Fecal Microbiota Transplantation (FMT) of FMP30 in Relapsing-Remitting Multiple Sclerosis: A Phase 1b Clinical Trial to Evaluate Feasibility, Safety, Tolerability and Effects on Immune Function
Phase: PHASE1
Conditions: Relapsing Remitting Multiple Sclerosis
Sponsor: Jeffrey Gelfand

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
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MS-BIOME 
 
Fecal Microbiota Transplantation (FMT) of FMP30 in 
Relapsing-Remitting Multiple Sclerosis: A Phase 1b 
Clinical Trial to Evaluate Feasibility, Safety, Tolerability 
and Effects on Immune Function 
 
 
 
Protocol Number: 17-23827 
National Clinical Trial (NCT) Identified Number: NCT03594487 
PRINCIPAL INVESTIGATOR 
Jeffrey M. Gelfand, MD, MAS, FAAN 
 
SUB-INVESTIGATORS 
 
Sergio Baranzini, PhD, UCSF Neurology 
James Ostroff, MD, UCSF 
Gastroenterology  
Priya Kathpalia, MD, UCSF 
Gastroenterology  
Stephen Hauser, MD, UCSF Neurology 
 
 
Funded by internal university funds (no external funding) 
Version Number: 5.7 
Date Approved: March 29, 2021 
 
 
 
 
 
 
 
 
 
 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
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Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
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BRIEF PROTOCOL SUMMARY 
 
 
Study Protocol Title 
Fecal Microbiota Transplantation (FMT) in 
Relapsing-Remitting Multiple Sclerosis: A 
Phase 1b Trial to Evaluate Feasibility, Safety, 
Tolerability, Dosing and Effects on Immune 
Function 
Short title 
MS-BIOME 
Clinical Phase 
Phase 1b 
Study Center 
UCSF MS Center 
Investigational Product 
Fecal Microbiota Transfer of donor stool 
(dosed as a single dose of 90 mL of FMP30) 
administered via colonoscopy. FMP30 donor 
stool will be obtained from OpenBiome, a 
Massachusetts-based nonprofit stool bank. 
Screening by OpenBiome excludes donors 
with known Multiple Sclerosis (MS) or other 
known autoimmune conditions and screened 
for transmissible pathogens. . 
 
Subjects will receive a 5-day oral antibiotic 
course of vancomycin, neomycin and 
metronidazole to precondition the gut as part of 
the FMT protocol, and FMT will then be 
delivered via a single colonoscopy. 
Methodology/Design 
Prospective, open label, single-group cohort 
study of a single fecal microbiota 
transplantation (FMT) of FMP30 donor stool 
administered via colonoscopy following 
preconditioning with oral antibiotics and 
standard bowel preparation for colonoscopy. 
The primary endpoints will be measured 
through 12 weeks; safety and biomarker follow- 
up will be collected through 48 weeks. 
 
A parallel observational control group of MS 
patients who otherwise satisfy study inclusion 
criteria based on their MS phenotype, 
demographics, disease duration and prior use 
of allowable MS therapies, will be recruited as 
a comparison/control arm to measure stability 
of the microbiome and immunological markers 
for 12 weeks or until time of initiation of MS 
disease modifying therapy clinically. Control 
subjects will not receive oral antibiotics, bowel 
preparation, colonoscopy or study MRI. 
 
 
 
Objectives 
Primary Objective 
 
To demonstrate that FMT in patients with 
relapsing-remitting MS is feasible, safe and 
tolerable 
 
To measure donor microbiome engraftment via 
changes in fecal microbiota community 

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structure at multiple time points following a 
single cycle of FMP30 delivered via 
colonoscopy in people with relapsing-remitting 
MS 
 
Secondary objectives 
 
To evaluate whether FMT of FMP30 
administered via colonoscopy can induce a 
shift from pro-inflammatory to 
immunomodulatory T cell profiles in patients 
with relapsing-remitting MS 
 
To evaluate whether FMT changes humoral 
function in patients with relapsing-remitting MS 
 
To begin to evaluate whether FMT favorably 
influences clinical and radiological endpoints in 
patients with relapsing-remitting MS 
Number of patients 
-10 patients treated with FMP30 
-10-20 patients in the observational 
comparison group control arm 
Diagnosis and inclusion criteria 
1. Age 18-60 inclusive (at time of 
screening) 
2. Diagnosis of relapsing-remitting 
multiple sclerosis (MS) by International 
Panel McDonald Criteria (2010)(1) 
incorporating 2017 revisions which 
reclassify select high-risk Clinically 
Isolated Syndromes under 2010 
criteria as RRMS under 2017 criteria, 
and Lublin criteria (2014)(2) 
3. Recent documented MS disease 
activity, defined as at least 1 clinical 
relapse within the past 1 year prior to 
baseline OR 2 clinical relapses in the 
past 2 years prior to baseline OR at 
least 1 new T2/FLAIR lesion on brain 
or spine MRI OR at least 1 gadolinium 
enhancing lesion on brain or spine MRI 
in the past 1 year prior to baseline 
4. Expanded Disability Status Scale 
(EDSS) less than or equal to 6.0; 
EDSS 5.5 or less if MS disease 
duration is greater than 15 years (no 
other disease duration restriction) 
5. Must have positive serology for 
Epstein-Barr Virus (EBV) (IgG anti- 
EBNA positive) at screening, indicating 
prior exposure 
6. No prior MS disease modifying therapy 
or a 12 week washout period for 
subjects on glatiramer acetate or 
interferon-beta therapy 
7. At least 4 weeks from baseline since 
last use of IV or oral glucocorticoids 

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8. Agree to maintain a stable diet during 
the course of the study (over the 
counter probiotics are allowable) 
9. Premenopausal women and women 
<12 months after the onset of 
menopause must have a negative 
serum pregnancy test unless they 
have undergone surgical sterilization 
10. Female subjects of childbearing 
potential who are sexually active with a 
non-sterilized male partner must agree 
to use a highly effective method of 
contraception; non-sterilized male 
subjects who are sexually active with a 
female partner of childbearing potential 
must agree to use a highly effective 
method of contraception 
11. Not actively participating in another 
interventional MS clinical trial 
(participation in other observational 
research studies is allowable) 
Exclusion Criteria 
1. Prior use of fingolimod, dimethyl 
fumarate, teriflunomide, natalizumab, 
alemtuzumab, mitoxantrone, 
cyclophosphamide, rituximab, 
ocrelizumab, daclizumab, 
methotrexate, azathioprine, 
mycophenolate mofetil, cyclosporine, 
leflunomide or induction chemotherapy 
2. No use of diuretics like furosemide 
(Lasix) 1 week before the first dose 
oral antibiotics. The use of 
hydrochlorothiazide (HCTZ) for 
hypertension at a dose < 50 mg/day is 
allowable. 
3. Progressive MS by Lublin criteria 
(2014) 
4. No oral or IV antibiotics within 8 weeks 
of screening and 12 weeks of 
scheduled of the planned FMT 
procedure if in the FMT arm or first 
stool collection if in control arm (note 
that topical, otic, ocular antibiotics are 
specifically allowable which is 
consistent with the IMSMS.org protocol 
for collaborative gut microbiome 
research in MS) 
5. Hypersensitivity or allergy to study 
antibiotics, conscious sedation 
medications or bowel preparation 
6. Contraindication to study procedures 
including MRI, anesthesia (ASA criteria 
IV and V), colonoscopy, phlebotomy 
7. History of inflammatory bowel disease 
(Crohn’s Disease, Ulcerative Colitis) 

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8. Active symptomatic C. Difficile 
infection (colonization is not an 
exclusion) 
9. Active gastrointestinal condition being 
investigated (i.e. GI bleeding, colon 
cancer, active GI workup); history of 
known or suspected toxic megacolon 
and/or known small bowel ileus, major 
gastrointestinal surgery (e.g. significant 
bowel resection) within 3 months 
before enrollment (note that this does 
not include appendectomy or 
cholecystectomy); or history of total 
colectomy or bariatric surgery 
10. History of malignancy (except excised 
cutaneous basal cell carcinoma or 
squamous cell carcinoma which are 
allowable) including no concurrent 
induction chemotherapy, radiation 
therapy or biological treatment for 
active malignancy 
11. Pregnant or lactating women or 
intention of getting pregnant during the 
trial period 
12. Active infection including untreated 
latent or active tuberculosis, HIV, 
hepatitis, syphilis or other major active 
infection 
13. Known immunodeficiency including 
CVID 
14. INR>1.5, Platelets<100, Hemoglobin 
<8.5, WBC<2.0, Absolute lymphocyte 
count <0.8, Absolute Neutrophil Count 
<0.5, CD4<200, eGFR<45. 
15. Any condition that in the opinion of the 
study PI could jeopardize the safety of 
the subject, would make it unlikely for 
the subject to complete the study or 
could confound the results of the study 
16. Unable or unwilling to comply with 
study protocol requirements 
Concomitant and Exclusionary Therapies 
Standard symptomatic MS medications are 
allowable as concomitant therapy, including 
dalfampridine or 4-aminopyridine, botulinum 
toxin, oral spasticity agents/muscle relaxants, 
pain medication, antidepressant and anti- 
anxiety medication, modafinil, armodafinil and 
amphetamines for fatigue/alertness. 
 
Enrolled subjects will be asked to consent to 
delay initiation of an MS disease modifying 
therapy (DMT) until the end of the 12-week trial 
period. The length of this feasibility study was 
specifically designed to be short in order to 
minimize time not on a MS DMT and is 
consistent with other delayed start protocol 

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designs in MS (for example, 
https://clinicaltrials.gov/show/NCT02688985). 
Subjects who experience breakthrough clinical 
worsening of MS after screening will be allowed 
to go on disease modifying therapy (DMT)      
at the discretion of their treating neurologist  
per routine medical management. If the 
decision to start a MS DMT occurs before the 
study intervention (antibiotics and/or FMT) this 
will be considered a screen failure and  
subjects will be excluded from the study and 
not included in further safety monitoring or in 
the pre-planned primary analysis. If the 
decision to start a MS disease modifying 
therapy occurs after any study intervention 
(antibiotics and/or FMT) has been 
administered, further study intervention will be 
discontinued but subjects will be invited and 
encouraged to complete the remaining study 
visits per protocol for microbiome, 
immunological and safety monitoring. For acute 
relapse management, PO or IV steroids will   
be allowable as part of routine medical 
management at the discretion of the treating 
neurologist. 
Duration of administration 
- 
5 day oral antibiotic preconditioning 
initiated 6 days before colonoscopy 
- 
GoLytely bowel prep initiated at day 6 
- 
Single dose of 90mls of FMP30 via 
colonoscopy at day 7 
Evaluation Criteria 
Primary Feasibility Endpoint 
- 
Proportion of subjects who complete 
the study protocol 
 
Primary biomarker endpoint 
- 
Engraftment à Change in fecal 
microbiota community structure at 
weeks 0, 2, 4, 8, and 12 
- 
Engraftment -> Comparison of change 
in fecal microbiota community structure 
between FMT treated patients and the 
observational control arm at weeks 0, 
4, 8, and 12 
 
Primary Safety endpoint 
Treatment-emergent adverse events 
including treatment-emergent serious 
and non-serious adverse events 
through week 12 defined as proportion 
of subjects who develop an adverse 
event of severity grade 2 or more by 
NIH CTCAE criteria 

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Primary biomarker endpoint 
- 
Engraftment à Change in fecal 
microbiota community structure at 
weeks 0, 2, 4, 8, 12 
- 
Secondary biomarker endpoints 
- 
Induction of T regulatory or Th2 cells 
and/or reduction of Th1 or Th17 cells 
at 0, 2, 4, 8 and 12 weeks 
- 
Plasma CD19+ and CD20+ B cell 
counts and serum immunoglobulin 
levels at weeks 0, 2, 4, and 12 weeks 
- 
New T2/FLAIR lesions, T2/FLAIR 
lesion load, T2/FLAIR lesion number at 
baseline and week 12 
- 
New gadolinium enhancing lesions, 
total gadolinium enhancing lesions at 
baseline and week 12 
 
Secondary clinical endpoints 
- 
Relapse rate through week 12 
- 
EDSS and sub scores at the screening 
visit, pre-treatment baseline visit, week 
2, week 4, week 8 and week 12 
- 
Fatigue score (abbreviated MFIS) at 
baseline, week 4, week 8 and week 12 
- 
Quality of life (MSQOL-54)] at the 
screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- 
Bowel symptoms (BWCS) at the 
screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- 
Bladder symptoms (BLCS) at the 
screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- 
Timed 25 foot walk at, pre-treatment 
baseline visit, week 2, week 4, week 8 
and week 12 
- 
Mood and Anxiety (MHI-5) and 
Columbia Suicide Rating Scale at the 
screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
Statistical Methodology 
Summary statistics will be calculated for the 
primary feasibility and safety analyses. For the 
primary biomarker analysis, Wilcoxon signed- 
rank (or paired T-test as appropriate) for paired 
pre-post analyses on immunological function in 
the FMT group will be used for the primary 
analysis. For the between group comparison of 
FMT treated vs the observational control arm, a 
t-test or Mann-Whitney/Wilcoxon rank sum 
non-parametric equivalent will be used as 
appropriate. For the paired analysis, we will 
have 80% power with an alpha of 0.05 to 

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detect at least a 1 SD change in pre-post 
outcomes. 
 
