Clinical trial NCT03219528
Conditions: Irritable Bowel Syndrome
Keywords: Irritable Bowel Syndrome Diarrhea Small Intestinal Bacterial Overgrowth Gut Microbiota
Sponsor: University of Michigan
Start date: 2018-02-13; Completion date: 2024-02-28
Enrollment: 74 participants; Allocation: RANDOMIZED; Intervention model: PARALLEL

Brief summary:
Diarrhea-predominant irritable bowel syndrome (IBS-D) is a highly prevalent but poorly understood condition with limited treatment options. Current therapies, including a nonabsorbable antibiotic rifaximin or diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP), show efficacy in 50% or less of patients. In this proposal, participants with IBS-D will be randomized to receive either rifaximin or low FODMAP dietary intervention.

Detailed description:
Diarrhea-predominant irritable bowel syndrome (IBS-D) is a highly prevalent but poorly understood condition with limited treatment options. Recent evidence has established small intestinal bacterial overgrowth (SIBO) and alterations in fecal microbiota as potential etiologies in the pathogenesis of IBS-D. Current therapies, including a nonabsorbable antibiotic rifaximin or diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP), show efficacy in 50% or less of patients \[1-4\]. It has been postulated that limited responses to therapies may stem from failure to identify distinct subgroups in IBS-D stratified by gut microbial profiles. In this proposal, participants with IBS-D will be randomized to receive either rifaximin or low FODMAP dietary intervention. The results of fecal microbiota-derived data as well as hydrogen breath tests will then be longitudinally followed to define SIBO. These methods will be used to test the hypotheses that: (i) distinct IBS-D phenotypes can be generated by defining fecal microbial populations as well as delineating the presence or absence of SIBO; and (ii) longitudinal analyses using microbe-derived metrics and SIBO status may relate to response to treatment with rifaximin or low FODMAP dietary intervention.

Arms: arm 1: Rifaximin 550 mg three times daily for 14 days arm 2: Low FODMAP diet for 4 weeks
Interventions: intervention 1: Rifaximin 550 MG intervention 2: Low FODMAP Diet
Intervention descriptions: intervention 1: Rifaximin 550 mg three times daily for 14 days intervention 2: Low FODMAP dietary intervention for 4 weeks

Protocol documents:
ICF_002.pdf: 
A Longitudinal Study to Identify IBS Phenotypes Using 
Fecal Microbiota and Hydrogen Breath Testing 
NCT03219528 
Date of IRB Approval: April 11, 2024 


