool will need to be collected 
prior to any contamination with the toilet bowl. The stool should then be kept in an airtight 
container which will be provided to you. 

The stool may be kept at room temperature if used within 6 hours or kept in a refrigerator 
for up to 24 hours. Stool sample must not be frozen. 

Stool is to be transported from the home to the hospital on ice packs. 

On the day of transplant, you will come to Stony Brook University Hospital’s Endoscopy 
Suite, located on the 14th Floor, and drop off the stool.  You will be asked if you had a fever 
in the previous 2 weeks or accidentally ingested _____________ (recipient allergen) in the 
past week. 
When you are first recruited for the study, you will be assigned a coded number. Stool samples 
collected from you will have your coded number, so your information will not be directly linked to 
your samples, medical or diet diary information.
RISKS / DISCOMFORTS 
The following risks/discomforts may occur as a result of you being in this study: 

When your blood is drawn, temporary pain and bruising where the needle enters the skin, 
and sometimes, fainting and/or infection. 

As part of the study, blood work to test for HIV (the virus that causes AIDS), Hepatitis B, 
Hepatitis C, and Syphilis will be performed. If these tests come back as positive, the results 
will be discussed with you in a confidential manner. If you do test positive for HIV infection, 
the importance of telling your sex or needle-sharing partners of possible exposure will be 
discussed. 

There is a rare possibility that confidential information about you may be accidentally 
disclosed.
BENEFITS
There is no direct benefit to you as a result of participating in this study.
The potential indirect benefits include helping the recipient feel better. Indirect benefits also 
include contributions to our knowledge regarding the safety, efficacy, and tolerability of fecal 
microbiota transplantation. Performing research studies on your stool may enable us to see if 
performing the stool transplant changed the composition of the recipient’s stool and may one day 
lead to creating medications that increase healthy bacteria in the colon or target harmful bacteria.
PAYMENT TO YOU
You will not be paid for your participation in this study. This research might create new tests, 
treatment, or cures. If it does, you will not get any money from those products.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 4 of 7
PAYMENT TO THE INSTITUTION
This project has no outside funding.
CONFIDENTIALITY
Protecting Your Privacy in this Study
We will take steps to help make sure that all the information we get about you is kept confidential. 
Your name will not be used wherever possible. We will use a code instead. All the study data that 
we get from you will be kept locked up. The code will be locked up too. If any papers and talks are 
given about this research, your name will not be used.
We want to make sure that this study is being done correctly and that your rights and welfare are 
being protected. For this reason, we will share the data we get from you in this study with the 
study team, Stony Brook University's Committee on Research Involving Human Subjects, applicable 
Institutional officials, and certain federal offices. However, if you tell us you are going to hurt 
yourself, hurt someone else, or if we believe the safety of a child is at risk, we will have to report 
this.
This study requires that we collect very private information about you. Therefore, we had the 
National Institutes of Health give us a Certificate of Confidentiality (COC). This piece of paper says 
that nobody can force the researchers to give out your information, even if a court of law asks for 
it. This will give you more protection. The only time information about you can be given out is:
If you are going to hurt yourself.
If you are going to hurt someone else.
If we believe the safety of a child is at risk.
If data about the fecal transplantation needs to be reported to the Food and Drug Administration.
If the data are required by other federal, state or local laws, such as for reporting of communicable 
diseases.
You should know that the Certificate of Confidentiality does not apply to information about your 
participation in research, including a consent form that is placed in your medical record (though 
HIPAA protection does apply). This information may be disclosed to individuals requesting your 
medical record.
This Certificate doesn’t mean you can’t talk about the study. If you give written permission, your 
insurance company, your boss, or your private doctor can be given the research information too.
While you are in this study we will get health data from the results of the tests you will have done 
in this study. You have a right to privacy but the data we get about your health in this study can be 
shared with the people referenced above (the study team, Stony Brook University’s Committee on 
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Stony Brook University Human Subjects Committee (IRB)

Page 5 of 7
Research Involving Human Subjects, applicable institutional officials, and certain federal offices) as 
well as:

Your private doctor

A board that reviews the safety of the study on an on-going basis.
Your health data are shared to make sure the study is being done correctly, costs are charged 
correctly, and to make sure your rights and safety are protected. Not all of these people are 
required by law to protect your health data. They might share it with others without your 
permission.
You have the right to stop allowing us to use or give out your health data. You can do this at any 
time by writing to Anupama Chawla, MD. If you do this, we will stop collecting any new health data 
from you, except if we need to keep an eye on a bad side effect you were having in the study. We 
will use any data we collected before you wrote your letter. When you sign the consent form at the 
end, it means:

That you have read this section.