For secondary outcomes that have repeated 
measures we will utilize multivariable linear 
regression mixed effects models with time as 
an interaction term for repeated-measures 
analyses and also compare outcomes in the 
FMT treatment arm with the non-interventional 
control comparison arm. 
Duration of subject participation 
FMT Treatment arm: 16 weeks in the active 
trial portion (up to 4 weeks for screening and 
baseline + 12 weeks post-FMT) with safety and 
biomarker follow-up for 1 year. 
Observational control comparison arm: 12 
weeks (8 weeks of observation and up to 4 
weeks for screening) 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
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STUDY SCHEMA 
 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
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Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
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TABLE OF CONTENTS 
BRIEF PROTOCOL SUMMARY ........................................................................................................................ 2 
STUDY SCHEMA ............................................................................................................................................. 9 
TABLE OF CONTENTS ................................................................................................................................. 11 
1. 
INTRODUCTION .................................................................................................................................. 13 
2. 
OBJECTIVES ....................................................................................................................................... 18 
       PRIMARY OBJECTIVES ................................................................................................................. 18 
       SECONDARY OBJECTIVES .......................................................................................................... 18 
3. 
STUDY DESIGN ..................................................................................................................................... 18 
       DESCRIPTION OF THE STUDY .................................................................................................... 18 
       RATIONALE FOR STUDY DESIGN ............................................................................................... 20 
       OUTCOME MEASURES ................................................................................................................ 20 
      Primary Outcome Measures ..................................................................................................... 20 
     Secondary Outcome Measures ................................................................................................. 21 
       SAFETY PLAN .................................................................................................................................. 21 
       COMPLIANCE WITH LAWS AND REGULATIONS ....................................................................... 22 
4. 
MATERIALS AND METHODS ............................................................................................................. 22 
       SUBJECTS ...................................................................................................................................... 22 
      Subject Selection ...................................................................................................................... 22 
     Inclusion Criteria ........................................................................................................................ 22 
     Exclusion Criteria ...................................................................................................................... 23 
       METHOD OF TREATMENT ASSIGNMENT .................................................................................... 24 
       STUDY TREATMENT ..................................................................................................................... 24 
      Supply, Preparation, Administration and Storage ..................................................................... 24 
       Donor Stool Formulation ................................................................................................... 24 
       Donor Stool Administration .............................................................................................. 25 
       Antibiotics ........................................................................................................................... 26 
     Dosage Modification .................................................................................................................. 26 
     Over Dosage ............................................................................................................................. 27 
       CONCOMITANT AND EXCLUDED THERAPY .............................................................................. 27 
       STUDY ASSESSMENTS ................................................................................................................ 27 
      Blood and Stool Samples for Research .................................................................................... 35 
       Blood Samples .................................................................................................................. 35 
       Stool Samples .................................................................................................................. 35 
       DISCONTINUATION OF PROTOCOL-SPECIFIED THERAPY ..................................................... 35 
       SUBJECT DISCONTINUATION ..................................................................................................... 36 
       STUDY DISCONTINUATION ......................................................................................................... 36 
       STATISTICAL METHODS .............................................................................................................. 36 
      Analysis of the Conduct of the Study ........................................................................................ 36 
     Efficacy Analysis .......................................................................................................................... 36 
     Safety Analysis ............................................................................................................................ 37 

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     Missing Data .............................................................................................................................. 38 
     Sample Size ................................................................................................................................. 38 
          DATA QUALITY ......................................................................................................................... 38 
5. 
ASSESSMENT OF SAFETY .................................................................................................................. 38 
       SAFETY VARIABLES ..................................................................................................................... 38 
       DEFINITION OF AN ADVERSE EVENT (AE) .................................................................................. 38 
       UNSOLICITED ADVERSE EVENTS .............................................................................................. 40 
       REPORTING OF ADVERSE EVENTS ........................................................................................... 40 
       RECORDING SAFETY VARIABLES .............................................................................................. 42 
      Adverse Event Reporting Period ................................................................................................. 41 
     Assessment of Adverse Events ................................................................................................. 41 
       REPORTING ADVERSE EVENTS ................................................................................................. 43 
       DATA SAFETY MONITORING PLAN .............................................................................................. 43 
6. 
REGULATORY CONSIDERATIONS ................................................................................................... 44 
       IND .................................................................................................................................................. 44 
       INFORMED CONSENT .................................................................................................................. 45 
       INSTITUTIONAL REVIEW BOARD OR ETHICS COMMITTEE APPROVAL ................................. 45 
       DATA COLLECTION ...................................................................................................................... 45 
       DISCLOSURE AND PUBLICATION OF DATA .............................................................................. 45 
       RETENTION OF RECORDS .......................................................................................................... 45 
7. 
REFERENCES ..................................................................................................................................... 47 
8. 
APPENDICES ......................................................................................................................................... 50 
Appendix A-1: Table of Assessments for Interventional FMT Treatment Group .......................................... 50 
Appendix A-2: Schedule of Assessments for Observational Control Arm (no FMT) .................................... 53 
Appendix B: Storage Controls and Material Specifications ........................................................................... 54 
Appendix C: Subject Adverse Event Diary .................................................................................................... 56 
Appendix D-1: Colombia-Suicide Severity Rating Scale (C-SSRS): Baseline/Screening ............................ 57 
Appendix D-2: Colombia-Suicide Severity Rating Scale (C-SSRS): Since Last Visit ................................... 60 
Appendix E: Mental Health Inventory (MHI-5) ............................................................................................... 63 
Appendix F: Modified Fatigue Impact Scale (MFIS) ..................................................................................... 64 
Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) ................................................. 67 
Appendix H: Bowel Control Scale (BWCS) ................................................................................................... 83 
Appendix I: Bladder Control Scale (BLCS) ................................................................................................... 84 
Appendix J: Food Frequency Questionnaire ................................................................................................. 85 
Appendix K: ASA Physical Status Classification System .............................................................................. 93 
Appendix L: OpenBiome Donor Screening Testing ...................................................................................... 94 
Appendix M: UCSF Post Approval Reporting Requirements ........................................................................ 95 
Appendix N: OpenBiome Amendments to BMF17195…………………..……………………………..………..96 
 
 

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1. 
INTRODUCTION 
 
Multiple Sclerosis (MS) is a chronic inflammatory/autoimmune disease of the 
central nervous system characterized by inflammatory-induced demyelination 
and neurodegeneration. In the United States, MS prevalence ranges from about 
40 to 191 per 100,000 population3. MS is a leading cause of non-traumatic 
disability in working age adults. About 85-90% of people with MS present with a 
relapsing-remitting phenotype, whereas 10-15% have primary progressive 
disease4. 
 
There are now several licensed injectable, oral and infusible disease modifying 
treatments for relapsing MS that reduce relapse rates, MRI T2/FLAIR and T1 
gadolinium enhancing lesions and disability progression, and all such therapies 
to date have a mechanism of action that works by modulating or suppressing 
systemic inflammation, particularly lymphocytes5. Currently available MS disease 
modifying therapies are designed to be taken chronically over the course of many 
years, if not decades, and all are only partially effective. Furthermore, safety, 
tolerability and perception of risk of currently available MS therapies varies 
widely5 leading some MS patients to decline to take currently available therapies. 
 
Genetics contributes to MS susceptibility, but a substantial proportion of MS 
disease risk remains unaccounted for by genetic factors alone and there has 
been increasing focus on environmental factors and gene-environmental 
interactions that contribute to MS risk and pathogenesis6. 
 
The human gastrointestinal system contains a massive population of microbes, 
and gut microbial organisms interact with the host immune system in a complex 
interplay that is commonly referred to as the gut microbiome. Changes in gut 
microbiota can affect immune function locally in the GI system, systemically, and 
in effector organs such as the central nervous system. The gut microbiome has 
been implicated in the pathogenesis of several autoimmune or inflammatory 
human conditions, including inflammatory bowel disease7, Type 1 Diabetes8,9, 
autoimmune hepatitis10, systemic lupus erythematosus11, juvenile idiopathic 
arthritis12, and neuromyelitis optica13. 
 
Emerging evidence has now converged to support the hypothesis that the gut 
microbiome contributes to MS pathogenesis14-16. In murine models of 
experimental autoimmune encephalomyelitis (EAE), the gut microbiome is 
essential for regulation and activation of immunity. Commensal gut bacteria are 
essential for triggering experimental autoimmune demyelination in mice driven by 
myelin-specific CD4 T cells, and recruitment and activation of autoantibody 
producing B-cells appears to depend in part on commensal microbiota17. Mice 
maintained under germ-free conditions exhibit significantly attenuated EAE 
compared to conventionally colonized mice, with germ-free animals producing 
less proinflammatory cytokines in the intestine and spinal cord (and reciprocally 

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greater T regulatory cells), whereas intestinal colonization of segmented 
filamentous bacteria in germ free mice restored ability to get EAE18 Alteration of 
gut microbiota with antibiotics reduces susceptibility to EAE19 and ameliorates 
EAE20. Oral treatment with polysaccharide A (PSA) a bacterial product expressed 
in the commensal bacteria Bacteroides fragilis attenuates EAE by affecting T 
regulatory function and migration21. Interferon-I produced by astrocytes in mice 
induced with EAE can combine with metabolites made by commensal gut flora 
derived from dietary tryptophan to suppress CNS inflammation22. Several studies 
in adult23-26 and pediatric-age27, 28 humans with MS also demonstrate dysbiosis of 
gut microbiota compared to unaffected controls that are associated with 
alterations in peripheral immune mechanisms implicated in MS pathogenesis. 
This has led to a “Chicken and Egg Dilemma” in the field about whether 
“dysbiosis precedes disease or, if in the contrary, an autoimmune disease such 
as MS can lead to gut dysbiosis29.” 
 
Work at UCSF (in the laboratory of co-investigator Dr. Sergio Baranzini) showed 
that in the microbiomes of 71 treatment-naïve MS patients and 71 healthy 
controls, specific bacterial taxa were significantly enriched in untreated relapsing 
MS patients (Fig. 1, manuscript submitted). In addition, Akkermansia muciniphila 
and Acinetobacter calcoaceticus, both increased in MS patients, induce 
proinflammatory responses in human PBMCs and in mono-colonized mice (Fig. 
2)39.  These observations suggest that the gut microbiome may be a viable target 
for therapy in multiple sclerosis, and measuring gut microbiota composition and 
host immunologic responses may provide insights into the patient’s response to 
therapy. 
 
 
 
Fig. 1: Changes in gut microbiota in relapsing MS. Systematic examination of 
relative abundances of individual microbial taxa between 71 untreated relapsing 
MS patients and 71 controls at the genus (A) and operational taxonomic unit 
(OTU) levels (B) by Wald test with Benjamini-Hochberg correction for multiple 
comparisons showed that 247 OTUs (16.89% of total) and 25 bacterial genera 
B

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(19.38% of total) were significantly increased or reduced in MS. Bacteria found to 
be significantly more prevalent in MS include Akkermansia and Acinetobacter. 
 
 
 
 
Fig. 2: Immunologic impact of MS-specific gut microbiota. (A) Peripheral blood 
mononuclear cells (PBMCs) from MS patients showed an impaired ability to 
differentiate or expand anti-inflammatory CD25+ FoxP3+ Treg populations. (B) 
Akkermansia muciniphila, which is increased in MS populations, significantly 
increased healthy donor PBMC differentiation into pro-inflammatory Th1 
lymphocytes. 
 
Fecal microbiota transplantation (FMT) is a medical procedure in which donor 
stool is transplanted into a host in order to alter the composition of gut 
microbiota. FMT is approved in the U.S. as a treatment for refractory C. Difficile 
infection, and several trials have been published documenting its safety and 
efficacy30, 31.  It is now also established that frozen donor stool (which is much 
easier to store and maintain) is non-inferior to fresh donor stool for efficacy 
treating C. Difficile infection32. FMT has also been studied for treatment of 
several other indications, including autoimmune diseases like Ulcerative Colitis in 
which FMT appears to be a promising rescue therapy33, whereas other studies 
(including those without antibiotic preconditioning before the FMT procedure) 
showed lower level engraftment after a single FMT34. FMT in HIV-treated 
individuals was well-tolerated but led to limited donor engraftment in a regimen 
without antibiotic preconditioning35. FMT from a single “rational” universal donor 
was beneficial and well-tolerated in a randomized study for treatment of hepatic 
encephalopathy36. 
 
In June 2019, the United States Food and Drug Administration (FDA) notified 
study investigators about two cases of serious multidrug-resistant organism 
(MRDO) infection in recipients of FMT. MDRO infection in those cases was 
reportedly transplanted from donor stool to the recipient through DMT and the 
infection then traveled from the gut into the bloodstream of the recipient causing 
serious infection. One patient died. The FDA instituted a mandate about 
 
 

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screening FMT donors for MDRO infection risk and to test FMT donor stool for 
MDRO infections. Our FMT supplier (OpenBiome) adheres to the FDA mandates 
but with any FMT procedure there may still be risk of transmitted MDRO infection 
despite such donor screening and testing, and these bacteria which are resistant 
to some antibiotics could be transmitted through FMT and cause serious infection 
or death. Informed consent forms were updated to reflect this FDA guidance and 
above warnings and responses to the advisory letter were provided to the FDA. 
 
     In March 2020 the FDA issued a safety alert regarding the possible transmission 
of Shiga Toxin-Producing E. coli (STEC) and Enteropathogenic E. Coli (EPEC). 
STEC is a type of E. coli that can produce a toxin called Shiga toxin. Shiga toxin 
can cause symptoms like abdominal pain, diarrhea (often bloody), vomiting, and 
mild fever. Most people develop symptoms within 3-4 days of acquiring the 
bacteria, and most get better within 5-7 days. EPEC is a type of E. coli that is 
generally carried asymptomatically but can sometimes cause transient watery 
diarrhea, similar to traveler’s diarrhea. Symptoms typically resolve in a matter of 
days. 
 