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Consent Subtitle: ________________________
Consent Version: 20230504
UNIVERSITY OF MICHIGAN
CONSENT TO BE PART OF A RESEARCH STUDY
1.  KEY INFORMATION ABOUT THE RESEARCHERS AND THIS STUDY  
Study title: A Longitudinal Study to Identify IBS Phenotypes Using Fecal Microbiota and Hydrogen Breath 
Testing (HUM00129427)
Company or agency sponsoring the study: Michigan Institute for Clinical and Health Research
Names, degrees, and affiliations of the principal investigator and study coordinator (if applicable): Principal 
Investigator: Allen Lee, MD, Department of Internal Medicine, University of Michigan
Study Coordinator: 
 Almo Regazi, Department of Internal Medicine, University of Michigan
Samantha Brehmer, Department of Internal Medicine, University of Michigan
1.1 Key Study Information
You may be eligible to take part in a research study.  This form contains important information that will help 
you decide whether to join the study.  Take the time to carefully review this information.  You should talk to 
the researchers about the study and ask them any questions you have.  You may also wish to talk to others 
such as your family, friends, or other doctors about joining this study.  If you decide to join the study, you will 
be asked to sign this form before you can start study-related activities.  Before you do, be sure you understand 
what the research study is about.
A research study is different from the regular medical care you receive from your doctor.  Research studies 
hope to make discoveries and learn new information about diseases and how to treat them.  You should 
consider the reasons why you might want to join a research study or why it is not the best decision for you at 
this time.  
Research studies do not always offer the possibility of treating your disease or condition.  Research studies also 
have different kinds of risks and risk levels, depending on the type of the study.  You may also need to think 
about other requirements for being in the study.  For example, some studies require you to travel to scheduled 
visits at the study site in Ann Arbor or elsewhere. This may require you to arrange travel, change work 
schedules, find child care, or make other plans.  In your decision to participate in this study, consider all of 
these matters carefully.  
This research collects health-related information, stool samples, and hydrogen breath test results to better 
understand irritable bowel syndrome with diarrhea (IBS-D). Additionally, if you consent to the optional studies 
listed in Section 4, colon tissue biopsies, saliva samples, and blood samples may be collected to better 
understand IBS-D. This research will investigate if Rifaximin and/or low FODMAP diet (FODMAP is an acronym 
that stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. FODMAP are 
sugars (carbohydrates) in the foods we eat that are poorly absorbed by the gut) will improve symptoms 
observed in IBS-D patients. We want to see if we can better classify IBS patients based on the results of 
hydrogen breath tests or by the composition of stool bacteria. If you choose to participate, you will be asked to 
either take Rifaximin or be on a low FODMAP diet (randomized), fill out surveys, record food diaries, collect 
stool samples, take hydrogen breath tests, answer questions online, and come to research visits at the 
hospital, and attend phone visits over the course of about 5 weeks.
This study involves a process called randomization.  This means that the treatment (Rifaximin or low FODMAP 
diet) you receive in the study is not chosen by you or the researcher.  The study design divides study 
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Consent Version: 20230504
participants into separate groups, based on chance (like the flip of a coin), to compare different treatments or 
procedures.  If you decide to be in the study, you need to be comfortable not choosing which study group you 
will be in.
This study may require you to stop taking certain medications before and possibly during the research study.  If 
you decide to be in the study, you should understand that some symptoms that were controlled by that 
medication may worsen.
There can be risks associated with joining any research study.  The type of risk may impact whether you decide 
to join the study.  For this study, these risks may include abdominal pain, bloating, dizziness, faint spells, and 
flatulence related to the drink consumed during the hydrogen breath test. General antibiotics side effects such 
as nausea, vomiting, diarrhea, etc may occur for patients taking Rifaximin. There could be pain or bruising 
associated with the optional blood draws. There are rare concerns about private information. More detailed 
information will be provided later in this document.
This study may offer some benefit to you now or others in the future by providing new insight into the causes 
and treatments of symptoms in IBS patients. Participants with IBS-D will receive glucose hydrogen breath tests 
to determine if they have small intestinal bacterial overgrowth (SIBO). Furthermore, IBS-D participants will be 
treated with well accepted treatments for IBS, including a non-absorbable antibiotic rifaximin or diets low in 
FODMAP. IBS-D subjects treated with low FODMAP diet will be provided education on a low FODMAP diet 
from a trained bio nutritionist and stool samples compensation. More information will be provided later in this 
document.
We expect the amount of time you will participate in the study will be approximately 5 weeks.
You can decide not to be in this study.  Alternatives to joining this study may include treatments such as anti-
spasmodic, anti-depressants, antibiotics, and dietary modification.  However, any alternative treatment option 
should be undertaken with appropriate continued medical supervision.
Even if you decide to join the study now, you are free to leave at any time if you change your mind.
More information about this study continues in Section 2 of this document.
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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2. PURPOSE OF THIS STUDY
2.1 Study purpose: 
Treatments such as a non-absorbable antibiotic called rifaximin or a diet low in FODMAP may improve 
symptoms in patients with irritable bowel syndrome (IBS).  We believe these treatments work by affecting the 
intestinal bacteria in our gut.  However, this has never been proven.  Also, we do not yet have a way to predict 
who will respond best to treatments in IBS, such as rifaximin or a low FODMAP diet.  We want to see if we can 
better classify IBS patients based on the results of tests, such as a glucose hydrogen breath test or by the 
composition of stool bacteria.   A hydrogen breath test is looking for a condition called small intestinal 
bacterial overgrowth (SIBO).  We also want to see if treatments for IBS lead to changes in the stool microbiome 
or hydrogen breath test results.
3. WHO MAY PARTICIPATE IN THE STUDY
Taking part in this study is completely voluntary.  You do not have to participate if you don't want to.  You may 
also leave the study at any time.  If you leave the study before it is finished, there will be no penalty to you, 
and you will not lose any benefits to which you are otherwise entitled. 
3.1 Who can take part in this study?
All adult subjects over the age of 18 years with diarrhea-predominant irritable bowel syndrome (IBS-D) are 
eligible to participate in this study.  You cannot have a history of celiac disease (allergy to wheat products), 
microscopic colitis, inflammatory bowel disease such as ulcerative colitis or Crohn’s disease, or other causes 
that might explain your symptoms.  
You should have had a colonoscopy or flexible sigmoidoscopy with colon biopsies within the past 2 years to 
rule out a condition called microscopic colitis. 
You will undergo an online survey for approximately seven days. You will be asked to fill out multiple choice 
questions about your IBS symptoms, and the study team will evaluate your symptoms to determine study 
eligibility. 
Subjects with a history of surgery to the GI tract, other than removal of the appendix, are not eligible to 
participate in this study.  Women who are pregnant or breastfeeding will not be allowed to participate in this 
study.  A urine pregnancy test will be performed in women capable of bearing children to exclude the 
possibility that you are pregnant.  In addition, you will not be eligible to participate in this study if you have 
been on antibiotics within the previous 3 months, such as rifaximin, or received dietary advice, such as a low 
FODMAP diet, for treatment of IBS or SIBO in the past.
In addition, adult IBS-D subjects and healthy adults who are scheduled for a colonoscopy are eligible to 
participate in an optional portion of the study where we will collect biopsy samples during your colonoscopy to 
determine how the microbiome (gut microbes) interact with the lining of the gut. 
3.2 How many people are expected to take part in this study?
225 subjects with IBS-D as well as 25 healthy subjects will participate in this study.
4.  INFORMATION ABOUT STUDY PARTICIPATION
4.1 What will happen to me in this study?  
You will undergo the following:
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Consent Subtitle: ________________________
Consent Version: 20230504
Pre-Visit (all subjects):