That you will allow the use and reporting of your health data as described above.

You have received a form from the University Hospital. It is called the Notice of Privacy 
Practices form.
COSTS TO YOU

You will be responsible for your stool and blood work for screening. Depending upon your 
insurance plan, the cost of this screening might not be covered and you may have to pay 
out of pocket for this process. We encourage you to contact your insurance company to 
discuss this potential cost prior to consenting to be in the study.

When you are approved to be the donor for the research study from your screening results, 
all stool tests thereafter for research purposes will be performed without any costs to you 
for participating in this study.
ALTERNATIVES

Your alternative to being in this study is to simply not participate.
IN CASE OF INJURY
If you are injured as a result of being in this study, please contact Dr. Anupama Chawla at 
telephone # 631-444-8115. The services of Stony Brook University Hospital will be open to you in 
case of such injury. However, you and/or your insurance company will be responsible for payment 
of any resulting treatment and/or hospital stay.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 6 of 7
CONSEQUENCES OF WITHDRAWING
You may withdraw your consent at any time by contacting Dr. Anupama Chawla. If you do this, we 
will stop collecting any new health data from you for research purposes but will continue to use the 
data we collected prior to your withdrawal. Your choice will not at any time affect the commitment 
of your health care providers to administer care. There will be no penalty or loss of benefits to 
which you are otherwise entitled.
YOUR RIGHTS AS A RESEARCH SUBJECT

Your participation in this study is voluntary. You do not have to be in this study if you don't 
want to be.

You have the right to change your mind and leave the study at any time without giving any 
reason, and without penalty.

Any new information that may make you change your mind about being in this study will be 
given to you.

You will get a signed and dated copy of this consent form to keep.

You do not lose any of your legal rights by signing this consent form.
QUESTIONS ABOUT THE STUDY OR YOUR RIGHTS AS A RESEARCH SUBJECT

If you have any questions, concerns, or complaints about the study, you may contact
Dr. Anupama Chawla, at telephone # (631-444-8115).

If you have any questions about your rights as a research subject or if you would like to 
obtain information or offer input, you may contact Stony Brook University Research Subject 
Advocate, Ms. Lu-Ann Kozlowski, BSN, RN, (631) 632-9036, OR by e-mail,
lu-ann.kozlowski@stonybrook.edu.

Visit Stony Brook University’s Community Outreach page, 
http://research.stonybrook.edu/orc/community.shtml#overview-of-volunteering-in-
research for more information about participating in research, frequently asked questions, 
and an opportunity to provide feedback, comments, or ask questions related to your 
experience as a research subject.
If you sign below, it means that you have read (or have had read to you) the information given in 
this consent form, and you would like to be a volunteer in this study.
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 7 of 7
Please initial your response to each statement below.____________________________________ 
1. I have been told about the risks, benefits, and alternatives to being screened for fecal microbiota 
transplantation, and I wish to be a donor.
Yes_____ No _____
2. I agree to give a stool specimen on the day of the fecal microbiota transplantation 
    
Yes_____ No _____
_________________________________       _____________________________________________
Subject Name (Printed) 
Subject Signature
            Date
_________________________________       _____________________________________________
Name of Person Obtaining Consent 
Signature of Person Obtaining Consent         Date
(Printed)
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 1 of 3
DONOR RESEARCH ASSENT FORM   (CDIFF/UC/IC)
Project Title: Fecal microbial transplantation in patients with medication-refractory Clostridium 
difficile and/or Ulcerative colitis or indeterminate colitis
Principal Investigator: Anupama Chawla, MD
You are being asked to be in a research study.
Purpose: To determine the safety and tolerability of fecal (stool) transplantation to treat 
Clostridium difficile and/or Ulcerative colitis or indeterminate colitis.
What Will Be Done: If you decide to be in this study, your part will involve: 

Answering a questionnaire to see if you are able to donate stool to the transplant recipient. 