     Several adverse event reports from OpenBiome have been received related to 
patients who were treated with investigational FMT for Clostridiodes 
difficile infection (rCDI). Four patients tested positive for STEC after being treated 
with FMT with material from a single donor. Two were hospitalized and have 
since been discharged; two were treated as outpatients and their symptoms have 
resolved. In addition, two patients who also received FMT from this donor have 
passed away. These individuals had multiple pre-existing conditions. Their 
deaths are likely unrelated to their FMT. Two additional adverse event reports for 
patients who received material from this donor were received that are likely 
unrelated to their FMT. Both had multiple pre-existing conditions. Both have 
passed away from unrelated causes. 
 
     In addition, two immunocompromised patients who were treated with FMT for 
rCDI later tested positive for EPEC. The patients were treated with material from 
two different donors. One patient was hospitalized for related symptoms; one was 
hospitalized for unrelated causes. Both have been discharged. 
 
     In response to these events and FDA guidance, OpenBiome notified sites with 
product that has tested positive and recalled unused units of product that tested 
positive. The study team has notified the one patient who received product that 
tested positive. OpenBiome has also made several changes to their routine 
donor screening, including a change in detection methods to PCR-based 
methods and the inclusion of additional stool pathogens and new organisms to 
their donor screening panel (see Appendix N: OpenBiome Amendments to 
BMF17195). 
 
On March 23, 2020 the FDA issued a safety alert regarding the potential for of 

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COVID-19 via stool. OpenBiome reports that their protocols and screening 
measures are compliant with all FDA guidance related to COVID-19. 
 
      A potential risk of fecal microbiota transplantation (FMT) is the transmission of 
SARS-CoV-2, a novel coronavirus that causes the disease COVID-19. Infection 
with SARS-CoV-2 could be transmitted through stool and could cause serious 
infection or death. It is possible for healthy, asymptomatic stool donors to 
potentially be infected with SARS-CoV-2. 
 
OpenBiome’s donors who provide stool for FMT routinely undergo regular stool, 
blood, and nasal screenings for many different infectious agents, including a 
nasal swab test for SARS-CoV-2 at a minimum of every 14 days. Each FMT is 
only made available when these screens do not detect these infectious agents in 
the donor at each of these time points. Donors also undergo regular clinical 
assessments for any risk factors associated with carrying SARS-CoV-2, such as 
review of recent travel to areas considered high risk for the virus, including 
visiting certain healthcare facilities, or other behaviors which may increase the 
risk of exposure. OpenBiome will continue to update its screening guidelines and 
procedures as additional data, assays, and information becomes available. 
 
For study subjects who received FMT from stool donations provided prior to 
December 1st, 2019, it is believed that the risk of SARS-CoV-2 virus being 
present in the FMT is very low and therefore no testing for the virus has been 
performed. All FMT products that were shipped to our site were manufactured 
before December 1, 2019, and we have not nor intend to use any FMT products 
donated after that date. 
 
 
 
To our knowledge, there are no peer-reviewed published studies of FMT in MS. 
A search of clinicaltrials.gov for “Fecal Microbiota Transplantation” revealed 365 
trials studying FMT, of which to date only two other studies are listed for 
relapsing-remitting MS. One study in the United Kingdom was listed as a Phase 
II trial with a crossover design treating with FMT (delivered via rectal enema by a 
trained nurse) in an early vs. delayed start at 6 months design. The study 
completion date is posted as January 25, 2019 and recruitment status has since 
been terminated (https://clinicaltrials.gov/ct2/show/NCT03183869, accessed 
March 12, 2021). Another study from Rush University Medical Center was an 
observational study of a single subject who underwent FMT outside the United 
States for the treatment of their MS. This study was completed May 1, 2020 
(https://clinicaltrials.gov/ct2/show/NCT03975413, accessed March 12, 2021). 
 
In 2016 and 2017, our UCSF MS Center team held detailed discussions with key 
experts and stakeholders, including UCSF gastroenterology and infectious 
disease collaborators (including Dr. Sarah Doernberg, director of antibiotic 
stewardship at UCSF, and Dr. Richard Jacobs in infectious disease), which 

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greatly contributed to development of this study protocol. 
 
A 2017 systematic review published in Annals of Internal Medicine37 of 85 FMT 
trials found that many trials suffer from gaps in reporting details, including 
“eligibility criteria for donors (47%), materials used for collecting stools and the 
period of collection (96%), methods used for conservation of stools (76%), the 
amount and type of stools used (for example, fresh or frozen), and duration of 
stool conservation (67%). Many (58%) did not report an analysis of microbiota 
composition.” We agree with the authors that FMT is a complex intervention and 
that detailed reporting is essential for advancing research in this field, particularly 
when applied to novel indications such as MS. Our trial is designed to try to 
collect such details with the intention of comprehensive reporting. 
2. 
OBJECTIVES 
 
   PRIMARY OBJECTIVES 
 
i. To demonstrate that FMT of FMP30 in patients with relapsing-remitting MS is 
feasible, safe and tolerable 
ii. To measure donor microbiome engraftment via changes in fecal microbiota 
community structure at multiple time points following FMT in people with 
relapsing-remitting MS. Stability of the microbiome in FMT treated patients will 
also be compared with an observational control arm of untreated MS patients not 
treated with FMT. 
 
 
     SECONDARY OBJECTIVES 
 
iii.  To evaluate whether FMT of FMP30 donor stool administered via 
colonoscopy can induce a shift from pro-inflammatory to immunomodulatory T 
cell profiles in patients with relapsing-remitting MS 
iv.  To evaluate whether FMT changes humoral function in patients with 
relapsing-remitting MS 
v.  To evaluate whether FMT favorably influences clinical and radiological 
endpoints in patients with relapsing-remitting MS 
 
 
3. 
STUDY DESIGN 
 
      DESCRIPTION OF THE STUDY 
 
In this Phase 1b open-label prospective clinical trial, patients with relapsing- 
remitting MS will undergo FMT of FMP30 (donor stool) via colonoscopy and 
immunological efficacy endpoints will be assessed at various time points. The 
active phase of the study will continue for 12 weeks post-FMT with safety and 
biomarker (engraftment) follow-up for 48 weeks. A parallel observational control 
arm of MS patients who otherwise satisfy study inclusion criteria based on their 
MS phenotype, demographics, disease duration and prior use of allowable MS 

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therapies, will be recruited as a comparison observational group to measure 
stability of stool and serum immunological measures. 
The primary hypotheses are that: 
1)  FMT will be safe and tolerable in patients with MS. 
2) FMT preceded by antibiotic preconditioning will lead to a change in fecal 
microbiota community structure 
Secondary hypotheses are that: 
1) FMT preceded by antibiotic preconditioning will induce a favorable shift from 
pro-inflammatory to immunomodulatory T cell profiles in patients with relapsing-
remitting MS 
2) That engraftment will not appreciably decay over time 
3) That FMT will favorably change humoral function 
4) That FMT will favorably influence short-term clinical and radiological 
endpoints. 
 
FMP30 donor stool will be obtained from OpenBiome (Somerville, MA; 
OpenBiome.org), an established nonprofit stool bank with stringent safety 
protocols and quality control. Donor stool will be obtained from donors without 
MS and without other known autoimmune diseases. OpenBiome will screen for 
transmissible pathogens according to their protocol (see Appendix L: OpenBiome  
Donor Screening Testing). As of January 25, 2021, OpenBiome has made 
amendments to their donor screening to include new organisms and change 
detection methods (see Appendix N: OpenBiome Amendments to BMF17195). 
UCSF has obtained an IND from the FDA for FMT of FMP30 donor stool in MS. 
After providing written informed consent and reviewing inclusion and exclusion 
criteria, subjects will participate in either the FMT Treatment Arm or the 
Observational Control Arm. 
Subjects in the FMT Treatment Arm will first undergo screening assessments 
according to the study schedule of activities and provide blood samples for 
eligibility and research, and stool samples for research. Subjects who pass 
screening will have their pre-treatment baseline visit with 21 days of their 
screening visit where they will have an MRI, safety and biomarker research blood 
sample collection, stool sample collection for research, complete study activities 
according to the study visit schedule, be given antibiotics, bowel preparation, a 
medication compliance diary and directions on when and how to start the 
antibiotics and bowel preparation before their scheduled FMT colonoscopy 
procedure. 
The week before their Baseline FMT visit, subjects will be contacted by study 
staff to review directions of when and how to initiate the 5 day oral antibiotic 
regimen, and to take the GoLytely bowel preparation to precondition the gut for 

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FMT and optimize engraftment of the donor microbiome. Study staff will ensure 
that the subjects understand how to complete their oral antibiotic regimen, 
compliance diary, and bowel preparation correctly. 
At the study Baseline Visit, following standard bowel preparation for colonoscopy, 
subjects will then undergo colonoscopy with FMT of FMP30 by an experienced 
gastroenterologist. Subjects will return 2 weeks, 4 weeks, 8 weeks, and 12 weeks 
after baseline for scheduled assessments of stool and blood sampling, 
questionnaires, physical examination, EDSS and MS rating scales. A follow-up 
MRI will be conducted at the Week 12 visit. The active study time of 12 weeks 
was designed to be short to minimize time off MS disease modifying therapies 
(should the subject wish to go on a MS disease modifying therapy). After the end 
of the 12 week active study time, subjects will be able to transition to other 
therapies such as disease modifying therapies (DMTs). Safety follow-up visits at 
weeks 24, 36, and 48 will include additional questionnaires, assessments, and 
safety and biomarker blood sample collection, and stool collection. The total 
study time will be 52 weeks (4 weeks screening + 12 weeks Active Treatment + 
36 weeks safety follow-up). 
Subjects participating in the Observational Control Arm will not undergo the 
interventional FMT treatment. Participants in this arm will have a total of 5 visits 
over the course of 12 weeks. At the Screening/Baseline visit, subjects will be 
asked about their Demographics and medical history, concomitant medications, 
provide blood samples to determine eligibility, undergo an EDSS neurological 
exam and MS Relapse assessment, and provide blood and stool samples for 
research along with other study activities according to the study visit schedule. 
Subjects will be provided a stool kit and pre-paid mailing label to collect their 
screening stool sample within 3 days after their screening visits and send it to Dr. 
 
Baranzini’s lab. At 2 weeks (± 2 days) post baseline/screening, subjects will 
collect and mail in another stool sample with a provided collection kit and prepaid 
mailing label. At weeks 4, 8, and 12, subjects will undergo an MS Relapse 
Assessment, review concomitant medications, and provide blood and stool 
samples. 
 
     RATIONALE FOR STUDY DESIGN 
 
We hypothesize that the gut microbiome influences MS disease activity and that 
modifying the gut microbiome via colonoscopically-delivered FMT sourced from 
donors without MS or other autoimmune disease will be favorable in MS. Data 
gained from this Phase 1b safety, tolerability and feasibility study will be 
instrumental for determining whether FMT can be developed into a promising 
new treatment strategy for MS and informing the design of a Phase 2 
randomized-controlled placebo-controlled trial of FMT in MS. 
 
     OUTCOME MEASURES 

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    Primary Outcome Measures 
 
Primary Feasibility Endpoint 
- 
Proportion of subjects who complete the study protocol 
 
Primary biomarker endpoint 
- 
Engraftment à Change in fecal microbiota community structure at weeks 
0, 2, 4, 8, and 12 
- 
Engraftment -> Comparison of change in fecal microbiota community 
structure between FMT treated patients and the observational control arm at 
weeks 0, 4, 8, and 12 
 
Primary Safety endpoint 
-Treatment-emergent adverse events including treatment-emergent serious 
and non-serious adverse events through week 12 defined as proportion of 
subjects who develop an adverse event of severity grade 2 or more by NIH 
CTCAE criteria 
 
    Secondary Outcome Measures 
     
Secondary biomarker endpoints 
- Induction of T regulatory or Th2 cells and/or reduction of Th1 or Th17 cells at 
0, 2, 4, 8 and 12 weeks 
- Plasma CD19+ and CD20+ B cell counts and serum immunoglobulin 
levels at weeks 0, 2, 4, and 12 weeks 
- New T2/FLAIR lesions, T2/FLAIR lesion load, T2/FLAIR lesion number at 
baseline and week 12 
- New gadolinium enhancing lesions, total gadolinium enhancing lesions at 
baseline and week 12 
 
 
Secondary clinical endpoints 
- Relapse rate through week 12 
- EDSS and sub scores at the screening visit, pre-treatment baseline visit, 
week 4, week 8 and week 12 
- Fatigue score (abbreviated MFIS) at baseline, week 4, week 8 and week 12 
- Quality of life (MSQOL-54)] at the screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- Bowel symptoms (BWCS) at the screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- Bladder symptoms (BLCS) at the screening, pre-treatment baseline visit, 
week 2, week 4, week 8 and week 12 
- Timed 25 foot walk at, pre-treatment baseline visit, week 2, week 4, week 8 
and week 12 
- Mood and Anxiety (MHI-5) and Columbia Suicide Rating Scale at the 
screening, pre-treatment baseline visit, week 2,  week 4, week 8 and week 12 

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     SAFETY PLAN 
 
Subjects will be evaluated at each study visit for the duration of their participation 
in the study (see Section 4.5 Study Assessments and Appendix A, Schedule of 
Assessments). 
Specific potential safety issues for this trial include antibiotic adverse reactions, 
complications and tolerability of colonoscopy, adverse reactions and worsening 
of the existing underlying disease, specifically MS relapse or MS MRI disease 
activity. 
See Section 5: Assessment of Safety, for complete details of the safety 
evaluation for this study. 
 
 
     COMPLIANCE WITH LAWS AND REGULATIONS 
 
This study will be conducted in accordance with U.S. Food and Drug 
Administration (FDA) Good Clinical Practices (GCPs), and local ethical and legal 
requirements, including approval by the UCSF Institutional Review Board. 
 
 
4. 
MATERIALS AND METHODS 
 
      SUBJECTS 
 
    Subject Selection 
 
Subjects will be recruited through the UCSF MS Center clinic and clinical 
research program. 
 
