A Phase 2 Study of Fecal Microbiota Transplantation (FMT) in Recipients After Allogeneic Hematopoietic Cell Transplantation (HCT)
Phase: PHASE2
Conditions: Allogeneic Hematopoietic Cell Transplantation (HCT)
Sponsor: Zachariah Michael DeFilipp

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DF/HCC Protocol #: 18-293
TITLE: A Phase 2 Study of Fecal Microbiota Transplantation (FMT) in Recipients after 
Allogeneic Hematopoietic Cell Transplantation (HCT)
*Principal Investigator (PI):
Zachariah DeFilipp, MD
Massachusetts General Hospital
zdefilipp@mgh.harvard.edu
Other Investigators:
Yi-Bin Chen, MD
Massachusetts General Hospital
ychen6@partners.org
Elizabeth Hohmann, MD
ehohmann@partners.org
Michael Mansour, MD, PhD
mkmansour@partners.org
IND #:  16857
IND Sponsor/Holder: Elizabeth Hohmann, MD
Protocol Version Date:
July 11, 2019
NCT03720392

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SCHEMA

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TABLE OF CONTENTS
SCHEMA.........................................................................................................................................2
1.
OBJECTIVES......................................................................................................................5
1.1
Study Design............................................................................................................5
1.2
Primary Objective....................................................................................................5
1.3
Secondary Objectives...............................................................................................5
2.
BACKGROUND .................................................................................................................5
2.1
HCT and the Microbiome........................................................................................5
2.2
FMT for Clostridium difficile infection...................................................................6
2.3
FMT to restore intestinal microbiome diversity following HCT.............................7
2.4
FMT for treatment of GVHD...................................................................................8
2.5
Rationale ..................................................................................................................8
2.6
Correlative Studies Background ..............................................................................8
3.
PARTICIPANT SELECTION.............................................................................................9
3.1
Eligibility Criteria....................................................................................................9
3.2
Exclusion Criteria ..................................................................................................10
3.3
Inclusion of Women and Minorities ......................................................................10
4.
REGISTRATION And Randomization PROCEDURES..................................................10
4.1
General Guidelines for DF/HCC Institutions ........................................................10
4.2
Registration Process for DF/HCC Institutions.......................................................11
5.
TREATMENT PLAN........................................................................................................11
5.1
Treatment Regimen................................................................................................11
5.2
Pre-Treatment Criteria ...........................................................................................13
5.3
Follow Up ..............................................................................................................13
5.4
General Concomitant Medication and Supportive Care Guidelines......................14
5.5
Criteria for Taking a Participant Off Protocol Therapy.........................................14
5.6
Duration of Follow Up...........................................................................................15
5.7
Criteria for Taking a Participant Off Study ...........................................................15
6.
DOSING DELAYS/DOSE MODIFICATIONS ...............................................................15
7.
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................15
7.1
Expected Toxicities................................................................................................17
7.2
Adverse Event Characteristics...............................................................................17
7.3
Expedited Adverse Event Reporting......................................................................18
7.4
Expedited Reporting to the Food and Drug Administration (FDA) ......................18
7.5
Reporting to Hospital Risk Management...............................................................19
7.6
Routine Adverse Event Reporting .........................................................................19
8.
PHARMACEUTICAL INFORMATION..........................................................................19
8.1
Fecal Microbiota Transplantation Capsules...........................................................19

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8.2
Placebo Capsules ...................................................................................................20
9.
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES ........................................21
9.1
Laboratory Correlative Studies..............................................................................21
9.2
Sample Collection and Storage..............................................................................22
10.
STUDY CALENDAR .......................................................................................................22
11.
MEASUREMENT OF EFFECT .......................................................................................24
11.1
Microbiome Diversity............................................................................................24
11.2
Survival..................................................................................................................24
11.3
Infection.................................................................................................................24
11.4
Acute GVHD .........................................................................................................24
12.
DATA REPORTING / REGULATORY REQUIREMENTS...........................................25
12.1
Data Management..................................................................................................25
12.2
Data Safety Monitoring..........................................................................................25
13.
STATISTICAL CONSIDERATIONS...............................................................................25
13.1
Primary endpoint....................................................................................................25
13.2
Secondary endpoints..............................................................................................26
13.3
Analysis plan..........................................................................................................26
13.4
Accrual...................................................................................................................26
14.
PUBLICATION PLAN .....................................................................................................26
REFERENCES ..............................................................................................................................27
APPENDIX A
PERFORMANCE STATUS CRITERIA ..................................................29
APPENDIX B
FMT Investigator’s Brochure ....................................................................29
APPENDIX C
FECAL DONOR TESTS...........................................................................34
APPENDIX D
INSTRUCTIONS FOR STOOL SAMPLE COLLECTION.....................36
APPENDIX E
STOOL COLLECTION PROCESSING FOR SEQUENCING 
ANALYSES, INCLUDING FUNGAL MICROBIOME ..................................................38
APPENDIX F
MAGIC CRITERIA FOR STAGING AND GRADING FOR ACUTE 
GVHD
39

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1. OBJECTIVES
1.1
Study Design
This is a randomized, double-blind, placebo controlled, phase II study evaluating the ability of 
third-party oral fecal microbiota transplantation (FMT) to improve microbiome diversity in adult 
recipients of allogeneic hematopoietic cell transplantation (HCT). FMT or placebo capsules will 
be administered prior to and following HCT.
A total of 48 evaluable patients will be randomized between the FMT arm and the placebo arm 
(24 evaluable patients per arm).
1.2
Primary Objective
To determine if FMT administration increases microbiome diversity – measured by urinary 3-
indoxyl sulfate (3-IS) levels at one month following the final post-HCT FMT – in recipients after 
allogeneic HCT as compared to patients receiving placebo. The primary endpoint is the proportion 
of participants who achieve gut microbiome diversity in each arm, measured at one month 
following the post-HCT FMT by urinary 3-IS levels, with 35 umol/mmol crea as the cutoff (≥ 35: 
diverse; < 35: not diverse). 
1.3
Secondary Objectives
Timepoints for all objectives are from the last dose of FMT or placebo given post-HCT. 

Cumulative incidence of acute graft-versus-host-disease (GvHD) at 6 months 

Cumulative incidence of non-relapse-mortality (NRM) at 6 months and at 12 months 

Cumulative incidence of infection at 100 days

Progression-free survival (PFS) and overall survival (OS) at 6 months and at 12 months

GVHD-free/relapse-free survival (GRFS) at 12 months
2. BACKGROUND
2.1
HCT and the Microbiome
Allogeneic hematopoietic cell transplantation (HCT) is a potentially curative treatment for a 
number of malignant and non-malignant hematologic conditions. Non-relapse mortality (NRM) is 
a major barrier to allogeneic HCT, complicating 10-40% of all transplants, depending on patient- 
and transplant-related factors [Jagasia 2012, Deeg 2007]. Despite substantial advances in HLA-
typing, immunosuppressive therapy, infectious disease management and supportive care, the 
leading causes of NRM remain GVHD and opportunistic infection. Thus, novel HCT approaches 
that can potentially limit such complications are of utmost importance. The recipient microbial 
flora may impact the development of acute GVHD [Peled, Blood 2016]. Recent focus on intestinal 
mucosal biology and advances in molecular techniques to simplify the complex mixtures of 
microorganisms have provided a better understanding of how a patient’s fecal microbiome may be 

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associated with certain complications and overall outcomes after HCT [Teshima 2016, Morgan 
2014, Taur 2015]. In HCT, the gastrointestinal mucosa is damaged, leading to an impaired 
intestinal microbiota with significantly reduced diversity. An analysis of fecal specimens taken 
from 80 recipients of allogeneic HCT at the time of engraftment showed that reduced intestinal 
microbiome diversity was associated with significantly worse survival outcomes (OS at 3 years 
was 36%, 60%, and 67% for low, intermediate and high diversity groups, respectively (p=0.019) 
[Taur 2014]. A subsequent study showed in 64 patients that increased bacterial diversity at 12 days 
after HCT was associated with reduced GVHD-related mortality. Furthermore, increased amounts 
of fecal bacteria belonging to the genus Blautia was specifically associated with reduced GVHD 
lethality [Jenq 2015]. More recently, a link between disease relapse after HCT and the abundance 
of several bacteria in the intestinal flora was demonstrated. In this study of 160 patients 
prospectively enrolled in a fecal collection protocol, Eubacterium limosum abundance was 
associated with less relapse and Enterococcus abundance was associated with more relapse [Peled, 
BBMT 2016]. While these associations between microbiome diversity and clinically important 
outcomes after HCT do not prove causality, the building pre-clinical evidence is compelling 
enough to investigate if these relationships can be altered to actually influence outcomes for 
patients.
Patients undergoing HCT have several reasons to have an altered microbiome, including: 1) prior 
and current use of antibiotics, 2) prior immediate hospitalizations, 3) use of chemotherapy and/or 
radiation, and 4) altered nutritional patterns. We hypothesize that approaches that restore a 
patient’s microbiome diversity after HCT may be able to influence and improve outcomes after 
HCT. While therapeutic approaches to restoring microbiome diversity are still investigational, 
FMT from a healthy individual carries promise, after initial studies have shown this to be a 
remarkably effective therapy for recurrent Clostridium difficile colitis [van Nood 2013, Rohlke 
2012]. At Massachusetts General Hospital (MGH), Dr. Elizabeth Hohmann has developed a novel 
protocol to produce and administer FMT via previously collected third-party frozen FMT capsules. 
The central hypothesis of our research is that empiric third party FMT after HCT can accelerate 
recovery of microbiome diversity and this may ultimately prevent infection and acute GVHD, 
thereby lowering NRM and improving overall outcomes after HCT.
2.2
FMT for Clostridium difficile infection
Clostridium difficile infection (CDI) is the predominant infectious cause of antibiotic-associated 
diarrhea, ranging in severity from mild diarrhea to death. Therapeutic approaches to restoring 
microbiome diversity have shown nearly complete cure in the treatment of recurrent Clostridium 
difficile colitis. The MGH Infectious Diseases Division has had a FMT program in place for 
recurrent CDI since 2012, initially demonstrating that frozen liquid fecal inocula from healthy 
volunteers can be administered by either the upper (NGT) or lower GI route (colonoscopy) with 
equivalent efficacy [Youngster CID 2014]. The FMT program subsequently transitioned to the 
generation of frozen, encapsulated inoculum from healthy unrelated donors to be delivered by the 
oral route. An initial pilot study of this novel third party FMT approach for recurrent CDI resulted 
in an overall 90% (95%CI, 68-98%) rate of clinical resolution of diarrhea (18 of 20 patients) 
[Youngster JAMA 2014]. To date, over 330 patients at MGH and partner institutions have been 
treated with third party freeze-dried capsule FMT for recurrent CDI. Overall cure rates in  subjects 
for whom follow-up is available, as measured by resolution of diarrhea at 8 weeks, is 93%, with 