To determine eligibility, you will undergo an online survey for approximately seven days. You will be 
asked to fill out multiple choice questions about your IBS symptoms. You will be asked questions about 
your social and medical history by a study coordinator. Depending on your symptoms, you may then 
be asked to come in/phone or video visit to go over the details of the study.

Consent could be obtained via email, fax, mail, or SignNow (a secure online application).

If you will undergo a colonoscopy to investigate the cause of your symptoms and you agree to 
participate in the optional sub study #2, you will also be asked to sign the consent form for optional 
sub study #2. During the colonoscopy, we may collect up to 12 mucosal biopsies during your routine 
colonoscopy. Each biopsy sample is about 0.2 cm in size which is approximately the size of a sesame 
seed. You are free to decline participation if you do not want to participate in this sub-study.

You will be given instructions and supplies for stool collection. The quantity of stool collections will 
vary based on your participation in other sub studies associated with this study. All subjects will collect 
a minimum of three stool samples and bring them to their next visit if you have an in-person visit or 
you can mail it back to us as soon as possible. 

Wash-out period: We will ask that you discontinue the following medications for at least 1 month prior 
to enrollment: narcotic pain medications (e.g. Norco, Percocet, Morphine); and probiotics.  We will ask 
that you stop antibiotics for at least 3 months prior to enrollment.
(Healthy Participants and IBS-D Subjects Undergoing Colonoscopy):

You will complete a one-time symptom questionnaire to look at the severity of your GI and 
psychological symptoms.  
(IBS-D Participants):

You will be randomized to either rifaximin or the low FODMAP diet arm of the study before your visit 
1. You will be told what treatment you have been randomized to. There is a 50:50 chance you will be 
put into either group, like a coin flip.