    Inclusion Criteria 
 
1) Age 18-60 inclusive (at time of screening) 
2) Diagnosis of relapsing-remitting multiple sclerosis (MS) by International 
Panel McDonald Criteria (2010)1 incorporating 2017 revisions which 
reclassify select high-risk Clinically Isolated Syndromes under 2010 
criteria as RRMS under 2017 criteria, and Lublin criteria (2014)2 
3) Recent documented MS disease activity, defined as at least 1 clinical 
relapse within the past 1 year prior to baseline OR 2 clinical relapses in 
the past 2 years prior to baseline OR at least 1 new T2/FLAIR lesion on 
brain or spine MRI OR at least 1 gadolinium enhancing lesion on brain or 
spine MRI in the past 1 year prior to baseline 
4) Expanded Disability Status Scale (EDSS) less than or equal to 6.0; EDSS 

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5.5 or less if MS disease duration is greater than 15 years (no other 
disease duration restriction) 
5) Must have positive serology (IgG anti-EBNA positive) for Epstein-Barr 
Virus (EBV) at screening (indicating prior exposure) 
6) No prior MS disease modifying therapy or a 12 week washout for subjects 
on glatiramer acetate or interferon-beta 
7) At least 4 weeks from baseline since last use of IV or oral glucocorticoids 
8) Agree to maintain a stable diet during the course of the study (over the 
counter probiotics are allowable) 
9) Premenopausal women and women <12 months after the onset of 
menopause must have a negative serum pregnancy test unless they have 
undergone surgical sterilization 
10) Female subjects of childbearing potential who are sexually active with a 
nonsterilized male partner must agree to use a highly effective method of 
contraception; nonsterilized male subjects who are sexually active with a 
female partner of childbearing potential must agree to use a highly 
effective method of contraception 
11) Not actively participating in another interventional MS clinical trial 
(participation in other observational research studies is allowable) 
 
 
    Exclusion Criteria 
 
1) Prior use of fingolimod, dimethyl fumarate, teriflunomide, natalizumab, 
alemtuzumab, mitoxantrone, cyclophosphamide, rituximab, ocrelizumab, 
daclizumab, methotrexate, azathioprine, mycophenolate mofetil, 
cyclosporine, leflunomide or induction chemotherapy 
2) No use of diuretics like furosemide (Lasix) 1 week before the first dose of 
oral antibiotics. The use of hydrochlorothiazide (HCTZ) for hypertension at 
a dose < 50 mg/day is allowable. 
3) Progressive MS by Lublin criteria (2014) 
4) No oral or IV antibiotics within 8 weeks of screening and 12 weeks of the 
planned FMT procedure (note that topical, otic, ocular antibiotics are 
specifically allowable) (which is consistent with the IMSMS.org protocol for 
collaborative gut microbiome research in MS) 
5) Hypersensitivity or allergy to study antibiotics, conscious sedation 
medications or bowel preparation 
6) Contraindication to study procedures including MRI, anesthesia (See 
Appendix K: ASA Criteria IV and V), colonoscopy, phlebotomy 
7) History of inflammatory bowel disease (Crohn’s Disease, Ulcerative 
Colitis) 
8) Active symptomatic C. difficile infection (colonization is not an exclusion) 
9) Active gastrointestinal condition being investigated (i.e. GI bleeding, colon 
cancer, active GI workup); history of known or suspected toxic megacolon 
and/or known small bowel ileus, major gastrointestinal surgery (e.g. 
significant bowel resection) within 3 months before enrollment (note that 

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this does not include appendectomy or cholecystectomy); or history of 
total colectomy or bariatric surgery 
10) History of malignancy (except excised cutaneous basal cell carcinoma or 
squamous cell carcinoma which are allowable) including no concurrent 
induction chemotherapy, radiation therapy or biological treatment for 
active malignancy 
11) Pregnant or lactating women or intention of getting pregnant during the 
trial period 
12) Active infection including untreated latent or active tuberculosis, HIV, 
hepatitis, syphilis, or other major active infection 
13) Known immunodeficiency including CVID 
14) INR>1.5, Platelets<100, Hemoglobin <8.5, WBC<2.0, Absolute 
lymphocyte count <0.8, Absolute Neutrophil Count <0.5, CD4<200, 
eGFR<45. 
15) Any condition that in the opinion of the study PI could jeopardize the 
safety of the subject, would make it unlikely for the subject to complete the 
study or could confound the results of the study 
16) Unable or unwilling to comply with study protocol requirements 
 
 
     METHOD OF TREATMENT ASSIGNMENT 
 
Eligible participants who wish to participate in the study and pass screening will 
receive the study intervention. Eligible participants who do not wish to receive 
FMT will be invited to enroll in the observational control arm to measure stool and 
blood biomarkers. 
 
     STUDY TREATMENT 
 
    Supply, Preparation, Administration and Storage 
 
   Donor Stool Formulation 
 
FMP30 donor stool will be obtained from OpenBiome (Somerville, MA; 
OpenBiome.org), a nonprofit stool bank. (See the Drug Master File BBMF-17195 
from OpenBiome,). 
 
Donors are screened by OpenBiome for the following risk factors per OpenBiome 
protocol and are excluded if they have any of the following (see also Appendix L: 
OpenBiome Donor Screening Testing): 
 
A. Infectious risk factors: 
1. Known human immunodeficiency virus (HIV), hepatitis A, B, or C infections 
or exposure. 
2. High-risk sexual behaviors. 
3. Use of illicit drugs. 

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4. Tattoo or body piercing within 6 months. 
5. Incarceration or history of incarceration. 
6. Known current communicable disease  (e.g.,  upper  respiratory  tract 
infection). 
7. Risk factors for variant Creutzfeldt Jakob disease. 
8. Travel within the last 3 months to areas of the world where diarrheal 
illnesses are endemic or risk of traveler’s diarrhea is high. 
B. Gastrointestinal and systemic comorbidities: 
1. History of inflammatory bowel disease, irritable bowel syndrome, idiopathic 
chronic constipation, or chronic diarrhea. 
2. History of GI malignancy or known polyposis 
3. Major immunosuppressive medications or systemic antineoplastic agents. 
4. Antibiotic use in the last 12 weeks. 
5. History of major gastrointestinal surgery (e.g., gastric bypass). 
6. Past history of Clostridium difficile infection. 
7. Metabolic syndrome with BMI > 30. 
8. Allergies and systemic autoimmunity (e.g., multiple sclerosis, connective 
tissue disease) and atopic diseases including asthma, eczema, and 
eosinophilic disorders. 
9. Past history of cancer including leukemia. 
 
As of January 25, 2021, OpenBiome has made amendments to their donor 
screening to include new organisms and change detection methods. (see Appendix 
N: OpenBiome Amendments to BMF17195). 
 
C. Laboratory Testing: 
OpenBiome has an established protocol for screening stool donors. This does 
not include all known viruses including cytomegalovirus (CMV) or Epstein-
Barr virus (EBV) or unknown viruses or unknown pathogens (see  Appendix L: 
Donor 
Screening 
List and Appendix N: OpenBiome Amendments to 
BMF17195). Our Phase 1 protocol excludes for 
pregnancy (acute 
cytomegalovirus (CMV) can be of major concern in pregnant women) and we 
exclude individuals who are EBV IgG anti-EBNA seronegative indicating prior 
exposure (rates of EBV positivity in adults with MS are very high as they are in 
the general population). Please also note that to our knowledge and per 
OpenBiome there have been no reported 
cases  of  CMV  or  EBV  infection  following  allogenic  FMT,  including  in 
immunocompromised patients40. 
 
 
   Donor Stool Administration 
 
The decision to deliver FMT via colonoscopy (as opposed to by enema or with 
oral capsules) was based on guidance from gastroenterology collaborators 
based on hypothesized better engraftment with colonoscopic delivery as well as 
tolerability (including with potential oral delivery given number of capsules 
required). The dosing selection of 3 x FMP30 was based on trying to maximize 

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potential engraftment while minimizing volume of stool needed to transplant and 
based on guidance from the OpenBiome Scientific Advisory board in designing 
this study protocol. 
 
According to FMP30 preparation instructions provided by OpenBiome, donor 
stool may be stored locally for up to 6 months in a standard -20°C laboratory 
freezer or up to 24 months in a -80°C laboratory freezer.  FMP30 will be prepared 
and thawed according to these instructions (see Appendix B: Storage Controls  
and Material Specifications). 
 
Once thawed, the material is ready for immediate administration. After thawing, 
material may remain at room temperature for up to 4 hours (or refrigerated/on ice 
for up to 8 hours). Samples should never be re-frozen. If thawed and not used 
within 8 hours, the material should be disposed of, as freeze thaw cycles may 
compromise viability. 
 
Recipients will undergo standard bowel preparation the day preceding FMT. The 
stool suspension will be introduced via colonoscopy and delivered by a study 
gastroenterologist into the cecum and ascending colon. 
 
 
   Antibiotics 
 
Emerging data from FMT trials for non-MS, non-Clostridium difficile indications 
demonstrates that engraftment of donor stool can be low when antibiotic 
preconditioning is not utilized34, 35. This protocol will therefore utilize antibiotic 
preconditioning prior to FMT and careful measurement of degree of engraftment 
as a primary biomarker endpoint. Antibiotic preconditioning using various 
regimens has been used in other FMT studies and is also widely used in the 
context of preparation for elective colorectal surgery (in which oral antibiotics 
have been shown to reduce surgical site infection rates and readmission rates)38. 
The selection of Neomycin and Metronidazole was based on standard usage in 
the context of bowel preparation for colorectal surgery and familiarity of use for 
other GI indications. (Ciprofloxacin, a fluoroquinolone, was considered as an 
alternative to neomycin and is sometimes used in the FMT context, but there are 
emerging safety concerns with fluoroquinolones as a class). Furthermore, both 
neomycin and vancomycin when administered orally tend to have poor systemic 
absorption and will therefore be expected to act mostly locally on colonic 
microbiota and potentially reduce risk of systemic side effects. Oral vancomycin 
was included with the goal of covering additional gram positive bacteria that are 
postulated to be important as part of the mechanism of action of FMT and are 
widely used in combination temporally with FMT in the Clostridium Difficile 
setting). Note that this same antibiotic protocol was also selected by UCSF GI 
investigators studying FMT in the context of ulcerative colitis, see  
https://clinicaltrials.gov/ct2/show/NCT03006809, accessed June 25, 2017). 
 
Summary Antibiotic Preconditioning Regimen: 

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Vancomycin 
500 mg PO BID 
X 5 days 
Metronidazole 
500 mg PO BID 
X 5 days 
Neomycin 
500 mg PO BID 
X 5 days 
All antibiotics to be started 6 days prior to FMT 
 
Oral antibiotics will be obtained through the UCSF Research pharmacy and 
delivered in secured packaging with labeling per pharmacy protocols. Subjects 
will be asked to complete a medication diary to document taking of home 
antibiotics.  Subjects will be required to complete the antibiotic regimen and the 
medication diary to receive the FMT study treatment. Failure of the subject to do 
so will result in exclusion from the study. 
 
    Dosage Modification 
 
Antibiotic dosages are protocolized; dosage modifications will not be permitted. 
FMT dosage via colonoscopy may include a lower amount of transplanted stool 
at the discretion of the study gastroenterologist if there are any peri-procedural 
safety or technical considerations. Total FMT dose (in mL) will be documented. 
 
    Over Dosage 
 
There is no data about over-dosage of FMT in humans. 
 
     CONCOMITANT AND EXCLUDED THERAPY 
 
Routine symptomatic MS therapies will be allowable, including dalfampridine or 
4-aminopyridine, botulinum toxin, oral spasticity agents/muscle relaxants, pain 
medications, antidepressants and anti-anxiety medication, modafinil and 
armodafinil or amphetamines for fatigue/alertness. 
 
Subjects will be asked to consent to not being on a MS disease modifying 
therapy during the 12 week study period. The length of this feasibility study was 
specifically designed to be short in order to minimize time not on a MS DMT. 
Subjects with a new clinical MS relapse or breakthrough clinical worsening of MS 
will be allowed to go on DMT at the discretion of their treating neurologist per 
routine medical management. If the decision to start a MS DMT occurs before 
the study intervention (antibiotics and/or FMT) this will be considered a screening 
failure and subjects will be excluded from the study and not included in further 
safety monitoring or in the pre-planned primary analysis. If the decision to start a 
MS disease modifying therapy occurs after any study intervention (antibiotics 
and/or FMT) has been administered, further study intervention will be 
discontinued but subjects will be invited and encouraged to complete the 
remaining observational period of the protocol for engraftment, immunological 
and safety monitoring. For acute relapse management, PO or IV steroids will be 

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allowable as part of routine medical management at the discretion of the treating 
neurologist. 
 
 
     STUDY ASSESSMENTS 
 
After providing written informed consent and reviewing inclusion and exclusion 
criteria, subjects will participate in either the FMT Treatment Arm or the 
Observational Control Arm. Study visits will take place at the Neuroscience 
Clinical Research Unit (NCRU) at the Sandler Neuroscience Center (675 Nelson 
Rising Lane, San Francisco, CA) on the UCSF Mission Bay Campus. 
Colonoscopy will take place at the UCSF Parnassus Endoscopy Unit (505 
Parnassus Avenue, San Francisco, CA). 
 