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only seven patients requiring two or more administrations.
Among the most vulnerable populations susceptible to CDI are HCT recipients, where the 
incidence of CDI is as high as 25%. Although FMT to treat CDI is becoming increasingly common 
in immunocompetent individuals, parts of the medical community have been reluctant to expand 
this therapy to include HCT patients, despite the increased risk of CDI- related morbidity and 
mortality. To date, nine HCT recipients (allogeneic= 7; autologous =2) referred from MGH and 
partner institutions with recurrent CDI have been treated with FMT with overall excellent success 
and limited adverse events. All patients were free of recurrent CDI at 8 weeks after FMT, although 
two patients eventually died of progression of their underlying malignancy, and one died of an 
intracranial hemorrhage. One patient did experience a spontaneous relapse of CDI at nine weeks 
after treatment. Side effects were primarily mild non-specific GI complaints after ingestion of 
capsules, which are common in patients with recurrent CDI. No transmission of infection was 
observed. CDI eradication in HCT individuals was associated with an increase in microbiome 
diversity, specifically an increase in Firmicutes and Bacteroidetes, and a decrease in 
Proteobacteria phyla [Zhu 2011]. These data provide preliminary evidence that FMT for HCT 
patients is mechanistically similar to CDI clearance in immunocompetent individuals, which 
supports clinical observations that FMT is safe and effective in HCT patients.
2.3
FMT to restore intestinal microbiome diversity following HCT
Following our experience with treating recurrent CDI with third-party cryopreserved FMT in HCT 
recipients, we conducted a pilot study administering empiric third party FMT after HCT. In this 
study, previously collected third party freeze-dried FMT was administered no later than 4 weeks 
after neutrophil engraftment and at least 48 hours after stopping systemic antibiotics. The absence 
of active acute GI GVHD was a pre-treatment criterion. Participants received a single standard 
dose of oral FMT, which was comprised of 30 FMT capsules administered over 2 consecutive 
days. The primary endpoint of this study was feasibility of empiric FMT in HCT recipients, which 
was defined as feasible if 80% or more of eligible participants were able to swallow 15 or more 
capsules. Correlative analyses were performed on serial stool (16s rRNA sequencing) and urine 
(liquid chromatography/tandem mass spectrometry for 3-IS) samples to measure microbiome 
diversity. We enrolled a total of 18 patients; 5 patients did not receive FMT capsules (aGVHD 
prior to planned FMT administration, n=3; patient withdrawn, n=2). All 13 participants who were 
given FMT were able to swallow all 30 FMT capsules. Clinical follow up is still ongoing, but thus 
far, FMT has been well tolerated, with only 1 treatment-related significant adverse event 
(abdominal pain). Analysis of correlative stool samples indicate expansion of donor operational 
Figure 1. Microbiome dynamics in pilot FMT study. Depiction of 16s rRNA sequencing of stool samples collected from 
same two patients, emphasizing origin of microbiota taxonomic units, classified as either being patient-derived, donor-
derived, both, or neither. 

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taxonomic units following FMT (Figure 1) with additional studies (urine 3-IS, clostridia 
abundance, Simpson’s Diversity Index) suggesting maintenance and recovery of intestinal 
microbiome diversity (Figure 2). The median pre-HCT 3-IS level in this study was 34.6 
umol/mmol crea, a level that 57% of patients have thus far achieved one month post-FMT, 
indicating that FMT may be associated with restoration of pre-HCT microbiome diversity. Thus, 
the preliminary results of our pilot study indicate that empiric third party FMT following 
allogeneic HCT appears to be feasible, safe, and associated with expansion of recipient 
microbiome diversity.
2.4
FMT for treatment of GVHD
A few small case series to date have described the use of FMT for patients with acute GVHD of 
the GI tract. In one pilot study, a total of 4 patients with steroid-resistant (n=3) or steroid-dependent 
gut aGVHD (n=1) received FMT. No severe adverse events attributed to FMT were observed. All 
patients responded to FMT, with 3 complete responses and 1 partial response (Kakihana 2016). In 
a separate case series, 3 patients with steroid-refractory GVHD of the gut received FMT. There 
were 2 complete responses and 1 partial response (Spindelboeck 2017). These two reports 
represent the initial descriptions of FMT for GVHD. Further studies are planned to further 
investigate the role of FMT in this population.
2.5
Rationale
There is growing evidence that commensal intestinal microbiota is dysregulated following 
allogeneic HCT and that low microbial diversity is associated with increased non-relapse mortality 
(NRM) and inferior survival. The central hypothesis of our research is that empiric third-party 
FMT can accelerate recovery of microbiome diversity early after HCT and this may prevent 
infection and acute graft-versus-host disease (GVHD), thereby lowering NRM and improving 
overall outcomes after HCT. Initial results of our pilot study demonstrate this approach is feasible, 
safe, and associated with expansion of recipient microbiome diversity. We therefore plan to further 
this research by performing a placebo-controlled trial in this population. 
2.6
Correlative Studies Background
In patients with C. diff infection and GVHD, the types of resident bacterial species or diversity in 
Figure 2. Longitudinal changes in A) urinary 3-IS, B) inverse Simpson index, and C) Clostridialis abundance prior to allo-
HCT and following FMT administration in the early post-transplant period.

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their gastrointestinal flora is altered (de Castro 2015, Taur 2014). This dysregulated flora is 
restored to a more diverse composition following FMT [de Castro 2015, Youngster 2014]. In order 
to define the large number of unique bacterial and fungal species, ribosomal sequencing is used. 
Sequencing16S rRNA, a component of bacterial and fungal ribosomes, is unique to each species 
allowing phylogenic and taxonomic categorization. We will use16S rRNA sequencing to 
determine gastrointestinal bacterial (microbiome) and fungal (mycobiome) diversity in HSCT 
patients before and after receiving FMT. These data will be correlated with clinical outcomes.
Urinary concentration of 3-indoxylsulfate (3-IS) is a clinically relevant biomarker of intestinal 
microbiota disruption after allogeneic HCT. Low levels of urinary 3-IS in the first 10 days after 
allogeneic HCT have been associated with higher transplant-related mortality (TRM) and worse 
overall survival, with the majority of TRM being related to acute GI GVHD [Weber 2015)].
3. PARTICIPANT SELECTION
3.1
Eligibility Criteria 
3.1.1
Men or women ≥ 18 and ≤ 80 years old 
3.1.2
Patients designated to undergo myeloablative or intermediate intensity allogeneic 
peripheral blood or bone marrow hematopoietic cell transplantation. Consent will be 
obtained prior to admission for HSCT. Patients receiving any donor source of stem cells 
are eligible. Eligible conditioning regimens are those defined as myeloablative by the 
ASBMT Consensus Criteria (Bacigalupo 2009) as well as the combination of fludarabine 
with melphalan (100-140 mg/mg2)  
3.1.3
Any GVHD prophylaxis regimen is allowed.  
3.1.4
ECOG performance status ≤ 2 (Karnofsky ≥ 60%, see Appendix A)  
3.1.5
Patients with adequate physical function as measured by 

Cardiac: Left ventricular ejection fraction at rest must be ≥ 40%, or shortening  fraction 
>25%

Hepatic:
o
Total Bilirubin ≤ 2.5 mg/dL, except for patients with Gilbert’s syndrome or 
hemolysis
o
ALT, AST, and Alkaline Phosphatase < 5 x ULN

Renal: Serum creatinine within normal range, or if serum creatinine is outside normal 
 range, then renal function (measured or estimated creatinine clearance or GFR) ≥ 
 40mL/min/1.73m2

Pulmonary: DLCO (corrected for hemoglobin), FEV1 and FVC ≥ 50% predicted
3.1.6
Women of child-bearing potential and men must agree to use adequate contraception 
(hormonal or barrier method of birth control; abstinence) prior to study entry and for the 
duration of study participation. Should a woman become pregnant or suspect she is 
pregnant while she or her partner is participating in this study, she should inform her 
treating physician immediately. Women of childbearing potential will have a urine 
pregnancy test, which must be negative, on Study Day 1, prior to receiving FMT. Men 
treated or enrolled on this protocol must also agree to use adequate contraception prior to 
the study and for 3 months after FMT.

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3.1.7
Ability to understand and the willingness to sign a written informed consent document, 
including the willingness to accept risk of unrelated donor stool.
3.1.8
Ability to swallow large capsules.
3.2
Exclusion Criteria 
3.2.1
Prior allogeneic hematopoietic stem cell transplantation. (Patients may have received a 
prior autologous hematopoietic stem cell transplant.)
3.2.2
Participants who are receiving any other investigational agents.
3.2.3
Uncontrolled intercurrent illness including, but not limited to, symptomatic congestive 
heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social 
situations that would limit compliance with study requirements.
3.2.4
Patients with active or uncontrolled bacterial, viral, or fungal infection(s) requiring 
systemic therapy.
3.2.5
Planned use of prophylactic donor lymphocyte infusion (DLI) therapy.
3.2.6
Delayed gastric emptying syndrome or large hiatal hernia
3.2.7
Known chronic aspiration
3.2.8
Participants with a history of significant allergy to foods not excluded from the donor diet 
(excluded foods are tree nuts, peanuts, shellfish, eggs)
3.2.9
Pregnant and breast-feeding women are ineligible because they are not eligible for 
hematopoietic stem cell transplantation.
3.2.10 HIV-positive participants are ineligible.
3.2.11 Participants who are unable to swallow pills.
3.2.12 Participants with end-stage liver disease (cirrhosis)
3.2.13 Participants with acute, active gastrointestinal infection (e.g., typhlitis, diverticulitis, 
appendicitis)
3.2.14 Participants with inflammatory bowel disease (e.g., ulcerative colitis, Crohn’s)
3.2.15 Prior total colectomy
3.3
Inclusion of Women and Minorities
Both men and women of all races and ethnic groups are eligible for this trial. Given the small size 
of our study there is insufficient power to detect small effects between groups.
4. REGISTRATION AND RANDOMIZATION PROCEDURES 
4.1
General Guidelines for DF/HCC Institutions
Institutions will register eligible participants in the Clinical Trials Management System (CTMS) 
OnCore. Registrations must occur prior to the initiation of any protocol-specific therapy or 
intervention. Any participant not registered to the protocol before protocol-specific therapy or 
intervention begins will be considered ineligible and registration will be denied.
An investigator will confirm eligibility criteria and a member of the study team will complete the 
protocol-specific eligibility checklist.