You will also learn how to complete the dietary recalls and fill them out over 3 days to determine your 
typical diet as well as an abdominal pain, bloating, and bowel movement log before your visit 1. 

We will also ask that you avoid Pepto-Bismol for at least 2 weeks, not eat or drink for at least 8 hours 
and not smoke for at least 6 hours prior to the Glucose Hydrogen Breath Test.

Participants not required to attend visit one in person will receive a hydrogen breath test kit and 
rifaximin via mail. 
Rifaximin Group:
Visit 1 (Phone or in person visit): 
You will be asked to complete questionnaires that determine the severity of your GI symptoms and drop 
off/mail your stool samples, three-day food diary, and logs.  We will also provide a glucose hydrogen breath 
test kit for you to perform at home for the duration of the pandemic. You will receive Rifaximin during visit one 
either in-person at the clinic or via mail if conducted remotely. Female participants capable of bearing children 
or consented to the optional sub study #2 and/or #3, will have visit one conducted in-person with an 
approximate duration of 30 minutes. Male participants and female participants not capable of bearing children 
who have not consented to optional sub study #2 and #3 will be able to conduct the visit remotely during the 
pandemic. 

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements only if visit is conducted in person. 

Urine pregnancy test – Women capable of bearing children will undergo a urine pregnancy test.
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Consent Subtitle: ________________________
Consent Version: 20230504

Please do not take Peptobismol for at least 2 weeks before the test. You also should fast for at least 8 
hours and should not smoke for at least 6 hours before the test. These restrictions will help improve 
the accuracy of the test.

There should be another person available in case there a side effects of dizziness or lightheadedness. 
There should also be snacks readily available.

Glucose Hydrogen Breath Test – you will be asked to drink a sugar water drink.  You will then be asked 
to blow into a tube every 15 minutes for 2 hours to measure whether you have overgrowth of bacteria 
in your small intestine. The hydrogen breath test will be done remotely with a take home test kit.

After you complete the glucose hydrogen breath test, you will then start on an antibiotic called 
rifaximin. You will take this medication three times per day for a total of 14 days.

Should you choose to participate in the optional sub-study #2, you will provide a saliva sample, which 
will be self-collected in a provided kit. The sample size will be about 2mL, or approximately ½ 
teaspoon. These samples will be stored for genetic analysis related to enzymes pertaining to IBS-D and 
may be shared with investigators at other institutions (Karolinska Institute and IKMB Kiel) to run 
specialized tests.  You are free to decline participation if you do not want to have your saliva sample 
stored.  You will have the ability to accept or decline separate permission at the end of this consent 
document.

Should you choose to participate in the optional sub-study #3, you will have your blood drawn. A 
trained phlebotomist will collect 1 tube, a total of about 10mL or 2 teaspoons of blood. These blood 
samples will be stored for future IBS-D research. You are free to decline participation if you do not 
want to have your blood sample stored.  You will have the ability to accept or decline separate 
permission at the end of this consent document.

You will be asked to record your stool frequency and form each day online or on paper log. 

You will also record the severity of your abdominal pain and bloating each day online or on paper log. 

You will also record your diet over a 24-hour period every week.
Visit 2 (Phone or In-Person Visit - Approximately one week after Visit 1):

You will be asked questions about your medication compliance.

You will continue to record your stool frequency and form, abdominal pain, and bloating online or on 
paper.

You will have completed your 24-hour food recall by this time.

You will be asked if you have experienced any adverse medical events since you last met the study 
team.       

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if the visit is conducted in person. 
Visit 3 (Phone or In-Person Visit - Approximately one week after Visit 2):

You will collect a stool sample before your third visit. You can return it to us in-person if you have an 
in-person visit or you will mail it to us as soon as possible.