FMT Treatment Arm: 
 
After providing written informed consent and reviewing inclusion and exclusion 
criteria, subjects will undergo screening visit assessments.  Screening can be 
extended to a total of 5 weeks if deemed necessary by the PI to repeat require 
screening diagnostic testing. These assessments include: 
 
Screening: 
- 
Medical history including documentation of MS history, past medical 
problems and diagnoses, past surgical history, family history, medication 
review, medication allergy review, social history, smoking history, and 
contraception data collection for subjects that are heterosexually active 
- 
Measurements of vital signs, weight and height 
- 
Electrocardiogram (ECG) 
- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Concomitant medication review 
- 
Physical examination including a general physical examination and 
neurological examination 
- 
MS relapse assessment 
- 
Expanded Disability Status Scale (EDSS) (a structured neurological exam) 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Food Frequency Questionnaire 
- 
Stool collection (2 stool collection kits will be provided at screening visit. 
Stool sample expected to be collected within 3 days of visit and sent in by 
the patient in pre-labeled packaging. The subject has the option of 
providing a stool sample at the pre-treatment baseline visit if one is not 
provided at screening.) 
- 
Urine collection for urinalysis and culture to assess kidney function 
- 
Blood draw via venipuncture: Up to a maximum of 150mL of venous blood 

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samples will be obtained at each visit for the assessments described 
below and as listed in the schedule of assessments for subsequent visits. 
 
About 15 ml of blood will be taken at the screening visit and subsequent 
visits according to the schedule of study activities for safety laboratory 
tests. Samples for the following screening safety and eligibility laboratory 
tests will be sent to UCSF’s Medical Center laboratory for analysis at the 
UCSF Mission Bay campus at 1975 4th Street, San Francisco, CA. 
o Serum pregnancy test (if the subject can become pregnant) 
o Hematology (hemoglobin, hematocrit, RBCs, WBC absolute and 
differential, ANC, and quantitative platelet count) 
o Prothrombin Time and International Normalized Ratio (PT/INR) 
o Chem-10 (sodium, potassium, CO2, chloride, BUN, Creatinine, 
Glucose, Magnesium, Calcium, phosphorus) 
o Lymphocyte Subsets 
o Liver function tests(Aspartate Aminotransferase (AST), Alanine 
Aminotransferase ( ALT), Total Bilirubin, Alkaline phosphatase, 
Creatinine) 
o Immunoglobulins (IgG, IgM, IgA) to evaluate for immunodeficiency 
o Tuberculosis screening (will be primarily analyzed by UCSF 
Mission Bay labs. Will be analyzed by Quest Labs if needed, as 
back up) 
§ 
Must be negative a screening 
o Viral serology 
§ 
HIV (Must be negative at screening) 
§ 
Hepatitis 
§ 
Must be negative for HBsAg and HepBAb, and 
HepCAb at screening visit 
§ 
Treponemal screen (must be negative for syphilis at 
screening visit) 
§ 
EBV IgG anti-EBNA must be positive at screening (indicating 
prior exposure) 
 
About 100 mL of blood will be drawn for biomarker and immunology 
research at screening and subsequent visits according to the study 
schedule of activities. 
 
Blood and stool research samples will be analyzed at the UCSF MS 
Immunology Research Lab located in the Sandler Neurosciences Center 
at 675 Nelson Rising Lane. 
 
Pre-treatment Baseline Visit: 
Within 21 days after screening, subjects will partake in pre-treatment baseline 
visit assessments. These assessments include: 
- 
Review of inclusion/exclusion criteria 
- 
Vital signs 
- 
Weight 

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- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Subjects will receive an Adverse Event Diary to record any adverse events 
that they subject experience throughout the study. Study staff will review 
this with the subject at all subsequent visits. 
- 
Concomitant medication review 
- 
Physical examination including a general physical examination and 
neurological examination 
- 
Brain, Cervical and Thoracic spine MRI, with and without contrast. 
- 
MS Relapse Assessment 
- 
Expanded Disability Status Scale (a structured neurological exam) 
- 
Timed 25 foot walk 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Stool collection (A stool sample is not required at this visit if the subject 
has already provided one at screening) 
- 
Urine pregnancy test (if the subject can become pregnant) 
- 
Blood draw via venipuncture for immunological research 
- 
Subjects will be given an oral antibiotic regimen and written instructions to 
take at home 6 days before their FMT colonoscopy procedure date. They 
will also be given an antibiotic compliance diary, and are required to 
record the dates and times they take their antibiotics and GoLytely Bowel 
Preparation. This will be reviewed by study staff on the FMT colonoscopy 
procedure date. 
- 
Subjects will receive GoLytely bowel preparation, a bowel preparation 
compliance diary and standardized instructions for bowel preparation per 
usual UCSF colonoscopy unit protocol. 
Subjects will be treated with oral antibiotics for gut preconditioning for 5 days 
before their FMT colonoscopy. The antibiotics will be provided by the UCSF 
research pharmacy and given to subjects at their pre-treatment baseline study 
visit. Subjects will be given written instructions to start taking them exactly 6 days 
prior to their scheduled FMT colonoscopy. Subjects will also receive a phone call 
by the study coordinator 1-3 days before they should start taking their antibiotics 
to confirm that the subject understands the instructions and are not experiencing 
any new health problems. 
 
GoLytely bowel preparation for colonoscopy will be self-administered at home the 
night before and morning of their FMT. Subjects will receive GoLytely bowel prep 
solution and standardized instructions for bowel preparation per usual UCSF 
colonoscopy unit protocol at their pre-treatment baseline visit. These instructions 
will also be reviewed via the reminder phone call before antibiotics have been 
initiated. 
 
To ensure bowel preparation compliance, subjects will be given a compliance 
diary to record the dates and times that they took their prescribed antibiotics and 
GoLytely bowel preparation. This will be collected and reviewed on the day of 

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their FMT colonoscopy procedure. If the compliance diary is incomplete the FMT 
procedure is subject to cancellation under the discretion of the Principle 
Investigator and study gastroenterologist. 
 
FMT Treatment Colonoscopy Baseline Visit: 
 
Depending on the availability, subjects may be asked to complete the following 
study assessments up to a week prior to their scheduled colonoscopy: 
- Stool Collection 
- Urine pregnancy test (if the patient can become pregnant) 
- Blood draw via venipuncture for safety labs 
- Urinalysis and culture 
 
The following assessments will be completed on the day of the FMT 
colonoscopy: 
- Vital signs 
- Weight 
- Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- Concomitant medication review 
- Antibiotic compliance diary collected and confirmed completed 
- Confirmation that bowel preparation was completed 
- Blood draw via venipuncture for immunology research samples 
 
After these assessments have been completed subjects will undergo the 
research-based FMT colonoscopy by a study gastroenterologist, per standard 
UCSF GI colonoscopy unit protocols to include administration of conscious 
sedation. At the discretion of the study gastroenterologist, up to 90 ml of FMP30 
donor stool will be administered for FMT via colonoscopy. A colonoscopy report 
generated by the study gastroenterologist will be included in the medical record 
with note of any abnormal findings. If there is a concerning finding during the 
colonoscopy that in the opinion of the gastroenterologist warrants timely biopsy, a 
biopsy will be performed. The sample will be sent to UCSF pathology for review 
and for a written report. The patient will be informed in the event of an abnormal 
finding. If a biopsy is conducted FMT will not be performed and the subject will be 
excluded from further active FMT treatment but offered to complete study visits 
for safety and biomarker follow-up. 
 
The study gastroenterologist and study P.I. will be notified at any point during 
recovery if the subject experiences: 
• Heart rate less than 60 or greater than 120 beats/min 
• Respiratory rate less than 12 or greater than 25 breaths/min 
• Systolic blood pressure is less than 90 mmHg or greater than 140 mmHg 
• If Glucose greater than 200 
• Diastolic blood pressure is less than 60 mmHg or greater than 90 mmHg 
• Temperature greater than 38.5 degrees Celsius 
 

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When endoscopy discharge criteria are met, the subject will be discharged from 
the endoscopy center. 
 
FMT Treatment Arm Post FMT Visits: 
 
Subjects in the FMT Treatment arm will come in for follow-up study visit 
assessments at weeks 2, 4, 8, and 12 following colonoscopy. These visit will 
include: 
- 
Vital signs 
- 
Weight 
- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Concomitant Medication Review 
- 
Physical examination including a general physical examination and 
neurological examination 
- 
Brain, Cervical and Thoracic spine MRI, with and without contrast at week 
12 
- 
MS Relapse Assessment 
- 
Expanded Disability Status Scale (a structured neurological exam) 
- 
Timed 25 foot walk 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Food Frequency Questionnaire at week 12 
- 
Stool collections 
- 
Pregnancy Test at weeks 2, 8, and 12 (if patient can become pregnant) 
- 
Blood draw via venipuncture for lab safety values and immunological 
research 
 
Safety Follow-Up Visits: 
After subjects complete the active portion of the study, they will enter the Safety 
Follow-Up period at weeks 24, 36, and 48. Assessments at these visits include: 
- 
Vital signs 
- 
Weight 
- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Concomitant medication review 
- 
Physical examination including a general physical examination and 
neurological examination (at week 48) 
- 
EDSS 
- 
Timed 25 foot walk 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Food Frequency Questionnaire 
- 
Stool collection 
- 
Urine pregnancy test (if the subject can become pregnant) 

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- 
Blood draw via venipuncture for clinical laboratory safety values and 
immunological studies for research 
After their week 48 safety follow-up visit, subjects in the FMT Treatment arm will 
have completed the study. 
 
Unscheduled Visits: 
In the case of a MS relapse or any other AE that the PI deems as a safety 
concern during the study, subjects will be asked to come in for an unscheduled 
visit. Assessments at this visit will include: 
- 
Vital signs 
- 
Weight 
- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Concomitant Medication Review 
- 
Physical examination including a general physical examination and 
neurological examination 
- 
Optional brain, cervical and thoracic spine MRI, with and without contrast 
- 
MS relapse assessment 
- 
EDSS 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Stool collection 
- 
Optional urine pregnancy test (if the subject can become pregnant) 
- 
Blood draw via venipuncture for lab safety values and optional 
immunology study samples 
 
Early Termination Visit: 
In the case of early termination, subjects will be asked to have an early 
termination visit.  Assessments during this visit include: 
- 
Vital signs 
- 
Weight 
- 
Assessment of Adverse Events (AEs) and Serious Adverse Events (SAEs) 
- 
Concomitant Medication Review 
- 
Physical examination including a general physical examination and 
neurological examination 
- 
Brain, Cervical and Thoracic spine MRIs, with and without contrast 
- 
EDSS 
- 
Timed 25 foot walk 
- 
MS symptom and disability questionnaires including the MFIS (Fatigue), 
MSQOL-54 (Quality of Life), BWCS (bowel symptoms), BCLS (bladder 
symptoms), MHI-5 (Mood and Anxiety) and the Columbia Suicide Rating 
Scale (suicidality) 
- 
Stool collection 
- 
Urine collection for pregnancy test and urinalysis lab safety values 
- 
Blood draw via venipuncture clinical laboratory safety values, and 
immunological studies for research 

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Observational Control Arm: 
 
Screening/Baseline Week 0 Visit: 
After providing written informed consent and reviewing inclusion and exclusion 
criteria, subjects will undergo the Screening/Week 0 visit assessments. These 
assessments include: 
- 
Demographics and medical history 
- 
Concomitant medication review 
- 
MS Relapse Assessment 
- 
EDSS 
- 
Food Frequency Questionnaire 
- 
Stool collection (Stool collection kits for screening, week 2 and week 4 will 
be provided at screening visit. The stool sample for screening will be 
expected to be collected within 3 days of visit and sent in by the patient in 
pre-labeled packaging.) 
- 
Blood draw via venipuncture: Up to a maximum of 150mL of venous blood 
will be obtained at each visit for the assessments described below and as 
listed in the schedule of assessments for subsequent visits.  About 15 ml 
of blood will be taken at the screening visit and subsequent visits 
according to the schedule of study activities for safety laboratory tests. 
Samples for the following safety and eligibility laboratory tests will be sent 
to UCSF’s Medical Center laboratory for analysis at the UCSF Mission 
Bay campus at 1975 4th Street, San Francisco, CA. 
o Hematology (hemoglobin, hematocrit, RBCs, WBC absolute and 
differential, ANC, and quantitative platelet count) 
o Lymphocyte Subsets 
o Immunoglobulins (IgG, IgM, IgA) to evaluate for immunodeficiency 
o Tuberculosis screening (will be analyzed by Quest Labs) 
§ Must be negative a screening 
o Viral serology 
§ HIV 
• Must be negative at screening 
§ Hepatitis 
• Must be negative for HBsAg and HepCAb prior to 
enrollment; 
§ Treponemal screen (must be negative for syphilis) 
§ EBV IgG anti-EBNA positive at screening, indicating prior 
exposure 
 
- 
About 100 mL of blood will be drawn for biomarker and immunology 
research at screening and subsequent visits according to the study 
schedule of activities. Blood and stool research samples will be analyzed 
at the UCSF MS Immunology Research Lab located in the Sandler 
Neurosciences Center at 675 Nelson Rising Lane. 
 
Week 2: 

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Participants will collect and mail in a stool sample in the packaging with a pre- 
paid air-bill provided by the study team at the screening visit. 
 
Weeks 4, 8, and 12 Visits: 
Subjects will return for follow up assessments at weeks 4, 8 and 12. These 
assessments include: 
- 
Concomitant medication review 
- 
MS Relapse Assessment 
- 
Food Frequency Questionnaire at week 12 
- 
Stool collection 
- 
Blood draw via venipuncture for safety labs and Immunological samples 
for research 
 
After their Week 12 visit, subjects in the observational control arm will have 
completed the study. 
 
 
 
 
    Blood and Stool Samples for Research 
 
   Blood Samples 
 
While the primary endpoint of this study (as in all phase 1 studies) is safety and 
tolerability, we also thought it important to include a scientific and mechanistic 
biomarker endpoint, in this case the T cell in vitro assay and a measurement of 
microbiome structure change.  They are generally accepted as a method to 
determine the overall inflammatory properties of microbiota and in immune 
dysregulation in people with MS. 
 