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An email confirmation of the registration will be sent to the Overall PI, study coordinator(s) from 
the Lead Site, treating investigator and registering person immediately following the registration.
Once registration is confirmed, the MGH FMT Core Lab will randomize per their “Randomization 
Scheme for FMT Clinical Trials.” 
Following registration, participants may begin protocol-specific therapy and/or intervention. 
Issues that would cause treatment delays should be discussed with the Overall Principal 
Investigator (PI). If the subject does not receive protocol therapy following registration, the subject 
must be taken off-study in the CTMS (OnCore) with an appropriate date and reason entered.  
4.2
Registration Process for DF/HCC Institutions
Applicable DF/HCC policy (REGIST-101) must be followed.  
5. TREATMENT PLAN
5.1
Treatment Regimen
There will be two treatment arms. Arm 1 participants will receive two doses of FMT after HCT. 
Arm 2 participants will receive placebo capsules instead of FMTs at the same time points. 
Participants will be randomized in a 1:1 ratio. Double-blinding will be maintained.
An individual not involved in patient assessments will receive the randomization assignment, take 
appropriate capsules (either FMT (Arm 1) or placebo (Arm 2)) from relevant freezer locations, 
and place them on dry ice for administration. Vials will be labeled “STUDY Caps” for 
administration so that neither physician, research nurse, nor participant will be able to identify 
FMT vs. placebo capsules. The certificate of analyses identifying capsules as FMT or placebo 
will then be sealed in an opaque envelope and saved for review at the time of unblinding. This will 
serve as a “double-check” on actual assignment. 
A total of 48 evaluable patients will be randomized between the FMT arm and the placebo arm 
(24 evaluable patients per arm).
Arm 1 will consist of two (2) doses of FMT given after HCT, starting within 4 weeks after 
engraftment after HCT.
Arm 2 will mirror Arm 1, using placebo capsules instead of FMT capsules. It will consist of two 
(2) doses of placebo, starting within 4 weeks after engraftment after HCT. 
In this protocol, a standard dose of oral FMT will be defined as 15 capsules administered during 
on a single day. Thus 2 doses of FMT will total 30 capsules. In our previous study of FMT in 
patients undergoing allogeneic HCT, thirty capsules contained microbial content of a median of 
38.6 g of feces (range, 24-56.7). 

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The FMT/placebo doses can be given within 4 weeks after engraftment after HCT. These 2 
doses of oral FMT/placebo will be administered as 15 capsules per day for two days (total 30 
capsules); the two days must occur within a 14 -day span – they can be consecutive, but they do 
not need to be.
Participants will be asked to fast for 2 hours prior to and 1 hour following capsule intake (drinking 
water will be allowed) There are not specific prohibited foods in associated with FMT 
administration. Capsules will be individually handed to participants by a research nurse or 
physician. Each capsule will be taken with a sip of water. Participants will be asked to drink at 
least 12 ounces of water during capsule administration to facilitate dilution of stomach contents 
and transit into the small intestine. Participants should swallow the daily allotment of FMT 
capsules within 1 hour.  
Capsules must not be crushed, chewed, or dissolved.
Capsules will be administered on an inpatient or outpatient basis. A record will be maintained of 
the time and date of each capsule administration. Participants will be evaluated for 15 minutes 
immediately following capsule administration. Immediate side effects have been very uncommon 
in our past experience in treating CDI or in our pilot study. Vomited doses will be counted and 
recorded. Substitute FMT capsules will not be administered to replace vomited doses.
Participants may not receive any anti-bacterial antibiotics (by any route) within 48 hours prior to 
the pre-HCT capsule administration and prior to the first day of the post-HCT administration. For 
subjects with renal dysfunction (CrCl < 60 ml/min/1.73m2) participants may not have received 
antibiotics within 72 hours prior to pre-HCT capsule administration and prior to the first day of 
the post-HCT administration. Specifically, if vancomycin is being given for prophylaxis of C. 
difficile infection, it must be stopped at least 48 hours prior to the first day of the FMT/placebo 
administration. Administration of trimethoprim / sulfamethoxazole for prevention of 
Pneumocystis pneumonia is not forbidden although the use of alternative measures – i.e. oral 
atovaquone or IV pentamidine – is preferred for the time around and immediately after capsule 
administration. 
Participants will undergo allogeneic hematopoietic stem cell transplantation according to 
institutional standards. Any donor source for stem cells and regimen for GVHD prophylaxis are 
allowed. 
The doses of FMT or placebo will commence only after neutrophil engraftment has occurred, 
defined as ANC ≥ 500/μL for three (3) consecutive days.  If the patient does not experience 
successful neutrophil engraftment, then the participant will not receive the second dose of FMT or 
placebo.
FMT/placebo administration must begin no later than 4 weeks after the date of neutrophil 
engraftment. 

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If the participant receives the first FMT placebo and then develops an infection requiring 
antibiotics, then the second dose of FMT/placebo will be delayed until 48 hours after the end of 
antibiotic dosing. In cases of infection requiring antibiotics, FMT or placebo must start within 2 
weeks after stopping systemic antibiotics.  Treatment with anti-viral agents, anti-fungal agents 
and/or trimethoprim / sulfamethoxazole is allowed at any time with no impact on FMT or Placebo 
administration. 
A minimum of 15 (out of the usual total number of 30) capsules must be swallowed for a dose of 
FMT or placebo to be considered successful. 
Subjects receiving any amount of FMT or placebo capsules will be followed for at least 6 months. 
5.2
Pre-Treatment Criteria
Prior to administration of the FMT or placebo capsules, the participant must meet the following 
criteria: 
ANC must be ≥ 1000/μL prior to each day of FMT/placebo. Use of growth factor 
supplementation is allowed.
ECOG performance status ≤ 3 (Karnofsky ≥ 40%, see Appendix A)
Participant must NOT receive any antibiotics within 48 hours prior to dose (72 hours for 
those with CrCl <60 ml/min/1.73m2)
Participant must NOT have a fever (temperature > 100.4 F) within 48 hours prior to 
FMT/placebo
Participant must NOT have uncontrolled intercurrent illness including, but not limited to, 
symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or 
acute psychiatric illness that could limit study compliance.
Participant must NOT have acute, active gastrointestinal infection (e.g., typhlitis, 
diverticulitis, appendicitis)
Participant must be able to swallow oral medications.
Additionally, this criterion must be met on day 1 only (does not apply on day 2):

Adequate hepatic function (Total Bilirubin ≤ 5 mg/dL; AST (SGOT) and ALT 
(SGPT) ≤ 5 x institutional upper limit of normal). An exception may be made for 
patients in whom a diagnosis of hemolysis or Gilbert’s is made.
Labs drawn on the day of FMT capsule/placebo administration must be reviewed and meet pre-
treatment criteria prior to treatment. There are no planned dose delays allowed if these pre-
treatment criteria are not met. Dosing delays are allowed for difficulty swallowing these many 
capsules as outlined in Section 6. 
5.3
Follow Up
Participants will be seen one week after the second day of the FMT or placebo dose, and then 
monthly for 6 months (1 month, 2 months, 3 months, 4 months, 5 months, 6 months), at 9 months 
and at 12-months after FMT or placebo (see Section 10, Study Calendar). Subjects who receive 

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FMT or placebo as outpatients will receive a phone call at 24-48 h after the second FMT or placebo 
dosing day. Standard physical exam, vitals, KPS, blood testing (CBC and chemistries), interval 
history, and GVHD assessment will take place at each study visit along with research toxicity 
assessments. Additionally, stool and urine samples for correlative studies will be collected at the 
1 week, 1 month, 2-month, 6-month and 12-month follow-up visits.
5.4
General Concomitant Medication and Supportive Care Guidelines
There are no required concomitant medications in this trial. Any concomitant medication 
administration is per the discretion of the treating physician(s). Participants may receive all 
concomitant therapy deemed necessary to provide optimal support.
Rarely, recipients of FMT have experienced fever after administration of FMT capsules. This is 
more common in younger individuals and children, and may represent an immunological reaction 
to a new intestinal flora. Participants who are febrile after FMT will have a clinical evaluation. 
Blood and other cultures will be performed as deemed clinically necessary. Such patients may be 
given antibiotics if they are hemodynamically unstable or clinically or microbiologically 
diagnosed with an active infection. Otherwise, it is recommended that they be observed.
Patients are allowed to be treated with any standard regimens for GVHD prevention as well as any 
post-HSCT therapies considered standard by the treating physician. Participants will not be 
allowed to be on any other investigational treatment protocol from admission for HCT until the 
final FMT vs placebo administration.
5.5
Criteria for Taking a Participant Off Protocol Therapy
After the second FMT or placebo administration (after HCT), the participant will be off protocol 
therapy. No further protocol therapy will be given. 
A participant may not receive all doses of FMT or placebo if any of the following criteria applies:

Intercurrent illness that prevents further administration of treatment

Unacceptable adverse event(s)

Participant demonstrates an inability or unwillingness to comply with the regimen 

Participant decides to withdraw from the protocol therapy

General or specific changes in the participant's condition render the participant 
unacceptable for further treatment in the judgment of the treating investigator
Participants will be removed from the protocol therapy when any of these criteria apply.  The 
reason for removal from protocol therapy and the date the participant was removed must be 
documented in the case report form (CRF). Alternative care options will be discussed with the 
participant.
When a participant is removed from protocol therapy and/or is off of the study, the relevant Off-
Treatment/Off-Study information will be updated in OnCore.