If you are eligible, you will be asked to have stool testing and blood tests done in a 
laboratory to see if you have harmful germs that might be transferred to the recipient by 
your stool. About 2-3 teaspoons of blood will be drawn from your arm vein for the blood 
tests. 

If all this testing is negative, then you and the stool recipient will be given a date for the 
stool transplant and you will be told to avoid _______________________ (recipient 
allergen) for up to one week before the transplant.

During the week before fecal transplantation, we will ask you to record everything you have 
eaten on a diet record which we will provide to you. 

On the night before or morning of fecal transplantation, you will be told to collect the stool 
using SaranTM Wrap, plastic hat, or a collection container. The stool will need to be collected 
before any contamination with the toilet bowl. The stool should then be kept in an airtight 
container which we will give you.

The stool may be kept at room temperature if used within 6 hours or kept in a refrigerator 
for up to 24 hours. Stool sample must not be frozen.

Stool is to be transported from the home to the hospital on ice packs.

On the day of transplant, you will come to Stony Brook University Hospital’s Endoscopy 
Suite, located on the 14th Floor, where you will drop off the stool and be asked if you had a 
fever in the previous 2 weeks or accidentally ate _____________ (recipient allergen) in the 
past week. 
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 2 of 3
Costs to You:
You may have to pay for the stool and blood tests, depending on your insurance plan. We 
encourage you or your parent/guardian to contact your insurance company to discuss this before 
you agree to be in the study. 
Payments to you: You will not be paid for being in this study. 
Risks/Discomforts: 

When your blood is drawn, temporary pain and bruising where the needle enters the skin, 
and sometimes, fainting and/or infection. 

As part of the study, blood work to test for HIV (the virus that causes AIDS), Hepatitis B, 
Hepatitis C, and Syphilis will be performed. If these tests come back as positive, the results 
will be discussed with you. If you do test positive for HIV infection, the importance of telling 
your sex or needle-sharing partners of possible exposure will be discussed. 

There is a rare possibility that confidential information about you may be accidentally 
disclosed. 
Benefits: There is no direct benefit to you as a result of participating in this study. 
The potential indirect benefits include helping the recipient feel better. Indirect benefits also 
include helping us learn more about the safety and effectiveness of fecal transplantation. 
Performing research studies on your stool may help us find out if performing the stool transplant 
changed the bacteria in the recipient’s stool and may one day lead to creating new medications 
that increase healthy bacteria in the colon or target harmful bacteria. 
In Case of Injury: If you are injured as a result of being in this study, please contact Dr. Anupama 
Chawla at telephone # 631-444-8115. The services of Stony Brook University Hospital will be open 
to you in case of such injury. However, you and/or your insurance company will be responsible for 
payment of any resulting treatment and/or hospital stay. 
Your Rights: 

The fact that you are in this study will be kept a secret. 

You do not have to be in this study if you do not want to be. 

You can change your mind at any time and leave the study without any problem and 
without telling us why. 

If we find out anything that may make you change your mind about being in this study, we 
will tell you. 
Questions: 
If you have any questions about this study, you can ask your parents, or talk to the study doctor,
Dr. Anupama Chawla at 631-444-8115. 
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Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)

Page 3 of 3
If you want to talk to someone about whether or not you have to be in this study or about other 
things about the study that you do not want to talk over with your parents or the study doctor, you 
can call Ms. Lu-Ann Kozlowski, 631-632-9036, or e-mail her at lu-ann.kozlowski@stonybrook.edu 
You can visit this webpage, http://research.stonybrook.edu/orc/community.shtml#overview-of-
volunteering-in-research for information about being in research studies. You can also ask 
questions or leave comments about how you feel about being a research subject in this study. 
If you sign below, it means that you have read this form and you would like to be in this study.
Please initial your response to each statement below._________________________________ 
1. I have been told about the risks, benefits, and alternatives to being screened for stool 
transplantation, and I wish to be a donor. 
Yes_____
 No _____ 
2. I agree to give a small part of my stool specimen on the day of the stool transplantation.
   
Yes_____ 
No _____ 
______________________________ 
______________________________      _______ 
Subject Name (Printed) 
Subject Signature 
        Date 
______________________________ 
______________________________     _______ 
Name of Person Obtaining Assent 
Signature of Person Obtaining Assent       Date
(Printed)
Approved: 7/3/2019
Expiration Date: 7/1/2020
Stony Brook University Human Subjects Committee (IRB)