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will be asked questions about your medication compliance. If you have been taking the medication 
as instructed, you should be finished with your rifaximin at this point.

You will continue to record your stool frequency and form, abdominal pain, and bloating online or on 
paper.
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Consent Subtitle: ________________________
Consent Version: 20230504

You will have completed your 24-hour food recall by this time.

You will be asked if you have experienced any adverse medical events since you last met the study 
team       

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if the visit is conducted in person.
Visit 4 (Phone or In-Person Visit - Approximately two weeks after Visit 3):

You will collect a stool sample before your fourth visit. You can return it to us in-person if you have an 
in-person visit or you will mail it to us as soon as possible.

You will have completed your 24-hour food recall by this time.

You will continue to record your stool frequency and form, abdominal pain, and bloating online.

You will be asked if you have experienced any adverse medical events since you last met with the 
study team.      

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse and 
temperature measurements if the visit is conducted in person.
Visit 5 (Phone or in person visit approximately one week after Visit 4):

You will collect a stool sample before your fifth visit. You can return it to us in-person if you have an in-
person visit or you will mail it to us as soon as possible.

You will undergo a physical examination and be asked questions about your medical history if visit is 
conducted in person.

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will be asked if you have experienced any adverse medical events since you last met with the 
study team.

The last hydrogen breath test is conducted at this visit. You will be given a take home hydrogen breath 
test kit to perform the test remotely. 

Please do not take Peptobismol for at least 2 weeks before the test. You also should fast for at least 8 
hours and should not smoke for at least 6 hours before the test. These restrictions will help improve 
the accuracy of the test.

There should be another person available in case there a side effects of dizziness or lightheadedness. 
There should also be snacks readily available.

Glucose Hydrogen Breath Test – you will be asked to drink a sugar water drink.  You will then be asked 
to blow into a tube every 15 minutes for 2 hours to measure whether you have overgrowth of bacteria 
in your small intestine. The hydrogen breath test will be done remotely with a take home test kit.       

Should you choose to participate in the optional sub-study #3, you will have your blood drawn at Visit 
5. A trained phlebotomist will collect 1 tube, a total of about 10mL or 2 teaspoons of blood. These 
blood samples will be stored for future IBS-D research. You are free to decline participation if you do 
not want to have your blood sample stored.  You will have the ability to accept or decline separate 
permission at the end of this consent document.

You will have completed your 24-hour food recall by this time.
Stool samples before, during, and after you have been on this diet will be stored for future research on IBS.  
You are free to decline participation if you do not want to have your stool sample stored.  You will have the 
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Consent Version: 20230504
ability to accept or decline separate permission at the end of this consent document.  This will be listed as 
“Optional Sub-Study #1”.
Low FODMAP Group:
Visit 1 (Phone or in person visit): 
You will be asked to complete questionnaires that determine the severity of your GI symptoms and drop 
off/mail your stool samples, three-day food diary, and logs.  We will also provide a glucose hydrogen breath 
test kit for you to perform at home for the duration of the pandemic. Female participants capable of bearing 
children or consented to the optional sub study #2 and/or #3, will have visit one conducted in-person with an 
approximate duration of 1.5 hours. Male participants and female participants not capable of bearing children 
who have not consented to optional sub study #2 and #3 will be able to conduct the visit remotely during the 
pandemic. You will receive low FODMAP diet consultation during this visit.

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if visit is done in person. 

Urine pregnancy test – Women capable of bearing children will undergo a urine pregnancy test.

You will meet with a nutritionist for education on a low FODMAP diet over phone or video for the 
duration of the pandemic.  The diet plan will be individualized to you based on the information from 
your diet questionnaires.

Please do not take Peptobismol for at least 2 weeks before the test. You also should fast for at least 8 
hours and should not smoke for at least 6 hours before the test. These restrictions will help improve 
the accuracy of the test.

There should be another person available in case there a side effects of dizziness or lightheadedness. 
There should also be snacks readily available.