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5.6
Duration of Follow Up
Participants will be followed for 12 months after the last day on which he/she received FMT or 
placebo capsules or until death, whichever occurs first.
5.7
Criteria for Taking a Participant Off Study
Participants will be removed from study when any of the following criteria apply:

Lost to follow-up

Withdrawal of consent for data submission

Death

Completion of the 12-month follow-up period
The reason for taking a participant off study, and the date the participant was removed, must be 
documented in the case report form (CRF). In addition, the study team will ensure Off 
Treatment/Off Study information is updated in OnCore in accordance with DF/HCC policy 
REGIST-101.
6. DOSING DELAYS/DOSE MODIFICATIONS
If a participant has a difficult time swallowing 15 capsules in one day, then capsule administration 
may be spaced out over three (3) days (10 capsules per day), instead of the standard dosing over 
two (2) days (15 capsules per day). This is a standard approach in capsule based FMT for recurrent 
C. difficile colitis, though it is noted that the vast majority of patients, including children and the 
elderly, are able to take 15 capsules in a single sitting. There will be no dose adjustment for 
participants unable to take 10 capsules per day. In the case of a dosing delay or dose modification, 
dosing and assessment schedules will remain unchanged (i.e., dosing day count will continue). 
Administration of the capsules with applesauce or pudding rather than water is also a standard 
approach, for subjects who have difficulty swallowing large capsules. The capsules are size 00 
(the size of a large pre-natal vitamin). Please note that subjects are fasting around the time of 
administration to minimize the risk and volume of potential emesis, which is rare. There is no 
reason food would alter the efficacy of FMT.
7. ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS 
An adverse event (AE) is any undesirable sign, symptom or medical condition or experience that 
develops or worsens in severity after starting the first dose of study treatment or any procedure 
specified in the protocol, even if the event is not considered to be related to the study.
Abnormal laboratory values or diagnostic test results constitute adverse events only if they induce 
clinical signs or symptoms or require treatment or further diagnostic tests.  Regardless of severity 
grade, only laboratory abnormalities that fulfill a seriousness criterion need to be documented as a 
serious adverse event.

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If a laboratory abnormality is one component of a diagnosis or syndrome, then only the diagnosis 
or syndrome should be recorded on the AE page/screen of the CRF.  If the abnormality was not a 
part of a diagnosis or syndrome, then the laboratory abnormality should be recorded as the AE. If 
possible, the laboratory abnormality should be recorded as a medical term and not simply as an
abnormal laboratory result (e.g., record thrombocytopenia rather than decreased platelets).
A qualified Investigator will evaluate all adverse events as to seriousness.  A serious adverse event 
(SAE) is any adverse event, occurring at any dose and regardless of causality that:

Results in death.

Is life-threatening. Life-threatening means that the person was at immediate risk of death 
from the reaction as it occurred, i.e., it does not include a reaction which hypothetically 
might have caused death had it occurred in a more severe form.

Requires or prolongs inpatient hospitalization (i.e., the event required at least a 24-hour 
hospitalization or prolonged a hospitalization beyond the expected length of stay). 
Hospitalization admissions and/or surgical operations scheduled to occur during the study 
period, but planned prior to study entry are not considered SAEs if the illness or disease 
existed before the person was enrolled in the trial, provided that it did not deteriorate in an 
unexpected manner during the trial (e.g., surgery performed earlier than planned).

Results in persistent or significant disability/incapacity. Disability is defined as a 
substantial disruption of a person’s ability to conduct normal life functions.

Is a congenital anomaly or birth defect; or
Is an important medical event when, based upon appropriate medical judgment, it may jeopardize 
the participant and require medical or surgical intervention to prevent one of the outcomes listed 
above. Examples of such medical events include allergic bronchospasm requiring intensive 
treatment in an emergency room or at home; blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse.
Events not considered to be serious adverse events are hospitalizations for:

A standard procedure for protocol therapy administration. However, hospitalization or 
prolonged hospitalization for a complication of therapy administration will be reported as 
an SAE.

Routine treatment or monitoring of the studied indication, not associated with any 
deterioration in condition, or for elective procedures

The administration of blood or platelet transfusion as routine treatment of studied 
Indication. However, hospitalization or prolonged hospitalization for a complication of 
such transfusion remains a reportable SAE.

A procedure for protocol/disease-related investigations (e.g., surgery, scans, endoscopy, 
sampling for laboratory tests, bone marrow sampling). However, hospitalization or 
prolonged hospitalization for a complication of such procedures remains a reportable SAE.

Elective or pre-planned treatment for a pre-existing condition that did not worsen

Emergency outpatient treatment for an event not fulfilling the serious criteria outlined 
above and not resulting in inpatient admission

Respite care

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For each SAE, the Investigator will provide information on severity, start and stop dates, 
relationship to IP, action taken regarding IP, and outcome.
AE monitoring and reporting is a routine part of every clinical trial.  The following list of reported 
and/or potential AEs (Section 7.1) and the characteristics of an observed AE (Section 7.2) will 
determine whether the event requires expedited reporting in addition to routine reporting.
All AEs and SAEs whether reported by the participant, discovered during questioning, directly 
observed, or detected by physical examination, laboratory test, or other means, will be recorded in 
the participant’s medical record and on the appropriate study-specific case report forms as per 
instructions.
7.1
Expected Toxicities
In prior experiences, participants undergoing Fecal Material Transplantation experienced 24 – 48 
hours of mild transient adverse events. Common events include fever, cramping, diarrhea, and gas. 
Rarely participants experience bacteremia after FMT. In our institutional experience with 
over 400 FMT recipients (various clinical indications), there was a single incident where 2 
subjects developed bacteremia from a relatively resistant organism (ESBL E. coli) that was 
later identified in the stool specimen from the same healthy FMT donor. This donor provided 
samples before specific screening for ESBL organisms was implemented.  Additional 
screening will minimize this risk, but we don’t believe it can be entirely eliminated.  
Based on our previous experience with these subjects, special attention will be given to 
patients who develop bacteremia with enteric organisms within 4 weeks of FMT dosing and 
additional testing may be performed to assist with assessment of attribution.
7.2
Adverse Event Characteristics 

CTCAE term (AE description) and grade:  The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
4.0 will be utilized for AE reporting. All appropriate treatment areas should have access to 
a copy of the CTCAE version 4.0.  A copy of the CTCAE version 4.0 can be downloaded 
from 
the 
CTEP 
web 
site 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm.

For expedited reporting purposes only:  
AEs that are listed above should be reported only if the adverse event varies in nature, 
intensity or frequency from the expected toxicity information that is provided. 

Expectedness. Adverse events can be ‘Expected’ or ‘Unexpected.’ 
o
Expected Adverse Event – An event that has been previously identified as resulting 
 from administration of the agent. For the purposes of this study, an adverse event 
is considered expected when it appears in the current adverse event list or is 
included in the informed consent document as a potential risk. Refer to section 7.1 

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for a listing of expected adverse events associated with the study agent.  
o
Unexpected Adverse Event – An event that varies in nature, intensity or frequency 
from information provided in the current adverse event list or when it is not 
included in the informed consent document as a potential risk.  

Attribution is the relationship between an adverse event and the study treatment. 
Attribution will be assigned as follows:
o
Definite – The AE is clearly related to the study treatment.
o
Probable – The AE is likely related to the study treatment.
o
Possible – The AE may be related to the study treatment.
o
Unlikely – The AE is doubtfully related to the study treatment.
o
Unrelated – The AE is clearly NOT related to the study treatment.
7.3
Expedited Adverse Event Reporting
7.3.1
Reporting to the PI
Investigators must report to the Overall PI any serious adverse event (SAE) that occurs after the 
initial dose of study treatment, and/or within 30 days of the last dose of treatment on the local 
institutional SAE form.
In the event of an unanticipated problem or life-threatening complications, treating investigators 
must immediately notify the Overall PI. 
7.3.2
DF/HCC Expedited Reporting Guidelines
Investigative sites will report AEs directly to the DFCI Office for Human Research Studies 
(OHRS) per the DFCI IRB reporting policy. 
The policy states that the following SAEs are required to be reported for all subjects enrolled and 
actively participating in the trial or when the SAE occurs within 30 days of the last study 
intervention: 

Grade 2 (moderate) and Grade 3 (severe) events - Only events that are Unexpected and 
Possibly, Probably or Definitely Related/Associated with the Intervention.

ALL Grade 4 (life-threatening or disabling) Events – Unless expected AND specifically 
listed in protocol as not requiring reporting.