Immune function will be measured in T cell in-vitro assays. Microbiota extracts 
will be co-cultured with blood peripheral mononuclear cells under different 
immune polarizing conditions to determine the pro-inflammatory properties of a 
given gut microbiota sample.  The potential clinical applicability of the T cell in- 
vitro assay has been observed in preclinical studies of microbiome differences 
between people with and without MS including as published by Dr. Baranzini’s 
lab at UCSF. 
 
 
   Stool Samples 
 
The clinical relevance of the fecal microbiota community structure is that it 
provides a mechanism of how microbiome alterations affect immune function in 
Multiple Sclerosis. It will be used as a measure of whether the subject’s 
microbiome changes with FMT intervention. Microbiota structure will be 
determined at each available time point by 16S ribosomal RNA sequencing on an 
Illumina Miseq instrument. Raw data files from the sequencer will be analyzed for 

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quality, and processed with the QIIME2 pipeline to obtain measures of alpha 
diversity (the richness of bacterial communities within a given sample), beta- 
diversity (how different two samples are when compared) (PcoA), individual 
organism testing, taxa representation, and differential abundance. With this 
method, the precise relative proportion of each identified organism can be 
assessed by creating a unique bacterial signature for each subject. If changes in 
community structure are detected, we will also explore how long these changes 
persist after the intervention. 
 
 
     DISCONTINUATION OF PROTOCOL-SPECIFIED THERAPY 
 
Protocol-specified therapy may be discontinued for any of the following reasons: 
• Unacceptable toxicity 
• Patient election to discontinue therapy (for any reason) 
• Patient election to start another MS disease modifying therapy 
• Physician’s judgment 
 
 
SUBJECT DISCONTINUATION 
 
Subjects will be removed from the study if there are any emergent safety 
concerns that in the opinion of the study investigators could negatively affect 
the welfare of the participant. 
 
Subjects with clinical MS relapses or breakthrough clinical worsening of MS will 
be allowed to go on disease modifying therapy (DMT) at the discretion of their 
treating neurologist per routine medical management. If the decision to start a 
MS DMT occurs before the study intervention (antibiotics and/or FMT) subjects 
will be considered a screening failure and excluded from the study and not 
included in further safety monitoring or in the pre-planned primary analysis. If 
the decision to start a MS disease modifying therapy occurs after any study 
intervention (antibiotics and/or FMT), any further study intervention will be 
discontinued and subjects will be invited to complete remaining study visits per 
protocol for safety and immunological monitoring. PO or IV steroids will be 
allowable as part of routine medical management for relapse activity. 
 
 
     STUDY DISCONTINUATION 
 
The Principal Investigator may elect to terminate the study at any time, including 
but not limited to unexpected adverse events that indicate the potential for a 
health hazard to subjects, failure to enroll or loss of financial support. 
 

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As of February 18, 2021, the study team decided to stop further recruitment 
early due to the challenges presented by the COVID-19 pandemic and in 
consideration that this is a Phase 1 study. 
 
     STATISTICAL METHODS 
 
    Analysis of the Conduct of the Study 
 
For study integrity, the following variables will be analyzed using 
descriptive/summary statistics: Enrollment, Dropouts, and Protocol Violations. 
 
Descriptive statistics will be used to describe baseline characteristics and 
demographics of the cohort. The t-test (or Wilcoxon Rank sum) or chi-squared 
(or Fisher exact) tests as appropriate will be used to analyze differences 
between the interventional and control groups. 
 
    Efficacy Analysis 
 
a. Primary Endpoint 
 
Summary statistics will be used to report primary safety and feasibility 
outcomes. For the primary biomarker immunology outcome, the Wilcoxon 
signed-rank (or paired T-test) will be used as a paired pre-post analysis of 
change in immunological function in the FMT treated arm. The t-test or Mann-
Whitney- U/Wilcoxon rank sum or chi-squared to Fisher Exact test will be 
used as appropriate to compare differences between the FMT treated arm 
and observational control arm. 
 
b. Secondary Endpoints 
 
Mixed effects linear regression modeling with time as the interaction term to 
leverage repeated measures will be used to analyze the following: 
- 
Fecal microbiota community structure at weeks 0, 2, 4, 8, 12 and 
for safety follow-up through an open label extension through 1 
year 
- 
Induction of T regulatory or Th2 cells and/or reduction of Th1 or Th17 
cells at 0, 2, 4 8 and 12 weeks and for safety follow-up through 1 year 
- 
Plasma CD19+ and CD20+ B cell counts and serum immunoglobulin 
levels at weeks 0, 2, 4, 8 and 12 weeks and for safety follow-up 
through 1 year 
- 
Fatigue score (abbreviated MFIS) at baseline, week 4, week 8 and 
week 12 
- 
Quality of life (MSQOL-54)] at baseline, week 4, week 8 and week 12 
- 
Bowel symptoms (BWCS) at baseline, week 4, week 8 and week 12 
- 
Bladder symptoms (BLCS) at baseline, week 4, week 8 and week 12 

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- 
Timed 25 foot walk at baseline, week 4, week 8 and week 12 
 
The Wilcoxon signed rank (or paired T test) will be used for the following pre-
post comparisons in the interventional, FMT treated arm: 
- 
New T2/FLAIR lesions, T2/FLAIR lesion load, T2/FLAIR lesion 
number at baseline and week 12 
- 
New gadolinium enhancing lesions, total gadolinium enhancing 
lesions at baseline and week 12 
- 
EDSS and sub scores at baseline and week 12 
- 
Timed 25 foot walk at baseline, week 4, week 8 and week 12 
- 
Mood and Anxiety (MHI-5) and Columbia Suicide Rating Scale 
and baseline, week 8 and week 12 
 
We will also analyze using comparison of means for pre-post treatment 
(student’s T-test or Wilcoxon rank sum or chi-squared or Fisher Exact as 
appropriate) 
 
    Safety Analysis 
 
Descriptive/summary statistics will be reported for safety endpoints and will 
include: 
- 
Summary of Adverse Events and Serious Adverse Events 
- 
Timing of AEs and Serious AEs 
 
    Missing Data 
 
Available data will be reported along with an accounting of missing data. There 
are no plans to use imputation or related strategies. 
 
    Sample Size 
 
We intend to recruit 10 subjects into the FMT treatment arm of this feasibility 
study. Using a Wilcoxon signed-rank (or paired T-test) for paired pre-post 
analyses on immunological function with a sample size of 10 subjects with 
complete data, we will have 80% power with an alpha of 0.05 to detect at least 
a 1 SD change in pre-post outcomes of change in T cell function. 
 
An observational control group of up to 20 subjects will be recruited to measure 
stool and serum biomarkers. 
 
As of February 18, 2021, the study team decided to stop further recruitment due 
to the challenges presented by the COVID-19 pandemic and in consideration 
that this is a Phase 1 study. Investigators are currently analyzing data obtained. 
Given this, data analyses will primarily be descriptive based on the number of 
subjects enrolled.  
 

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  DATA QUALITY 
 
Data quality will be ensured through the use of standard practices and 
procedures through the UCSF MS Clinical research program. 
 
 
5. 
ASSESSMENT OF SAFETY 
 
      SAFETY VARIABLES 
 
Patients will be evaluated clinically and with standard laboratory tests before the 
study and at regular intervals during the study. Safety evaluations will consist of 
medical interviews, recording of adverse events, physical examinations, and 
standard laboratory measurements. 
Adverse events (AEs) and serious adverse events (SAEs) that are considered 
related to the FMT intervention will be monitored and reported. 
 
     DEFINITION OF AN ADVERSE EVENT (AE) 
 
Adverse events (AEs) will be recorded at each regular scheduled study visit in 
the study patient record (source document) as well as on a specific AE case 
report form (CRF). An AE is any untoward medical occurrence in a study patient 
or clinical investigation participant administered a pharmaceutical product. An AE 
does not necessarily have a causal relationship with this treatment. An AE can 
therefore be any unfavorable and unintended sign (including an abnormal 
laboratory finding), symptom, or disease temporally associated with the use of a 
medicinal product, whether or not related to the medicinal product, e.g.: 
• any new clinical diagnosis 
• any symptom that requires medical clarification or leads to in-patient 
admission (surgery or accident) 
• any suspected adverse drug reaction (ADR) 
• any symptom that appears on the study patient’s medical records 
• any event related in time with the application of the study medication and 
affecting the health of the study patient (including laboratory value 
changes) 
If there is any doubt as to whether a clinical observation is an AE, the event 
should be reported. 
 
AEs must be graded for severity and relationship to study product. Adverse 
events of special interest (AESI) will be defined as newly acquired transmissible 
infectious diseases, newly acquired autoimmune disease, and worsening of the 
underlying disease state. 
 
AEs will be assessed by the clinician using the NIH Common Terminology 
Criteria for Adverse Events (CTCAE) Version 4.0 defined grading system (Briefly, 
the criteria for estimating adverse event severity grade: 

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• 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: Severe or medically significant but not immediately life- 
threatening; hospitalization or prolongation of hospitalization indicated; 
disabling; limiting self-care ADL. 
• Grade 4, Life threatening: Places the patient or subject at immediate risk 
of death. It does not include an adverse event that, had it occurred in a 
more severe form, might have caused death. 
• Grade 5, Death 
 
*Based on the most recent version of NCI NIH CTCAE (v4.0), which can be found 
at: http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm 
 
All adverse events, regardless of relatedness should be reported. All adverse 
events should be evaluated for relatedness when reporting and documenting on 
the CRF. The following guidelines of relatedness will be utilized: 
 
n Definitely Related: The adverse event is clearly related to the FMT material - 
i.e. an event that follows a reasonable temporal sequence from administration 
of the FMT material or follows a known or expected response pattern to the 
FMT material, that is confirmed by improvement on stopping and 
reappearance of the event on repeated exposure, and that could not be 
reasonably explained by the known characteristics of the patient's clinical 
state. 
n Possibly Related: An adverse event that follows a reasonable temporal 
sequence from administration of the FMT material or follows a known or 
expected response pattern to the suspected intervention, but that could have 
been produced by other factors. 
 
In addition to open-ended questions on adverse events meeting the above 
definitions, specific potential adverse events will be inquired about during the 
safety follow up period (following the 12 week active portion of the study through 
to 48 weeks. 
 
An adverse event or suspected adverse reaction is considered “serious” if, in the 
view of either the site PI or lead PI, it results in any of the following outcomes: 
• Death 
• Life-threatening adverse event* 
• Inpatient hospitalization or prolongation of existing hospitalization 
• A congenital anomaly/birth defect 
• Persistent or significant disability or incapacity or substantial disruption of 

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the ability to conduct normal life function 
• Important medical events that, may not result in death, be life-threatening, 
or require hospitalization may be considered when, based upon 
appropriate medical judgement, they may jeopardize the patient or subject 
and may require medical or surgical intervention to prevent one of the 
outcomes listed in this definition 
*Life-threatening adverse event. An adverse event is considered “life- 
threatening” if, in the view of either the site PI or lead PI, its occurrence places 
the patient or participant at immediate risk of death. It does not include an 
adverse event which, had it occurred in a more severe form, might have caused 
death. 
Any adverse event or suspected adverse reaction that meets the criteria for 
serious adverse event will be: 
• recorded on the appropriate SAE CRF 
• followed through resolution by a study clinician 
• reviewed and evaluated by a study clinician 
 
 
     UNSOLICITED ADVERSE EVENTS 
 
On enrollment in the study, the study participants will be instructed to contact the 
site PI if an AE occurs. These include fever, chills, abdominal pain, abdominal 
distention, excessive flatulence, constipation, nausea, and vomiting. These 
unsolicited, unrelated non-serious adverse events occurring from the time of FMT 
until 12 weeks (for the active period of the study) and 52 weeks (for the safety 
follow-up). Patients will be given a patient diary with date, time, details and action 
taken to help with data collection. This diary be taken to the site PI for evaluation 
at each follow-up visit and patients instructed to seek immediate medical 
attention if indicated. 
 
     REPORTING OF ADVERSE EVENTS 
 
Study participants will be instructed to contact the study team if any serious or 
unexpected adverse event occurs. Study staff will enquire about AEs at each 
study visit. Reported AE’s will be recorded in detail in an AE CRF. 
AE information to be collected in the AE CRF: 
• Nature of the event 
• Time of onset: date, time 
• Concomitant treatment: product (generic name), indication, dosage, 
dosage interval, presentation, mode of administration, administration 
regimen 

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• Duration of the AE 
• Severity 
• Seriousness 
• Causality 
• Outcome 
The course and outcome of the adverse event will be commented on as follows: 
• Recovered without sequelae 
• Not yet recovered 
• Recovered with sequelae 
• Fatal 
Any SAE (including death, irrespective of the cause) occurring during the study 
will be immediately reviewed by the study PI. 
 
If determined to be a SUSAR (Suspected Unexpected Serious Adverse 
Reaction) by the study PI, the event will be reviewed by the Data Safety 
Committee. All unexpected fatal or life-threatening events associated with the 
use of the trial drugs will be reported to the regulatory agencies and competent 
authorities via telephone or fax within 7 calendar days after being notified of the 
event. Also, all related but unexpected SAEs including non-death/non-life- 
threatening related but unexpected SAEs associated with the use of the trial 
medication will be reported to the appropriate authorities and investigators by a 
written safety report within 15 calendar days of notification.  The UCSF IRB will 
be notified of SUSARs in accordance to the Post-Approval Reporting 
Requirements policy of the UCSF Office of Ethics and Compliance (see Appendix 
M: UCSF Post-Approval Reporting Requirements). 
 
In case of a SAE (non-SUSAR), the study PI will record the event for review and 
compilation. The Data Safety Committee will review all SAE every 6 months or 
ad hoc depending on the clinical case at the discretion of the study PI. A specific 
SAE CRF will be provided. The report must contain a detailed description of the 
symptoms observed and the concomitant treatment administered. Furthermore, 
the report must comment on a possible causative relationship between the AE 
and the trial medication. Each SAE must be followed until it is resolved or can be 
explained satisfactorily. 
 