Glucose Hydrogen Breath Test – you will be asked to drink a sugar water drink.  You will then be asked 
to blow into a tube every 15 minutes for 2 hours to measure whether you have overgrowth of bacteria 
in your small intestine. The hydrogen breath test is done remotely and you will be given a test kit to 
take home. 

After you complete the glucose hydrogen breath test, you will then start on a low FODMAP diet for the 
next 4 weeks.

Should you choose to participate in the optional sub-study #2, you will provide a saliva sample, which 
will be self-collected in a provided kit. The sample size will be about 2mL, or approximately ½ 
teaspoon. These samples will be stored for genetic analysis related to enzymes pertaining to IBS-D and 
may be shared with investigators at other institutions (Karolinska Institute and IKMB Kiel) to run 
specialized tests.  You are free to decline participation if you do not want to have your saliva sample 
stored.  You will have the ability to accept or decline separate permission at the end of this consent 
document.

Should you choose to participate in the optional sub-study #3, you will have your blood drawn. A 
trained phlebotomist will collect 1 tube, a total of about 10mL or 2 teaspoons of blood. These blood 
samples will be stored for future IBS-D research. You are free to decline participation if you do not 
want to have your blood sample stored.  You will have the ability to accept or decline separate 
permission at the end of this consent document.

You will be asked to record your stool frequency and form each day online or on paper log. 

You will also record the severity of your abdominal pain and bloating each day online or on paper log. 

You will also record your diet over a 24-hour period every week.
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Visit 2 (Phone or In-Person Visit - Approximately one week after Visit 1):

You will be asked questions about your dietary compliance.

You will continue to record your stool frequency and form, abdominal pain and bloating online or on 
paper.

You will have completed your 24-hour food recall by this time.

You will be asked if you have experienced any adverse medical events since you last met the study 
team.       

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if the visit is conducted in person. 
Visit 3 (Phone or In-Person Visit - Approximately one week after Visit 2):

You will collect a stool sample before your third visit. You can return it to us in-person if you have an 
in-person visit or you will mail it to us as soon as possible.

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will be asked questions about your dietary compliance. 

You will also have a consultation with a U of M nutritionist via phone or video for the duration of the 
pandemic. They will answer any questions you have about the diet and check in on your progress. 

You will continue to record your stool frequency and form, abdominal pain, and bloating online or on 
paper.

You will have completed your 24-hour food recall by this time.

You will be asked if you have experienced any adverse medical events since you last met with the 
study team       

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if the visit is conducted in person.
Visit 4 (Phone or In-Person Visit - Approximately two weeks after Visit 3):

You will collect a stool sample before your fourth visit. You can return it to us in-person if you have an 
in-person visit or you will mail it to us as soon as possible.

You will be asked questions about your dietary compliance.

You will have completed your 24-hour food recall by this time.

You will continue to record your stool frequency and form, abdominal pain, and bloating online.

You will be asked if you have experienced any adverse medical events since you last met with the 
study team.      

You will be asked questions about your physical health and wellbeing. 

You will undergo a basic physical examination to measure height, weight, blood pressure, pulse, and 
temperature measurements if the visit is conducted in person.
Visit 5 (Phone or in person visit approximately one week after Visit 4):

You will collect a stool sample before your fifth visit. You can return it to us in-person if you have an in-
person visit or you will mail it to us as soon as possible.

You will undergo a physical examination and be asked questions about your medical history if visit is 
conducted in person.
Study ID: HUM00129427   IRB: IRBMED   Date Approved: 4/11/2024   Expiration Date: 4/10/2025


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Consent Version: 20230504

Questionnaires – you will complete eight questionnaires to look at the severity of your GI and 
psychological symptoms.  

You will be asked if you have experienced any adverse medical events since you last met with the 
study team.       

The last hydrogen breath test is conducted at this visit. You will be given a take home hydrogen breath 
test kit to perform the test remotely. 