ALL Grade 5 (fatal) Events  
Grade 2 and Grade 3 laboratory abnormalities that are considered by the investigator to be 
clinically insignificant and do not require therapy, or adjustment in prior therapy, do not need to 
be reported to the DFCI IRB as an SAE.
7.4
Expedited Reporting to the Food and Drug Administration (FDA)
The IND holder / physician study sponsor, Dr. E. Hohmann, will be responsible for all 
communications with the FDA. She will report any serious adverse event that meets the FDA’s 

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criteria for expedited reporting following the reporting requirements and timelines set by the FDA.
Unexpected fatal or life-threatening experiences associated with the use of the study treatment will 
be reported to FDA as soon as possible but in no event later than 7 calendar days after initial receipt 
of the information.
All other serious unexpected experiences associated with the use of the study treatment will be 
reported to FDA as soon as possible but in no event later than 15 calendar days after initial receipt 
of the information.
Events will be reported to FDA by email and in hard copy as formal submissions to our IND 
(16895). 
7.5
Reporting to Hospital Risk Management
Participating investigators will report to their local Risk Management office any participant safety 
reports, sentinel events or unanticipated problems that require reporting per institutional policy. 
7.6
Routine Adverse Event Reporting
All Adverse Events must be reported in routine study data submissions to the Overall PI on the 
toxicity case report forms.  AEs reported through expedited processes (e.g., reported to the 
IRB, FDA, etc.) must also be reported in routine study data submissions.
8. PHARMACEUTICAL INFORMATION
A list of the adverse events and potential risks associated with the investigational agent 
administered in this study can be found in Section 7.1.
8.1
Fecal Microbiota Transplantation Capsules
8.1.1
Donor Screening
Donors are healthy, nonpregnant adults aged 18 to 50 years, taking no medications, and with a 
normal body mass index (18.5-25 [calculated as weight in kilograms divided by height in meters 
squared]). Volunteers are excluded for any significant medical history (with the exception of 
resolved traumatic injury) or for any use of antibiotics in the preceding 6 months, and cannot be 
healthcare workers active full time in a clinical setting. Candidates must pass the American 
Association of Blood Banks donor questionnaire, then undergo physical examination and general 
laboratory screening tests. Refer to Appendix C for a summary of the testing performed on donor 
blood and stool. Volunteers are asked to refrain from eating common allergens within 5 days of 
stool donation but otherwise not to alter their diets. At the time of donation, subjects have an 
interim health query for febrile, systemic, and gastrointestinal symptoms and were deferred for 
any change in health status. All donations are stored without use for an additional 4 weeks to allow 
retesting of donors for human immunodeficiency virus, hepatitis A, B and C, and syphilis prior to 
clinical use of the inoculum. Testing includes evaluation of donor’s plasma viral load for EBV and 

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CMV before and after donations, and assessment of pre- and post-donation fecal samples for 
VRE, MRSA, ESBL, and carbapenemase producing Enterobacteraceae (CRE) using 
commercially available chromogenic agars. A complete list and timing of screening tests is 
given in Appendix C, and approved by the FDA.  See also the current IDB (Appendix B). 
8.1.2
Preparation of Frozen Inocula
Processing is carried out under aerobic conditions. A fecal suspension is generated in normal saline 
without preservatives using a commercial blender. Materials are sequentially sieved to remove 
particulate material. The final microbial slurry is concentrated by centrifugation and resuspended 
in saline at one-tenth the volume of the initial sample with 40% glycerol added as a bacterial 
cryoprotectant. The concentrated microbial solution is pipetted into size 0 capsules (650 μL), 
which are closed and then secondarily sealed in size 00 capsules. Capsules are stored frozen at 
−80°C (−112°F). Capsules are transported to the clinic or bedside on dry ice. Commercially 
available acid-resistant hypromellose capsules (DRCaps, Capsugel) are used. Stability of capsules 
in an acid environment mimicking the stomach has been tested by evaluating trypan blue–filled 
capsules. At 37°C (99°F) and a pH of 3 or less, the capsules are stable for 115 minutes before dye 
is released. Each inoculum is prepared from the feces of a single donor and a full treatment of 30 
capsules contains sieved, concentrated material derived from approximately 48 g of fecal matter 
(mean per capsule, 1.6 g; range, 1.0-2.05 g). Capsules are odorless and tasteless. 
8.1.3
Storage and Stability
We do not expect, and have not previously observed a decrement in the viability or efficacy of the 
capsules, which will be stored at -80 C in an alarmed freezer. Capsules will be discarded if not 
used by their expiration date which is 9 months after encapsulation. Capsules which are not 
structurally intact cannot be used (see Certificate of Analysis). Representative FMT Capsules are 
saved for analysis in the event of infection transmission. FMT Capsule lots where numbers allow 
have assessment of aerobic colony forming units over time (0 and 9months) as a measure of 
stability. 
8.1.4
Administration
Participants will receive FMT capsules, 15 each on 2 days. Participants will be NPO for at least 2 
hours prior to and 1 hour following capsule administration. Administration will be with at least 12 
ounces of water.
8.2
Placebo Capsules
8.2.1
Capsule Preparation
Placebo capsules consist of a combination of food grade powdered cocoa and gelatin in normal 
saline (IV grade) / USP glycerol (same vehicle as FMT capsules). Gelatin is added to make the 
placebo solution more viscous and physically fill the capsules in the same way that the standard 
FMT inoculum does for appearance purposes. Placebo capsules are identical in appearance to FMT 
capsules, and are produced as described in IND #16011 (E. Hohmann MD).
8.2.2
Administration
Participants will receive placebo capsules, 15 each on 2 days. Participants will be NPO for at least 
2 hours prior to and 1 hour following capsule administration. Administration will be with at least 
12 ounces of water.

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9. BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES
9.1
Laboratory Correlative Studies
9.1.1
Urinary 3-indoxyl sulfate levels
Urinary 3-indoxyl sulfate (3-IS) levels will be measured at baseline and at one month following 
the final post-HCT FMT administration. Analysis will be done via reverse-phase liquid 
chromatography – electrospray ionization - tandem mass spectrometry in negative ion multiple 
reaction monitoring mode as has been demonstrated previously [Weber 2015, Taur 2012].  
9.1.2
16s rRNA Sequencing
To determine the fecal microbiome and mycobiome diversity, stool samples will be analyzed using 
a standard sequencing method that identifies unique signatures from each bacterial or fungal 
species. Specifically, the bacterial species are determined by sequencing 16S ribosomal RNA 
(rRNA) using V4-V5 PCR amplification. Fungal species will be identified using internal 
transcribed spacer sequences (ITS).
V4–V5 variable region of the 16S rRNA from isolated ITS DNA from each fecal specimen will 
be determined using PCR containing purified DNA, Taq DNA polymerase, and forward and 
reverse primers. Following amplification, the PCR product will be sequenced, analyzed and 
grouped into operational taxonomic units for classification.
Microbial diversity will be estimated from stool sequencing data by calculating the inverse 
Simpson index, an ecological estimate of α diversity, calculated to represent the reciprocal of the 
expected probability of two randomly selected bacterial sequences as belonging to the same 
operational taxonomic unit [Magurran 2004].
9.1.3
MAGIC GVHD biomarkers
In recent years, diagnostic and prognostic blood biomarkers have emerged for acute GVHD. 
In an exploratory analysis, we will evaluate GVHD biomarker profiles, using a validated 
algorithm of 2 Mount Sinai Acute GVHD International Consortium (MAGIC) biomarkers 
(ST2 and REG3α). Blood biomarker profiles will be evaluated for patients receiving FMT or 
placebo at multiple time-points post-transplant. We will also explore associations between 
biomarker profiles and microbiome diversity and composition, as evaluated from urine and 
stool specimens.
Blood sample collections (one red top tube with 5 mL blood for serum at each time point) for 
MAGIC GVHD biomarker evaluations will be collected at Day 0, Day +7, Day +14, Day +21, 
Day +28, Day +56, and Day +90. All these time points are in relation to BMT date. 
Participants are exempt from collection of these samples as part of this protocol if they are 
co-enrolled on the MAGIC Database and Bioreposity protocol. 
 
9.1.4
Neutrophils functional analyses
An exploratory analysis of neutrophil function will be examined posttransplant. Blood will 

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only be collected at 2 months post second FMT/Placebo (+/- 14 days). One 10mL EDTA tube.
9.2
Sample Collection and Storage
Samples will be collected at the following timepoints: 

Baseline; between 14 days prior to first FMT/placebo until first stool after the first FMT 
dose

1 week post HSCT (+/- 4 days)

1 week following the second day of the post-HCT FMT or placebo administration (+/- 3 
days)

1 month following the second day of the post-HCT FMT or placebo administration (+/- 14 
days)

2 months following the second day of the post-HCT FMT or placebo administration (+/- 
14 days)

6 months following the second day of the post-HCT FMT or placebo administration (+/- 
28 days)

12 months following the second day of the post-HCT FMT or placebo administration (+/- 
28 days)
Stool will be collected by the study participant using the instructions in Appendix E. Urine will 
also be collected at each of these timepoints.
If for any reason a participant does not receive the second day of capsules for FMT/placebo, then 
subsequent sample collections will be benchmarked from the first day of the post-HCT FMT. 
Because bacteria and fungi require different analyses, the storage of the collected specimens differs. 
For fungal analysis, stool will be collected and then directly frozen at -80oC. For bacterial analysis, 
90% ethanol solution will be added to the stool, which will then be frozen. See appendix E for more 
information. Urine specimens will be frozen at -80oC and stored for future analysis. 
Universal precautions will be used when handling all specimens. All specimens will be labeled in a 
de-identified manner. 
10. STUDY CALENDAR
Baseline
(within 42 
days prior 
to 
admission 
for HSCT)
1-week 
post 
HSCT
FMT/ 
placebo 
Day 1
FMT/ 
placebo 
Day 2
1-week 
post 2nd 
FMT/ 
placebo
(I)
Follow 
up 
(H)
12 months 
post 2nd 
FMT/ 
placebo
(I)

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Informed consent
X
Medical History
X
Physical Exam
X
X
X
X
X
X
X
Vital Signs (A)
X
X
X
X
X
X
X
Performance Status
X
X
X
X
X
X
X
CBC w/ diff, PLTs
X
X
X
X
X
X
X
Serum chemistry (B)
X
X
X
X
X
X
X
Pregnancy Test (C)
X
X
Hepatitis B, hepatitis C, HIV 
testing
X
Con Meds
X
FMT or Placebo Capsule 
administration
X
X
AE/Toxicity Evaluation
X
X
X
X
X
X
Stool and urine samples for 
correlatives (D)
X
X
X
X (D)
X
Blood sample collection for 
MAGIC GVHD biomarker 
evaluation (E)
X
X
X
X
Blood for correlatives (F)
X
Screen for AROs (G)
X
Acute GVHD evaluation
X
X
X
X
X
X
(A) Must include temperature, heart rate, blood pressure, respiratory rate  
(B) Albumin, alkaline phosphatase, total bilirubin, bicarbonate, BUN, calcium, creatinine, 
 glucose, magnesium, phosphorus, potassium, total protein, SGOT (AST), SGPT (ALT), 
 sodium.
(C) Pregnancy test on FMT day 1 should be resulted prior to FMT administration
(D) Stool and urine samples for correlatives are required only at the following visits: 