For non-serious adverse reactions (definitely related, possibly related, not 
related) the study PI will record the event for review and compilation. All non- 
serious adverse reactions will be reviewed by the Data Safety Committee every 6 
months or ad hoc depending on the clinical case at the discretion of the study PI. 
 
In accordance with safety requirements, the study PI will inform the local IRB. 
The following instructions must be heeded: 
• In the case of an intolerable SAE, the study patient must, at the 
decision of the study PI, be withdrawn from further treatment, and 
symptomatic treatment must be administered. The participant may opt 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
43 
 
 
to voluntarily provide additional samples for duration of study. 
• The measures taken must be recorded on the CRF. 
 
In accordance with local legislation, the study PI will submit copies of the final 
SAE-report to the Regulatory Authorities concerned, if necessary. 
 
     RECORDING SAFETY VARIABLES 
 
The principal investigator will be responsible for ensuring that all AEs and SAEs 
that are observed or reported during the study are collected and reported to the 
UCSF IRB and the FDA in accordance with CFR 312.32 (IND Safety Reports). 
 
    Adverse Event Reporting Period 
 
The study period during which all AEs and SAEs must be reported begins after 
informed consent is obtained and study intervention initiation, defined in this 
study as the first dose of antibiotic pre-treatment. AE monitoring ends 16 weeks 
following the last administration of study treatment or study 
discontinuation/termination, whichever is earlier.  
 
    Assessment of Adverse Events 
 
All AEs and SAEs whether volunteered by the subject, discovered by study 
personnel during questioning, or detected through physical examination, 
laboratory test, or other means will be reported. Each reported AE or SAE will be 
described by its duration (i.e., start and end dates), regulatory seriousness 
criteria if applicable, suspected relationship to FMT procedure and actions taken. 
 
To ensure consistency of AE and SAE causality assessments, investigators 
should apply the following general guideline: 
 
Yes 
There is a plausible temporal relationship between the onset of the AE and 
administration of FMT procedure (including antibiotic preconditioning and bowel 
preparation), and the AE cannot be readily explained by the subject’s clinical 
state, intercurrent illness, or concomitant therapies; and/or the AE follows a 
known pattern of response to the FMT procedure. 
 
No 
Evidence exists that the AE has an etiology other than the FMT procedure (e.g., 
preexisting medical condition, underlying disease, intercurrent illness, or 
concomitant medication); and/or the AE has no plausible temporal relationship to 
the FMT procedure. 
 
     REPORTING ADVERSE EVENTS 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
44 
 
 
A. Deaths 
 
All deaths that occur during the protocol-specified AE reporting period will be 
reported. 
 
B. Preexisting Medical Conditions 
 
A preexisting medical condition is one that is present at the start of the study. 
Such conditions will be reported as part of the medical and surgical history. 
Preexisting conditions will be reassessed throughout the trial and reported as an 
AE or SAE if the frequency, severity, or character of the condition worsens during 
the study. 
 
C. Hospitalizations for Medical or Surgical Procedures 
 
Any AE that results in hospitalization or prolonged hospitalization will be 
documented and reported as an SAE. Hospitalization for diagnostic or elective 
surgical procedures for preexisting conditions will not be reported. 
 
D. Pregnancy 
 
If a female subject becomes pregnant during the course of the study, this will be 
reported as an AE, and appropriate reporting will also be made to the UCSF IRB. 
 
      DATA SAFETY MONITORING PLAN 
 
This study will adhere to a pre-specified IRB-approved data safety monitoring 
plan with the goal of ensuring participant and monitoring data quality. As this 
study is a single-center open label Phase 1 clinical trial for which the 
local investigator will have access to all data, an independent data safety 
monitoring board is not required per UCSF IRB guidance 
(https://irb.ucsf.edu/data-and-safety-monitoring-plans-and-boards). The study PI 
will review patient safety and data on a near real-time basis as part of routine 
study conduct. 
 
The study will be halted pending review and discussion by the Data Safety 
Committee if at any point during the study a serious adverse event (SAE) at least 
possibly related to study treatment or a suspected or proven infection at least 
possibly related to the study treatment is identified. 
 
In addition, to ensure participant safety, the data safety monitoring plan will 
include additional review by a Data Safety Committee consisting of the study PI 
(Dr. Jeffrey Gelfand), Dr. Sergio Baranzini and GI co-investigators (Drs. James 
Ostroff and Priya Kathpalia) at the following intervals for interim analyses: 
n Within 2 weeks of when the first 3 FMT treated patients have reached 4 
week post-FMT 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
45 
 
 
n Within 3 weeks after each 3 sequential FMT-treated subjects reach 12 
weeks post-FMT 
n Semi-annually to review all study progress up to that date 
n At study completion 
 
The Data Safety Committee will review clinical data, adverse events, and 
any anticipated or unanticipated problems involving risk to participants and will 
have access to all primary study data upon request. PI can request additional 
ad hoc meetings as needed. Immunological efficacy outcomes as available will 
be shared with the committee as available but may not be available at every 
timeline, especially earlier time points, given the need for batched analyses. 
The study PI provides assurance that the research team will adhere to all 
required UCSF IRB reporting requirements as well as those that may be 
required by the FDA. 
 
 
6. 
REGULATORY CONSIDERATIONS 
 
      IND 
 
An IND will be obtained from the FDA for FMT of donor stool in MS. Reporting of 
AEs will be in accordance with IND and UCSF IRB guidelines. 
     INFORMED CONSENT 
 
Written informed consent will be obtained from all subjects. A copy of the ICF will 
be provided to each subject along with a UCSF IRB approved Human Subjects 
Bill of Rights. Subjects will also be required to sign appropriate HIPAA release 
documentation for medical record review. 
 
     INSTITUTIONAL REVIEW BOARD OR ETHICS COMMITTEE 
APPROVAL 
 
This study protocol, informed consent forms and supporting documentation will 
be submitted to the UCSF IRB for review before the study is initiated. The study 
will be conducted in accordance with U.S. FDA, applicable national and local 
health authorities, and UCSF IRB requirements, including for applicable 
reporting. 
     DATA COLLECTION 
 
Data will be collected using a combination of hard copy case report forms and 
electronic case report forms with database programs using REDCap, a web- 
based platform approved and encouraged by UCSF for use in human subject 
research. 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
46 
 
 
     DISCLOSURE AND PUBLICATION OF DATA 
 
Disclosure will be in accordance with UCSF IRB guidelines and approved 
protocols. Some data created by the study will be added to the medical record, 
including clinical laboratory results and MRI reports (which are read out by UCSF 
neuro-radiologists for safety). Medical information obtained from the study may 
also be given to the subject’s treating physician or health-care provider with the 
subject’s permission. 
Data generated by this study will be made available to relevant authorities, 
including the U.S. FDA, local or national health authorities or the UCSF IRB. 
It is the intention of the investigators that the results of this study will be 
presented at scientific meetings and published in peer-reviewed medical journals. 
No names or identifying information will be used in presenting trial results. 
The study will be registered with clinicaltrials.gov. 
 
     RETENTION OF RECORDS 
 
Records will be obtained per current UCSF IRB and U.S. FDA guidelines, with 
the current standard to retain records for at least 2 years after completion of the 
study. 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
47 
 
 
7. 
REFERENCES 
 
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Howard J, Trevick S, Younger DS. Epidemiology of Multiple Sclerosis. 
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Czaja AJ. Factoring the intestinal microbiome into the pathogenesis of 
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Verwoerd A, Ter Haar NM, de Roock S, Vastert SJ, Bogaert D. The 
human microbiome and juvenile idiopathic arthritis. Pediatr Rheumatol Online J. 
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Cree BA, Spencer CM, Varrin-Doyer M, Baranzini SE, Zamvil SS. Gut 
microbiome analysis in neuromyelitis optica reveals overabundance of 
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Ochoa-Reparaz J, Mielcarz DW, Begum-Haque S, Kasper LH. Gut, bugs, 
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Joscelyn J, Kasper LH. Digesting the emerging role for the gut microbiome 
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Tremlett H, Bauer KC, Appel-Cresswell S, Finlay BB, Waubant E. The gut 
microbiome in human neurological disease: A review. Annals of neurology. 
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Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
48 
 
 
17. 
Berer K, Mues M, Koutrolos M, Rasbi ZA, Boziki M, Johner C, et al. 
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Ochoa-Reparaz J, Mielcarz DW, Haque-Begum S, Kasper LH. Induction 
of a regulatory B cell population in experimental allergic encephalomyelitis by 
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Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami 
P, et al. CD44 deletion leading to attenuation of experimental autoimmune 
encephalomyelitis results from alterations in gut microbiome in mice. Eur J 
Immunol. 2017. 
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Wang Y, Begum-Haque S, Telesford KM, Ochoa-Reparaz J, Christy M, 
Kasper EJ, et al. A commensal bacterial product elicits and modulates migratory 
capacity of CD39(+) CD4 T regulatory subsets in the suppression of 
neuroinflammation. Gut Microbes. 2014;5(4):552-61. 
22. 
Rothhammer V, Mascanfroni ID, Bunse L, Takenaka MC, Kenison JE, 
Mayo L, et al. Type I interferons and microbial metabolites of tryptophan 
modulate astrocyte activity and central nervous system inflammation via the aryl 
hydrocarbon receptor. Nat Med. 2016;22(6):586-97. 
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Jangi S, Gandhi R, Cox LM, Li N, von Glehn F, Yan R, et al. Alterations of 
the human gut microbiome in multiple sclerosis. Nat Commun. 2016;7:12015. 
24. 
Miyake S, Kim S, Suda W, Oshima K, Nakamura M, Matsuoka T, et al. 
Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking 
Depletion of Species Belonging to Clostridia XIVa and IV Clusters. PLoS One. 
2015;10(9):e0137429. 
25. 
Cantarel BL, Waubant E, Chehoud C, Kuczynski J, DeSantis TZ, 
Warrington J, et al. Gut microbiota in multiple sclerosis: possible influence of 
immunomodulators. J Investig Med. 2015;63(5):729-34. 
26. 
Chen J, Chia N, Kalari KR, Yao JZ, Novotna M, Soldan MM, et al. Multiple 
sclerosis patients have a distinct gut microbiota compared to healthy controls. Sci 
Rep. 2016;6:28484. 
27. 
Tremlett H, Fadrosh DW, Faruqi AA, Zhu F, Hart J, Roalstad S, et al. Gut 
microbiota in early pediatric multiple sclerosis: a case-control study. Eur J Neurol. 
2016;23(8):1308-21. 
28. 
Tremlett H, Fadrosh DW, Faruqi AA, Hart J, Roalstad S, Graves J, et al. 
Gut microbiota composition and relapse risk in pediatric MS: A pilot study. J 
Neurol Sci. 2016;363:153-7. 
29. 
Ochoa-Reparaz J, Magori K, Kasper LH. The chicken or the egg dilemma: 
intestinal dysbiosis in multiple sclerosis. Ann Transl Med. 2017;5(6):145. 
30. 
Smits LP, Bouter KE, de Vos WM, Borody TJ, Nieuwdorp M. Therapeutic 
potential of fecal microbiota transplantation. Gastroenterology. 2013;145(5):946- 
53. 
31. 
Kelly CR, Khoruts A, Staley C, Sadowsky MJ, Abd M, Alani M, et al. Effect 
of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
49 
 
 
Clostridium difficile Infection: A Randomized Trial. Ann Intern Med. 
2016;165(9):609-16. 
32. 
Lee CH, Steiner T, Petrof EO, Smieja M, Roscoe D, Nematallah A, et al. 
Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of 
Diarrhea in Patients With Recurrent Clostridium difficile Infection: A Randomized 
Clinical Trial. JAMA. 2016;315(2):142-9. 
33. 
Uygun A, Ozturk K, Demirci H, Oger C, Avci IY, Turker T, et al. Fecal 
microbiota transplantation is a rescue treatment modality for refractory ulcerative 
colitis. Medicine (Baltimore). 2017;96(16):e6479. 
34. 
Damman CJ, Brittnacher MJ, Westerhoff M, Hayden HS, Radey M, Hager 
KR, et al. Low Level Engraftment and Improvement following a Single 
Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative 
Colitis. PLoS One. 2015;10(8):e0133925. 
35. 
Vujkovic-Cvijin I, Rutishauser RL, Pao M, Hunt PW, Lynch SV, McCune 
JM, et al. Limited engraftment of donor microbiome via one-time fecal microbial 
transplantation in treated HIV-infected individuals. Gut Microbes. 2017:0. 
36. 
Bajaj JS, Kassam Z, Fagan A, Gavis EA, Liu E, Cox IJ, et al. Fecal 
Microbiota Transplant from a Rational Stool Donor Improves Hepatic 
Encephalopathy: A Randomized Clinical Trial. Hepatology. 2017. 
37. 
Bafeta A, Yavchitz A, Riveros C, Batista R, Ravaud P. Methods and 
Reporting Studies Assessing Fecal Microbiota Transplantation: A Systematic 
Review. Ann Intern Med. 2017. 
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Bowel Preparation Significantly Reduces Surgical Site Infection Rates and 
Readmission Rates in Elective Colorectal Surgery. Ann Surg. 2015;261(6):1034- 
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39. 
Cekanaviciute, E. et al. Gut bacteria from multiple sclerosis patients 
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40. 
Kelly CR, Ihunnah C, Fischer M, et al. Fecal Microbiota Transplant for 
Treatment of Clostridium difficile Infection in Immunocompromised Patients. The 
American journal of gastroenterology. 2014;109(7):1065-1071. 
doi:10.1038/ajg.2014.133. 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
50 
 
 
 
 
 