Baseline (between 14 days prior to first FMT/placebo until first stool after first FMT 
dose) 

1 week post HSCT (+/- 4 days)  

1 week post second FMT/placebo (+/- 3 days)  

1 month post second FMT/placebo (+/- 14 days)  

2 months post second FMT/placebo (+/- 14 days)  

6 months post second FMT/placebo (+/- 28 days)  

12 months post second FMT/placebo (+/- 28 days)
(E) Blood sample collections for MAGIC GVHD biomarker evaluations will be collected at 
Day 0, Day +7, Day +14, Day +21, Day +28, Day +56, and Day +90. All these time points are 
in relation to BMT date. If are exempt from collection of these samples as part of this 
protocol if they are co-enrolled on the MAGIC Database and Bioreposity protocol. One red 
top tube with 5 mL blood for serum at each time point. 
(F) Blood will only be collected at 2 months post second FMT/Placebo (+/- 14 days). One 
10mL EDTA tube
(G) Screen for Antibiotic-Resistant Organisms including VRE, MRSA
(H) Follow up schedule: Participants receiving FMT/placebo will have a follow up visit at 1, 

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2, 3, 4, 5, 6, 9, and 12 months post last dose of study drug.
(I) Windows for visits / evaluations are as follows: 

1-week post-FMT/placebo, 1-week post-HSCT: +/- 3 days  

Follow up visits: months 1-6: +/- 14  days  

Follow up visits: months 9 and 12: +/- 28 days
11. MEASUREMENT OF EFFECT
11.1
Microbiome Diversity
Microbiome diversity will be measured by urinary 3-indoxyl sulfate (3-IS) levels at one month 
following the final post-HCT FMT. The cutoff for gut microbiome diversity is a urinary 3-IS level 
of ≥ 35 umol/mmol crea (≥ 35 = diverse; < 35 = not diverse).
11.2
Survival
Overall Survival: Overall Survival (OS) is defined as the time from the first dose of FMT or 
placebo to death due to any cause, or censored at date last known alive. OS will be assessed at 6 
and 12 months. 
Progression-Free Survival: Progression-Free Survival (PFS) is defined as the time from first dose 
of FMT or placebo to the earlier of underlying disease progression or death due to any cause. 
Participants alive without disease progression are censored at date of last disease evaluation. PFS 
will be assessed at 6 and 12 months. 
GVHD-Free/Relapse-Free Survival: GVHD-Free/Relapse-Free Survival (GRFS) is defined as the 
time from first dose of FMT or placebo to the earlier of diagnosis of GVHD or disease progression 
or relapse. Patients who have not experienced any of these events will be censored at date of last 
disease evaluation. GRFS will be assessed at 12 months. 
Non-relapse mortality: Non-relapse mortality (NRM) is defined as the time from first dose of FMT 
or placebo to death without relapse or progression or underlying disease. Deaths from any cause 
without prior progression are considered as NRM events. NRM will be assessed at 6 and 12 
months. 
11.3
Infection
Infections (bacteremia, C. difficile, and others) will be diagnosed per clinical norms, and testing 
will be at the discretion of treating physicians. Data will be collected from medical records 
continuously, to assess possible concurrent infection.  Bacteremia with organisms typically arising 
from the GI tract and C. difficile infection are diagnoses of special interest.  There will be no 
specific microbiological screening tests ordered for the purpose of this study. 
 
11.4
Acute GVHD

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The cumulative incidence of overall grades II-IV and grades III-IV acute GVHD will be assessed 
through six months after last dose of FMT or placebo. Grading is as detailed in Appendix F. 
12. DATA REPORTING / REGULATORY REQUIREMENTS
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 7.0 
(Adverse Events: List and Reporting Requirements).
12.1
Data Management
The Office of Data Quality (ODQ) will collect, manage, and perform quality checks on the data 
for this study. 
12.2
Data Safety Monitoring
The DF/HCC Data and Safety Monitoring Board (DSMB) will review and monitor study progress, 
toxicity, safety and other data from this study. The Board is chaired by a medical oncologist from 
outside of DF/HCC and its membership composed of internal and external institutional 
representation. Information that raises any questions about participant safety or protocol 
performance will be addressed by the Overall PI, statistician and study team. Should any major 
concerns arise, the DSMB will offer recommendations regarding whether or not to suspend the 
study.
The DSMB will meet twice a year to review accrual, toxicity, response and reporting information. 
Information to be provided to the DSMB may include: participant accrual; treatment regimen 
information; adverse events and serious adverse events reported by category; summary of any 
deaths on study; audit results; and a summary provided by the study team. Other information (e.g. 
scans, laboratory values) will be provided upon request. 
13. STATISTICAL CONSIDERATIONS
13.1
Primary endpoint
The primary endpoint is the proportion of patients who achieve gut microbiome diversity at one 
month following the final post-HCT FMT, measured by a urinary 3-IS levels (≥35 umol/mmol 
crea: gut microbiome diversity achieved; <35: gut microbiome diversity not achieved). A total of 
48 evaluable patients will be randomized between the FMT arm and the placebo arm (24 evaluable 
patients per arm). Patients who are able to swallow at least one capsule will be considered as 
evaluable. This will give 80% power to detect a 30% improvement (20% on the placebo arm vs. 
50% in the FMT arm) in the proportion of patients who achieve gut microbiome diversity at one 
month, with one-sided type 1 error rate of 0.12. In the primary analysis, patients who are 
considered as evaluable but do not have one month urinary 3-IS data available due to any reason 
(e.g., early death) will be included in the denominator in calculating the proportion of patients who 
achieve gut microbiome diversity, and will be considered as failing to achieve gut microbiome 
diversity at one month. A secondary analysis will also be performed, which will only include those 
patients with one month 3-IS data available.

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13.2
Secondary endpoints
Secondary endpoints include acute GVHD at 6 months, NRM at 6 and 12 months, 100 day 
infection rate, PFS, OS and GRFS. All time to event outcomes will use the date of first 
administration of FMT (or placebo) as time 0. Definitions for these endpoints are given in section 
11.
13.3
Analysis plan 
The proportion of patients achieving gut microbiome diversity at one month will be compared 
between the FMT and the placebo arm, using a Fisher’s exact test at one-sided significance level 
0.12, The estimated proportions will be calculated along with 90% confidence intervals for each 
arm. This analysis will be performed for all evaluable patients, as well as within the subset of 
patients with one month 3-IS data available
The cumulative incidence of acute GVHD (using early deaths as competing risks), NRM (using 
relapse as competing risks), and infections (using early deaths as competing risks), will be 
compared between the two arms using the Gray test, The cumulative incidence for each type of 
endpoints will be estimated along with 90% confidence intervals for each arm.  PFS, OS and GRFS 
will be compared using the Log-rank test, and will be estimated using the Kaplan-Meier method 
along with 90% confidence intervals for each arm. 
13.4
Accrual
Accrual rate is expected to be approximately 24 evaluable patients per year, therefore it will take 
approximately 2 years to complete accrual of 48 evaluable patients.
13.5
Stopping Rule to do Death
If a participant dies due to a bloodstream infection with enteric organisms occurring within 4 weeks 
of final FMT dosing, the participant will be unblinded in order to determine if FMT or placebo 
capsules were administered. If the participant received placebo capsules, the death will not be 
attributed to study treatment.  If the patient received FMT capsules, additional testing will be 
performed to assist with assessment of attribution of the infectious death. If 1 additional participant 
experiences a grade 5 treatment-related adverse event, the study will be terminated.
14. PUBLICATION PLAN
The results should be made public within 24 months of reaching the end of the study. The end of 
the study is the time point at which the last data items are to be reported, or after the outcome data 
are sufficiently mature for analysis, as defined in the section on Sample Size, Accrual Rate and 
Study Duration. If a report is planned to be published in a peer-reviewed journal, then that initial 
release may be an abstract that meets the requirements of the International Committee of Medical 
Journal Editors. A full report of the outcomes should be made public no later than three (3) years 
after the end of the study. 

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REFERENCES
de Castro CG Jr, Ganc AJ, Ganc RL, et al. Fecal microbiota transplant after hematopoietic SCT: 
report of a successful case. Bone Marrow Transplant. 2015 Jan;50(1):145.
Deeg, HJ. How I treat refractory acute GVHD. Blood, 2007. 109(10): p. 4119-26.
Jagasia M, Arora M, Flowers ME, Chao NJ, McCarthy PL, Cutler CS, Urbano-Ispizua 
A, Pavletic SZ, Haagenson MD, Zhang MJ, Antin JH, Bolwell BJ, Bredeson C, Cahn JY, Cairo 
M, Gale RP, Gupta V, Lee SJ, Litzow M, Weisdorf DJ, Horowitz MM, Hahn T. Risk factors for 
acute GVHD and survival after hematopoietic cell transplantation. Blood, 2012. 119(1): p. 296-
307.
Jenq, RR, Taur Y, Devlin SM, Ponce DM, Goldberg JD, Ahr KF, Littmann ER, Ling 
L, Gobourne AC, Miller LC, Docampo MD, Peled JU, Arpaia N, Cross JR, Peets TK, Lumish 
MA, Shono Y, Dudakov JA, Poeck H, Hanash AM, Barker JN, Perales MA, Giralt SA, Pamer 
EG, van den Brink MR. Intestinal Blautia Is Associated with Reduced Death from Graft-versus-
Host Disease. Biol Blood Marrow Transplant, 2015. 21(8): p. 1373-83.
Kakihana K, Fujioka A, Suda W, eta l. Fecal microbiota transplantation for patients with steroid-
resistant/dependent acute graft-versus-host disease of the gut. Blood. 2016 Oct 20;128(16):2083-
2088.
Magurran A. Measuring biological diversity. 2004, Malden, MA: Blackwell Publishing.
Morgan XC, Huttenhower C. Meta'omic analytic techniques for studying the intestinal 
microbiome. Gastroenterology, 2014. 146(6): p. 1437-1448 e1.
Peled, JU, Devlin SM, Staffas A, Lumish M, Khanin R, Littmann ER, Ling L, Kosuri S, Maloy 
M, Slingerland JB, Ahr KF, Porosnicu Rodriguez KA, Shono Y, Slingerland AE, Docampo 
MD, Sung AD, Weber D, Alousi AM, Gyurkocza B, Ponce DM, Barker JN, Perales MA, Giralt 
SA, Taur Y, Pamer EG, Jenq RR, van den Brink MRM. Members of the Intestinal Microbiota 
Are Associated with Relapse after Allogeneic Hematopoietic Stem Cell Transplantation. Biol 
Blood Marrow Transplant, 2016. 22(3): p. S23-S24.
Peled, JU, Hanash AM, Jenq RR. Role of the intestinal mucosa in acute gastrointestinal GVHD. 
Blood, 2016. 128(20): p. 2395-2402.
Rohlke F, Stollman N. Fecal microbiota transplantation in relapsing Clostridium difficile 
infection. Therap Adv Gastroenterol, 2012. 5(6): p. 403-20.
Spindelboeck W, Schultz E, Uhl B. Repeated fecal microbiota transplantations attenuate diarrhea 
and lead to sustained changes in the fecal microbiota in acute, refractory gastrointestinal graft-
versus-host disease. Haematologica. 2017. 
Taur Y, Jenq RR, Ubeda C, van den Brink M, Pamer EG. Role of intestinal microbiota in 
transplantation outcomes. Best Pract Res Clin Haematol, 2015. 28(2-3): p. 155-61.
Taur Y, Jenq RR, Perales MA, Littmann ER, Morjaria S, Ling L, No D, Gobourne A, Viale 
A, Dahi PB, Ponce DM, Barker JN, Giralt S, van den Brink M, Pamer EG.The effects of 
intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell 
transplantation. Blood, 2014. 124(7): p. 1174-82.
Taur, Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, Lee YJ, Dubin KA, Socci 

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ND, Viale A, Perales MA, Jenq RR, van den Brink MR, Pamer EG. Intestinal domination and 
the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. 
Clin Infect Dis, 2012. 55(7): p. 905-14.
Teshima T, Reddy P, Zeiser R. Acute Graft-versus-Host Disease: Novel Biological Insights. Biol 
Blood Marrow Transplant, 2016. 22(1): p. 11-6
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser 
CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ. Duodenal 
infusion of donor feces for recurrent Clostridium difficile. N Engl J Med, 2013. 368(5): p. 407-
15.
Weber D, Oefner PJ, Hiergeist A, Koestler J, Gessner A, Weber M, Hahn J, Wolff D, Stämmler 
F, Spang R, Herr W, Dettmer K, Holler E. Low urinary indoxyl sulfate levels early after 
transplantation reflect a disrupted microbiome and are associated with poor outcome. Blood, 
2015. 126(14): p. 1723-8.
Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB, Alm EJ, Gevers D, Russell 
GH, Hohmann EL. Fecal microbiota transplant for relapsing Clostridium difficile infection using 
a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin 
Infect Dis, 2014. 58(11): p. 1515-22.
Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen 
fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA, 2014. 
312(17): p. 1772-8.
Zhu W, Stevens AP, Dettmer K, Gottfried E, Hoves S, Kreutz M, Holler E, Canelas AB, Kema 
I, Oefner PJ. Quantitative profiling of tryptophan metabolites in serum, urine, and cell culture 
supernatants by liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem, 2011. 
401(10): p. 3249-61.

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APPENDIX A
PERFORMANCE STATUS CRITERIA
ECOG Performance Status Scale
Karnofsky Performance Scale
Grade
Descriptions
Percent
Description
100
Normal, no complaints, no evidence 
of disease.
0
Normal activity.  Fully active, able 
to carry on all pre-disease 
performance without restriction.
90
Able to carry on normal activity; 
minor signs or symptoms of disease.
80
Normal activity with effort; some 
signs or symptoms of disease.
1
Symptoms, but ambulatory.  
Restricted in physically strenuous 
activity, but ambulatory and able 
to carry out work of a light or 
sedentary nature (e.g., light 
housework, office work).
70
Cares for self, unable to carry on 
normal activity or to do active work.
60
Requires occasional assistance, but 
is able to care for most of his/her 
needs.
2
In bed <50% of the time.  
Ambulatory and capable of all 
self-care, but unable to carry out 
any work activities.  Up and about 
more than 50% of waking hours.
50
Requires considerable assistance and 
frequent medical care.
40
Disabled, requires special care and 
assistance.
3
In bed >50% of the time.  Capable 
of only limited self-care, confined 
to bed or chair more than 50% of 
waking hours.
30
Severely disabled, hospitalization 
indicated.  Death not imminent.
20
Very sick, hospitalization indicated. 
Death not imminent.
4
100% bedridden.  Completely 
disabled.  Cannot carry on any 
self-care.  Totally confined to bed 
or chair.
10
Moribund, fatal processes 
progressing rapidly.
5
Dead.
0
Dead.
APPENDIX B
FMT INVESTIGATOR’S BROCHURE 
Investigators Brochure 
MGH FMT Frozen Capsules
Hohmann Laboratory 
Jackson 518 
Infectious Disease Division

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Department of Medicine
Massachusetts General Hospital
Principal Investigator: Elizabeth L. Hohmann MD
Version: 9.0
Date: June 4, 2019 
The purpose of this document is to provide co-investigators with concise, current 
information about FMT capsules, direction for dosing, and active state of knowledge 
about their use. Information included is current as of June 4, 2019 and includes subjects 
receiving one or more doses of FMT capsules. 
This document will be updated at least annually. 
Capsule Overview
FMT capsules are made from stool donated by healthy individuals 18-50 who must pass 
a careful health screening, including blood banking questionnaire, medical history, 
physical exam, and numerous blood and fecal tests as shown below. Fecal material is 
blenderized in sterile preservative-free saline, and then sieved, pelleted, and re-
suspended in sterile saline/40% glycerol and double encapsulated in pharmaceutical 
grade, nested vegan hypromellose capsules designed to open in neutral pH 
environments (Capsugel). Capsules are then frozen. One standard dose of thirty 
capsules contains soluble material harvested from approximately 40 grams of fecal 
material. Manufacturing details are in separate Clinical Manufacturing and Control 
documents. 
General Health Laboratory Tests
C-Reactive protein, high sensitivity
Lipid panel
Comprehensive metabolic panel
CBC with differential
ANA – sent out to Mayo
HTLV I & II antibodies
Done at screening 
within 30 days of start 
of donations
Pregnancy test by HCG if female
Stool Tests
Clostridium difficile testing by PCR
Stool culture for enteric pathogens* – includes Yersinia, 
Vibrio cholerae, V. parahemolyticus, and E. coli O157
Rotavirus antigen detection by ELISA
Ova and parasites – includes giardia and cryptosporidium
Norovirus
Adenovirus
VRE rectal screen
MRSA nasal screen
Done at screening 
within 30 days of start 
of donations
*re-done with stool 
samples from first and 
last donations
Helicobacter pylori – sent out to Mayo

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MRSA plating*
Listeria plating*
CRE plating*
ESBL plating*
Serologic Tests
Hepatitis A (IgG + IgM)
Hepatitis B (surface Ag + surface Ab)
Hepatitis C (IgG)
HIV ½ (IgG)
Done at screening 
within 30 days of start 
of donations
Repeated 28-40 days 
after last donation
Syphilis TrepSure ELISA
Viral Loads
Epstein-Barr virus
Done at the time of the 
first and last donations
Cytomegalovirus
Oral Glucose Tolerance Test – Optional
Glucose (fasting)
Hemoglobin A1C
Optional – done at 
screening
Glucose tolerance test, 2 hours post glucola ingestion
Appearance
Exemplary capsules are shown below. 
Storage
Capsules are frozen and stored at -80◦C and shipped on dry ice. A dated certificate of 
analysis which includes lot number, and manufacture date, acceptance of donor testing, 
and structural integrity of capsules at the time of shipment or in person delivery on dry 
ice to an investigator for a specific recipient will be filed. It is recommended that capsule 
be stored no longer than 30 days at -20◦C, in a FROST-FREE freezer. Capsules should 
be discarded 9 months after manufacture. Capsules should be promptly transported on 
dry ice once removed from the freezer, for administration to subjects. 
Animal testing
No animal testing has been performed on FMT capsules. 
Solubility
FMT capsules and prototypes with aqueous dyes are demonstrated to be relatively 
stable in an acid environment and release payload under neutral conditions. It is 

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therefore NOT required nor recommended that subjects take antacids, bicarbonate or 
other acid- suppressing medications prior to administration. Taking these medications 
are not contraindications to administration of FMT capsules however. 
Instructions for Use 
Subjects must meet study-specified inclusion and exclusion criteria. Subjects should be 
NPO for 4 hours prior to and one hour after administration of capsules. 
For treatment of C. difficile infection (CDI)
 A single dose is considered 30 capsules when treating CDI. Capsules may be 
administered on 2 successive days (15 each day) or 3 successive days (10 each day), 
at the choice of subject/physician. For simple convenience most people prefer 2 days. 
Subjects or parents should sign a clinical consent form. Follow-up phone calls and 
completion of the 2-sided follow-up Case Report Form provided are required at the 
following intervals 
in the 24-96 hours window after administration
at 7-14 days 
at 8 weeks (+/- 5 days)
at 6 mo (+/- 2 weeks)
and subjects should be seen in person as dictated by a physician’s clinical judgment. 
Physicians who do not complete and return follow-up forms in a timely manner will not 
be provided additional capsules. 
For other applications, doses will be defined within specific clinical protocols, but will 
generally follow the above timing for safety assessments. 
Acute reactions after dosing in 403 subjects treated for C. difficile
The capsules are tasteless and odorless. Five adult subjects and two children of 403 
total have vomited within 8-12 h after capsule administration and not brought up 
feculent material or intact capsules. One cancer patient with chronic vomiting of 
medications vomited up all 15 capsules of his second dose, after tolerating the first dose 
well. Diarrhea and irritable bowel- like symptoms are commonly reported after FMT for 
CDI and often resolve over time. Subjects may be discharged after explanation of 
follow-up and advised re diet, relapse and AE’s to monitor which usually takes about 20 
minutes. 
Total Adverse Events in 395 subjects reaching 8 weeks follow-up
Most subjects treated for CDI have some ongoing GI symptoms, typically minor (Grade 
1). It is impossible to determine if these symptoms are related to resolving CDI, post-
infectious irritable bowel syndrome, or the capsules themselves. See Chart 1 below. 
One IBD flare requiring intensified treatment has been noted and deemed related. 
EVENT 
Number Percentage 
Fevers - transient 
9
3%
Hospitalizations 
44
16%
Deaths
24
8%