8. 
APPENDICES  
Appendix A-1: Table of Assessments for Interventional FMT Treatment Group 
 
 
 
 
Week 
Screening 
Treatment Period 
 
 
Early 
Termin- 
ation 
Visit 
Safety Follow-Up 
 
 
 
- 4 
Pre- 
Treatment 
Baseline 
Visit 
 
Pre-FMT 
Phone 
Call 
Baseline 
FMT 
Week 0 
 
Post FMT 
Phone 
Call 
 
 
 
2 
 
 
 
4 
 
 
 
8 
12 
(End of 
Active 
Portion) 
 
 
Unsched- 
uled visit 
24 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 36 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 48 
(OLE 
SAFETY 
FOLLOW- 
UP) 
 
 
Day 
 
 
-28 
Within 21 
Days After 
Screening 
 
 
-7(±1) 
0 
 
 
2 (±1) 
 
 
14 (±2) 
 
 
28 (±7) 
 
 
56 (±7) 
84 (±7) 
 
 
168 (±7) 
252  (±7) 
 
 
336 (±7) 
Informed Consent 
X 
Review 
Inclusion/Exclusion 
Criteria 
X 
X 
 
 
 
 
 
 
 
 
 
Demographics, 
Medical History, 
Smoking History, 
Reproductive 
Status, & 
Contraception 
X 
 
 
 
 
 
 
 
 
 
 
Vital Signs 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Weight, Height 
(height only 
collected at 
screening) 
X 
X 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
ECG (for safety) 
with cardiology 
read 
X 
 
 
 
 
 
 
 
 
 
 
Adverse Event 
Reporting 
X 
X 
(Provide 
Subject with 
AE Diary) 
X 
(telephone 
visit) 
X 
X 
(telephone 
visit) 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant 
Medication Review 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Physical 
Examination 
X 
X 
 
 
X 
X 
X 
X 
X 
X 
 
X 
IMAGING 
MRI Brain, Cervical 
and Thoracic Spine 
with contrast 
(includes 3 formal 
neuroradiology 
reads) – also 
includes SF SIGMA 
spine sequences 
 
X 
 
 
 
 
 
X 
X 
(optional) 
X 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
51 
 
 
 
 
 
 
 
 
 
Week 
Screening 
Treatment Period 
 
 
Early 
Termin- 
ation 
Visit 
Safety Follow-Up 
 
 
 
- 4 
Pre- 
Treatment 
Baseline 
Visit 
 
Pre-FMT 
Phone 
Call 
Baseline 
FMT 
Week 0 
 
Post FMT 
Phone 
Call 
 
 
 
2 
 
 
 
4 
 
 
 
8 
12 
(End of 
Active 
Portion) 
 
 
Unsched- 
uled visit 
24 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 36 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 48 
(OLE 
SAFETY 
FOLLOW- 
UP) 
 
 
Day 
 
 
-28 
Within 21 
Days After 
Screening 
 
 
-7(±1) 
0 
 
 
2 (±1) 
 
 
14 (±2) 
 
 
28 (±7) 
 
 
56 (±7) 
84 (±7) 
 
 
168 (±7) 
252  (±7) 
 
 
336 (±7) 
CLINICAL ASSESSMENTS 
MS Relapse 
Assessment 
X 
X 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
EDSS 
X 
X 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Timed 25 foot walk  
X 
 
 
X 
X 
X 
X 
 
X 
X 
X 
X 
Questionnaires 
(MSQOL-54, MFIS, 
MHI-5, C-SSRS, 
BWCS, BLCS ) 
X 
(Use 
Baseline/S- 
creening 
Visit version 
of C-SSRS) 
X 
(Use Since 
Last Visit 
version of 
C-SSRS) 
 
 
X 
(Use 
Since 
Last 
Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last 
Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last 
Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last Visit 
version 
of C- 
SSRS) 
 
X 
(Use 
Since 
Last 
Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last Visit 
version 
of C- 
SSRS) 
X 
(Use 
Since 
Last Visit 
version 
of C- 
SSRS) 
Food Frequency 
Questionnaire 
X 
 
 
 
 
 
 
X 
 
 
X 
X 
X 
LABORATORY ASSESSMENTS 
Stool Collection 
(microbiome) 
X (can be 
collected at 
pre- 
treatment 
visit) 
X (optional 
if not 
collected at 
screening) 
 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Pregnancy test 
(Serum test at 
screening. Urine 
test at all other 
visits) 
X 
X 
 
X 
 
X 
 
X 
X 
X 
(optional) 
X 
X 
X 
X 
CBC/diff 
X 
X 
X 
X 
X 
X 
X 
X 
Urinalysis + culture 
X 
 
 
X 
 
 
 
 
X 
X 
(optional) 
X 
 
 
HIV 
X 
X 
X 
Treponemal 
Screen 
X 
 
 
 
 
 
 
X 
 
X 
 
 
EBV IgG anti- 
EBNA Screen 
X 
 
 
 
 
 
 
 
 
 
 
Immunoglobulins 
(IgG, IgM, IgA) 
X 
 
 
X 
 
X 
X 
X 
X 
 
X 
 
 
Hepatitis B and C 
screening 
X 
 
 
 
 
 
 
X 
 
X 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
52 
 
 
 
 
 
 
 
 
 
Week 
Screening 
Treatment Period 
 
 
Early 
Termin- 
ation 
Visit 
Safety Follow-Up 
 
 
 
- 4 
Pre- 
Treatment 
Baseline 
Visit 
 
Pre-FMT 
Phone 
Call 
Baseline 
FMT 
Week 0 
 
Post FMT 
Phone 
Call 
 
 
 
2 
 
 
 
4 
 
 
 
8 
12 
(End of 
Active 
Portion) 
 
 
Unsched- 
uled visit 
24 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 36 
(OLE 
SAFETY 
FOLLOW- 
UP) 
Week 48 
(OLE 
SAFETY 
FOLLOW- 
UP) 
 
 
Day 
 
 
-28 
Within 21 
Days After 
Screening 
 
 
-7(±1) 
0 
 
 
2 (±1) 
 
 
14 (±2) 
 
 
28 (±7) 
 
 
56 (±7) 
84 (±7) 
 
 
168 (±7) 
252  (±7) 
 
 
336 (±7) 
Lymphocyte 
Subsets (CD 3, 4, 
8, 19) 
X 
 
 
X 
 
X 
X 
X 
X 
X 
X 
 
 
INR/PT(Blood 
Clotting) 
X 
 
 
 
 
 
 
 
 
 
 
LFTs (AST, ALT, 
AlkP, T bili) 
X 
 
 
X 
 
X 
X 
X 
X 
X 
(optional) 
X 
 
 
Quantiferon Gold 
X 
Chem-10 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Immunology 
studies (Baranzini 
Lab) 
X 
X 
 
X 
 
X 
X 
X 
X 
X 
(optional) 
X 
X 
X 
X 
Intervention 
Oral Antibiotic 
Regimen (taken at 
home) 
 
X 
(give meds, 
directions, 
and diary to 
subject) 
X 
(telephone 
call; review 
antibiotic 
directions) 
X 
(antibiotic 
diary 
collection) 
 
 
 
 
 
 
 
 
Bowel Preparation 
(taken at home) 
 
X 
(give to 
subject with 
directions) 
X 
(telephone 
call; review 
bowel prep 
directions) 
X 
(bowel 
regimen 
taken at 
home) 
 
 
 
 
 
 
 
 
Colonoscopy 
X 
FMT with donor 
stool 
 
 
 
X 
 
 
 
 
 
 
 
 
Conscious sedation 
for FMT 
 
 
 
X 
 
 
 
 
 
 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
53 
 
 
 
 
Appendix A-2: Schedule of Assessments for Observational Control Arm (no FMT) 
 
 
 
 
Week 
Screening/Baseline 
Observation Period 
 
 
Week 0 
 
 
Week 2 
 
 
Week 4 
Week 8 
Week 12 
END OF 
OBSERVATIONAL 
PORTION 
Day 
0 
14 (±2) 
28 (±7) 
56 (±7) 
84(±7) 
Informed Consent 
X 
Review 
Inclusion/Exclusion 
Criteria 
X 
 
 
Demographics and 
Medical History 
X 
 
 
EDSS 
X 
 
 
Medication Review 
X 
X 
X 
X 
MS Relapse 
Assessment 
X 
 
X 
X 
X 
Frequency 
Questionnaire 
X 
 
 
X 
LAB 
ASSESSMENTS  
 
 
Stool Collection 
(microbiome) 
X 
X 
(subject 
will mail 
in 
sample) 
X 
X 
X 
Immunology 
studies (Baranzini 
Lab) 
X 
 
X 
X 
X 
HIV 
X 
Treponemal 
Screen 
X 
 
 
EBV IgG anti- 
EBNA Screen 
X 
 
 
Hepatitis B and C 
screening 
X 
 
 
CBC/diff 
X 
X 
X 
X 
Immunoglobulins 
(IgG, IgM, IgA) 
X 
 
X 
X 
X 
Lymphocyte 
Subsets (CD 3, 4, 
8, 19) 
X 
 
X 
X 
X 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
 
54 
 
 
Appendix B: Storage Controls and Material Specifications 
 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
 
55 
 
 
Appendix B: Storage Controls and Material Specifications (cont.) 
 

Protocol Title: MS-BIOME Study 
Protocol Number: 17-23827  
NCT: 03594487 
Version 5.7  March 29, 2021 
 
56 
 
 
Appendix C: Subject Adverse Event Diary 
Subject Adverse Event Diary 
Subject Initials   
 
 
 
 
Page 
of   
 
 
Instructions: Please record any symptoms or changes in your health you may be feeling 
throughout this study. Please bring this diary to all study appointments. Contact study staff for 
any questions or concerns that you may have. 
 
AE 
# 
 
AE Description 
Onset 
Date/Time 
Resolution 
Date/Time 
Action Taken to 
Resolve 
Outcome 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Appendix D-1: Colombia-Suicide Severity Rating Scale (C-SSRS): 
Baseline/Screening 
 
 

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Appendix D1: Colombia-Suicide Severity Rating Scale (C-SSRS): 
Baseline/Screening (cont.) 
 
 

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Appendix D1: Colombia-Suicide Severity Rating Scale (C-SSRS): 
Baseline/Screening (cont.) 
 

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Appendix D-2: Colombia-Suicide Severity Rating Scale (C-SSRS): Since 
Last Visit 
 

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Appendix D2: Colombia-Suicide Severity Rating Scale 
(C-SSRS): Since Last Visit (cont.) 
 

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Appendix D2: Colombia-Suicide Severity Rating Scale 
(C-SSRS): Since Last Visit (cont.) 
 

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Appendix E: Mental Health Inventory (MHI-5) 
 
 
 

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Appendix F: Modified Fatigue Impact Scale (MFIS) 
 
 

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Appendix F: Modified Fatigue Impact Scale (MFIS) (cont.) 
 

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Appendix F: Modified Fatigue Impact Scale (MFIS) (cont.) 
 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 
 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 
 

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Appendix G: Multiple Sclerosis Quality of Life Questionnaire (MSQOL-54) 
(cont.) 
 
 
 
 

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Appendix H: Bowel Control Scale (BWCS) 
 
 
 
 

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Appendix I: Bladder Control Scale (BLCS) 
 
 

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Appendix J: Food Frequency Questionnaire 
 
 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 
 

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Appendix J: Food Frequency Questionnaire (cont.) 
 
 
 
 

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Appendix K: ASA Physical Status Classification System 
 

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Appendix L: OpenBiome Donor Screening Testing 
Table 1: 
Donor Screening Testing 
 
Pathogen 
Method 
Serological 
Testing 
HIV-1/2 
IA 
Hepatitis A, IgM 
IA 
Hepatitis B, anti-HBc, IgM antiHBc, HBsAg 
IA 
Hepatitis C 
IA 
Treponema pallidum 
Antibody cascading reflex 
Strongyloides 
EIA 
Stool Testing 
Multi-Drug Resistant 
Organisms 
VRE 
Culture 
CRE 
Culture 
ESBL 
Culture 
Salmonella spp 
Culture 
Shigella spp 
Culture 
Campylobacter spp 
Culture 
Vibrio spp 
Culture 
Rotavirus A 
EIA 
Cryptosporidium spp 
EIA 
Shiga Toxin 
PCR 
Enteropathogenic Escherichia coli (EPEC) 
PCR 
Giardia lamblia 
EIA 
Adenovirus 
EIA 
Norovirus 
PCR 
Clostridium difficile Toxin B 
RT-PCR 
Cryptosporidium spp 
EIA 
Helicobacter pylori 
EIA 
Ova and parasites 
Microscopic exam 
Cyclospora and Isospora 
Microscopic exam 
Microsporidia 
Microscopic exam 
Bristol Stool Type assessment 
Visual 
Nasal Swab 
Multi-Drug Resistant 
Organisms 
MRSA 
Culture 
Additional 
Screening 
Liver Function Panel 
Serological testing 
ALT 
AST 
ALP 
Albumin 
Bilirubin (Total, direct, indirect) 
CBC and Differential 
Mini Health Questionnaire 
Documentation 
Random Clinical Health Checks 
Clinical assessment 
IA = Immunoassay, EIA = Enzyme immunoassay; VRE = Vancomycin-resistant 
enterococci; CRE = carbapenem-resistant Enterobacteriaceae; ESBL = Extended- 
spectrum beta-lactamases; RT-PCR = reverse-transcription polymerase chain 
reaction; qPCR = qualitative polymerase chain reaction; ALT = Alanine 
Aminotransferase; AST = Aspartate Aminotransferase; ALP = Alkaline Phosphatase; 
CBC = Complete Blood Count 

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Appendix M: UCSF Post Approval Reporting Requirements 
 
 
 

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Appendix N: OpenBiome Amendments to BMF17195 
 
 
 
 
 

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