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Diarrhea 
145
48%
Nausea/bloating 
78
25%
Ulcerative colitis flare
3
0.01%
Expected resolution of symptoms of C. difficile. 
This is variable. The occasional individual has fever, cramping, borborygmi and 
occasional diarrheal bowel movements after dosing. Patients with significant abdominal 
pain as part of their presenting or ongoing symptoms may have a component of Irritable 
Bowel Syndrome. Episodic pain or nonspecific abdominal discomfort may persist. Some 
subjects resolve diarrhea but have ongoing frequent formed stools compared with 
baseline. In the MGH experience, some subjects have cleared stool of C. difficile based 
upon repeated testing, but had slow resolution of other symptoms over weeks. Cure is 
defined as resolution of diarrhea at 8 weeks (3 stools or less per day). 
Definition of Relapsed CDI
A relapse qualifying for re-dosing must meet the following criteria:

Relapsed or ongoing diarrhea (more than 4 bowel movements of Bristol Grade 3 
or higher AND 

A positive stool test for C. diffile (toxin or PCR) on day 5 or later (Day 0 = initial 
dose day). Routine rescreening of stools in the absence of significant symptoms 
is not recommended. 
Clinical Results (as of June 4, 2019)
Of the total 395 patients currently followed to the 8-week time frame 89% were cured 
with a single dose and an additional 9% were cured with a second dose (98% total). 
Notable other observations are below. 

One 62 y.o. man with a history of 2 prior small bowel obstructions had another, 1 
month after successful FMT, which resolved with conservative management and 
no operation. This was deemed unrelated. There was no relapse. 

A total of 19 patients over the age of 90 have been treated (successfully).

A total of 19 children (age range 7-17) have been treated with capsules. 

One man with chronic inflammatory arthritis on immunosuppression was treated 
and did well for weeks, but then relapsed shortly after more rituximab was given 
(with our and others agreement). He was readmitted with severe ileus and 
relapsed C.difficile. He was subsequently retreated with enema FMT by flexible 
sigmoidoscopy but ultimately came to operation for the ileus, where Crohns was 
considered based upon gross findings but not confirmed on pathology. These 
findings were deemed unrelated to FMT. Intestinal TB was recommended as a 
possible diagnosis to the treating clinicians. 

13 patients with prior bone marrow transplant were treated, though two 
subsequently developed relapsed malignancy and died of that, and one died of 
an intracranial hemorrhage.

10 solid organ transplant patients were treated successfully, though some 
required more than a single dose. 

One 67 y.o. woman with massive polycystic liver disease and a history of 
bacteremia of unclear origin with GI organisms was admitted with the same 

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(Enterococcal bacteremia) 3 weeks after FMT. The presumed source was 
biliary/liver. 

There has been NO transmission of infection or suspicion of that. 

Two immunocompromised adults (one who received chemotherapy and one with 
cirrhosis) who received FMT products as part of clinical studies developed 
bloodstream infection caused by extended-spectrum beta-lactamase (ESBL)-
producing Escherichia coli (E.coli). One of the individuals subsequently died. The 
FMT products used in these two individuals were prepared from stool obtained 
from the same donor. The donor stool and resulting FMT products used in these 
two individuals were not tested for ESBL-producing gram-negative organisms 
prior to use. After these adverse events occurred, stored preparations of FMT 
product from this stool donor were tested and found to be positive for ESBL-
producing E. coli identical to the organisms isolated from the two patients. 

Caution is warranted in individuals with immunocompromise.
APPENDIX C
FECAL DONOR TESTS
(All performed at MGH Clinical Labs unless noted below) 

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General Health Laboratory Tests 
(within 1 mo. of donation)
C-Reactive Protein, high sensitivity
Lipid Panel
Comprehensive Metabolic Panel 
CBC w. Differential 
ANA (Send out to Mayo – 
Approved by Kent Lewandrowski
HCG (if female)
Serologic Testing 
(within 2 weeks of donations; repeated 28 to 40 days after completing donations)
Hep A (IgG + IgM) 
Heb B Surface Ag 
Hep B Surface Ab
Hep C Ab 
HIV Antibody 
Syphilis Ab Screen
HTLV 1&2 ab
Swabs (within 1 mo. of donations)
VRE Rectal Screen 
MRSA Nasal Screen 
Stool Testing 
(within 1 mo. of donations; repeated with first and last donations)
Clostridium difficile toxin by PCR 
Stool Culture (include vibrio cholerae, V. parahaemolyticus, yersinia, E coli O157)
Rotavirus Antigen Detection ELISA
Ova & Parasites (include Giardia & Cryptosporidium)
Norovirus
Adenovirus
H. Pylori (Send out to Mayo – Approved by Kent Lewandrowski)
Hohmann Lab Plates 
(within 1 mo. of donations; repeated with first and last donations)
MRSA Plating
Listeria Plating
CRE Plating
ESBL Plating

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APPENDIX D
INSTRUCTIONS FOR STOOL SAMPLE COLLECTION
Sample collection supplies you will receive:

Stool collection device including collection frame, containers and lids

Black sharpie pen
Step 1: Stool sample collection preparation 
You should wear disposable gloves during the following steps.
Set up the Stool Collection system as follows:

Raise the toilet seat and place the collection frame on the bowl. 

Then place the collection container in the frame and lower the toilet seat.
Step 2: Collection of Stool Sample

Please collect a stool sample on the morning of your visit to the clinic.

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
You should urinate before collecting the stool.

Pass your entire stool into the clean, dry collection container. 
o
Please collect a minimum of 10 grams of stool (approximately ½ stick of butter). 
If this is not possible, please provide as much as possible.

Do not mix toilet paper, soap, urine or water with your sample.

After collection place the collection container on a flat surface and then
close the lid tightly to ensure that the sample does not leak during transit.

Discard the gloves and wash hands with soap and water
Step 3: Post Stool Sample Collection

Using the Sharpie pen, write your initials, the date and the time (including
am/pm) of your bowel movement on the container.

Put the closed collection container into a plastic bag, zip or tie it closed, and bring it to 
the lab as soon as possible (preferably within 3 hours of sample production). 
o
There is no need to refrigerate or freeze the sample. 
o
Transport the sample in the sealed container, and place it in a plastic bag 
additionally. 

Repeat hand washing and if necessary.
Our research coordinator can be reached at 617-724-8625 Monday through Friday between 
9:00 a.m. and 5:00 pm, if you have any questions about this process.
Thank you for your participation.  We would appreciate if you bring in samples on the following 
days:

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APPENDIX E
STOOL COLLECTION PROCESSING FOR SEQUENCING 
ANALYSES, INCLUDING FUNGAL MICROBIOME
Stool samples will be aliquoted and stored frozen in two formats to facilitate varied analytical 
methods.  Some processors prefer neat stool frozen with no preservatives (fungal and shotgun 
sequencing), some use RNA later and some utilize 95% ethanol.  We will store samples neat and 
in 95% ethanol.  Duplicates of each sample are made. Samples are aliquoted in a biosafety hood 
and immediately frozen. 
 
Protocol
Supplies:  2 mL microfuge tubes with a screw cap or locking cap for long-term freezer storage. 
1. Fill 4 (four) 2 mL microfuge tubes about half full with stool.  These specimens do not 
need to be weighed.
 
2. Fill 4 (four) 4 ml microfuge tubes with 2 ml 95% ethanol. Add stool such that vials are 
approximately ¾ full, allowing space for expansion during freezing.   
3. Place stool specimens at -80oC until needed for sequencing at which point specimens will 
be shipped on dry ice.  It is absolutely critical that these specimens stay frozen during the 
entire shipping duration.  
4. Fungal ribosomal DNA will be prepared from all specimens simultaneously to ensure 
uniform procedure and quality of the prep from 2 of the 4 samples.
5. The remaining 2 stool specimens will be held in -80oC storage as back up. 

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APPENDIX F
MAGIC CRITERIA FOR STAGING AND GRADING FOR ACUTE 
GVHD
Stage
Skin
(Active Erythema 
Only)
Liver 
(Bilirubin)
Upper GI
Lower GI
(Stool output/Day)
0
No active 
(erythematous) 
GVHD rash
< 2 mg/dL
No or intermittent 
nausea, vomiting 
or anorexia
< 500 mL/day or 
less than 3 episodes 
per day
1
Maculopapular 
rash < 25% BSA
2 – 3 mg/dL
Persistent nausea, 
vomiting, or 
anorexia
500 – 999 mL/day or 
3-4 episodes per day
2
Maculopapular 
rash 25-50% BSA
3.1 – 6 mg/dL
-
1000-1500 mL/day 
or 5-7 episodes per 
day
3
Maculopapular 
rash > 50% BSA
6.1 – 15 mg/dL
-
> 1500 mL/day or > 
7 episodes per day
4
Generalized 
erythroderma (> 
50% BSA) plus 
bullous formation 
and desquamation 
> 5% BSA
> 15 mg/dL
-
Severe abdominal 
pain with or without 
ileus or grossly 
bloody stool 
(regardless of stool 
volume)
Overall clinical grade (based on most severe target organ involvement) 
Grade 0: No stage 1-4 of any organ.
Grade I: Stage 1-2 skin without liver, upper GI, or lower GI involvement
Grade II: Stage 3 rash and/or Stage 1 liver and/or Stage 1 upper GI and/or Stage 1 lower GI
Grade III: Stage 2-3 liver and/or Stage 2-3 lower GI, with Stage 0-3 skin and/or Stage 0-1 upper GI. 
Grade IV: Stage 4 skin, liver or lower GI involvement, with Stage 0-1 upper GI.