Please do not take Peptobismol for at least 2 weeks before the test. You also should fast for at least 8 
hours and should not smoke for at least 6 hours before the test. These restrictions will help improve 
the accuracy of the test.

There should be another person available in case there a side effects of dizziness or lightheadedness. 
There should also be snacks readily available.

Glucose Hydrogen Breath Test – you will be asked to drink a sugar water drink.  You will then be asked 
to blow into a tube every 15 minutes for 2 hours to measure whether you have overgrowth of bacteria 
in your small intestine. The hydrogen breath test will be done remotely with a take home test kit. 

Should you choose to participate in the optional sub-study #4, you will have your blood drawn at Visit 
5. A trained phlebotomist will collect 1 tube, a total of about 10mL or 2 teaspoons of blood. These 
blood samples will be stored for future IBS-D research. You are free to decline participation if you do 
not want to have your blood sample stored.  You will have the ability to accept or decline separate 
permission at the end of this consent document.

You will have completed your 24-hour food recall by this time.
Stool samples before, during and after you have been on this diet will be stored for future research on IBS.  
You are free to decline participation if you do not want to have your stool sample stored.  You will have the 
ability to accept or decline separate permission at the end of this consent document.  This will be listed as 
“Optional Sub-Study #1”.
As a subject participating in this research study, you have certain responsibilities that may apply to this study, 
such as ensuring that you arrive at all of your scheduled appointments, take your study medication as directed, 
and report any adverse reactions you may have during the study. 
Besides the information about the main study, the following information is specific to optional sub-studies.  
We would like to better define the reason why patients may or may not respond to IBS-D treatments.  To do 
this, we would like your permission to study your colon tissue (with biopsies from your colonoscopy), saliva, 
blood, and/or medical information.  Biopsies will be used to create “colonoid” models to understand enzymes 
that may potentially be involved with IBS-D.  Saliva will also be used to study enzymes that could be involved 
with IBS-D. Blood will be used to better understand immune markers that may be involved in IBS-D.  You can 
take part in the main study even if you don’t participate in any of the optional sub studies.
Optional sub-study #1: The sub-study is looking to analyze metabolomics differences from the stool samples. 
This sub-study aims to learn about the physical processes that lead to microbiome changes seen in IBS 
patients. Participants consented to this sub-study will collect a stool sample at visits 1, 3, 4, and 5. We will also 
collect a one-time stool sample and symptom questionnaires from healthy controls. Samples will then be 
stored for long-term storage.
Optional sub-study #2: This sub-study is looking to understand enzymes that may potentially be involved with 
Irritable Bowel Syndrome with Diarrhea. It requires a one-time collection of saliva sample on visit 1. 
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Optional sub-study #3: This sub-study requires blood collections to better understand immune markers that 
may potentially be involved with Irritable Bowel Syndrome with Diarrhea.  We will collect 10 mL 
(approximately 2 teaspoons) of blood at visit 1 and 5.
Optional sub-study #4: This sub-study requires tissue collection. Biopsies will be taken from eligible subjects 
who are scheduled to undergo a colonoscopy for clinical purposes (e.g. to rule out alternative causes of 
symptoms or screening for colon cancer). Biopsies will be utilized to generate human intestinal enteroids to 
study host-microbial interactions determining response to treatment in IBS. Twelve mucosal biopsies will be 
obtained for research purposes in addition to any clinically indicated biopsies.
There may be risks involved in the optional sub-studies. The risks are explained in section 5. 
Even if you give us permission now to keep some of your colon tissue, saliva, and blood and medical 
information, you can change your mind later and ask us to destroy it. Keep in mind, however, that once we 
have analyzed your colon tissue, saliva, and blood, we may not be able to take the information out of our 
research. Also, if we have shared some of your colon tissue, saliva, and blood and medical information with 
other researchers, we will not be able to get it back.  
We will not tell you the results of the analysis of your colon tissue, saliva, and or blood. Allowing us to study 
your colon tissue, saliva, and blood and medical information to better understand Irritable Bowel Syndrome 
with Diarrhea will not benefit you directly.   
With appropriate permissions, your samples and collected information may also be shared with other 
researchers, here, around the world, and with companies.
Your identifiable private information or identifiable biospecimens may be stripped of identifiers and used for 
future research studies or distributed to another researcher for future research studies without additional 
informed consent. 
Research can lead to new discoveries, such as new tests, drugs, or devices. Researchers, their organizations, 
and other entities, including companies, may potentially benefit from the use of the data or discoveries. You 
will not have rights to these discoveries or any proceeds from them.
4.2 How much of my time will be needed to take part in this study?  
You will either come in or have a phone visit for the baseline evaluation and undergo testing which will take 
approximately 2.5-3.5 hours.  You will then start on treatments for IBS and will report your symptoms and 
answer questionnaires either in person or via phone for three additional visits.  Each visit will take 
approximately 30 minutes.  During the final visit, you will undergo repeat questionnaires and glucose hydrogen 
breath tests which will take approximately 2.5 hours.  Patients participating in the sub-study with optional 
saliva collection will spend approximately 1 minute providing the sample.  Patients participating in the sub-
study with optional phlebotomy will spend approximately 5 minutes at Visits 1 and 5 providing a blood sample.  
Patients who participate in sub study 2 will add approximately five to ten minutes onto their procedure length.
4.3 When will my participation in the study be over? 
Once you have been on treatment for IBS for 4 weeks and have completed all of the testing.  Most subjects will 
complete their part in the study around 5 weeks.  The entire study is expected to last about 2 years.
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4.4 What will happen with my information and/or biospecimens used in this study?
With appropriate permissions, your biospecimens and collected information may also be shared with other 
researchers, here, around the world, and with companies.
Your identifiable private information or identifiable biospecimens may be stripped of identifiers and used for 
future research studies or distributed to another researcher for future research studies without additional 
informed consent. 
5.  INFORMATION ABOUT STUDY RISKS AND BENEFITS
5.1 What risks will I face by taking part in the study?  What will the researchers do to protect me against 
these risks?
The known or expected risks are:
A). MAIN STUDY RISKS:

Glucose Breath Hydrogen Test:
The most common side effects (occurring in more than 10% of patients) are: 
Bloating, abdominal discomfort/pain, and passing gas/wind , nausea, fainting during/after the test, 
fainting spells and dizziness

Rifaximin:
Rifaximin is an antibiotic which may lead to bacterial resistance to other antibiotics. However, rifaximin 
is minimally absorbed from the GI tract and studies have shown there is low risk for bacterial 
resistance. In addition, studies comparing rifaximin with placebo have not shown significant 
differences in the rate of side effects. General antibiotics side effect, such as nausea, vomiting, 
diarrhea, etc may occur. Finally, oral contraception may not be as effective when taken with rifaximin. 

FODMAP:
A low FODMAP diet may change the bacteria in our gut. However, multiple studies examining the low 
FODMAP diet in IBS have shown that it is both safe and effective for the treatment of IBS. However, 
oral contraception may not be as effective when the gut bacteria change.
B). OPTIONAL SUB-STUDY RISKS

Stool collection (less than 1%):
fainting at the site of the stool collection

Saliva Collection:
If you choose to participate in the optional sub-study for collection of saliva, there are potential risks 
you should be aware of. First, these samples may be shared with investigators at other centers called 
Karolinska Institute and IKMB Kiel. There are potential risks including loss of privacy. We will try to 
minimize these risks by removing any identifiable information (e.g. your name, date of birth, address, 
etc.) on the saliva samples. We will not share any of this information with the investigators at the 
Karolinska Institute and IKMB Kiel. This part of the study is optional and you do not have to agree to 
participate in this optional sub-study. 

Blood Collection:
If you choose to participate in the optional sub-study for the blood collection, there are some risks you 
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may be familiar with. This could be pain, bruising, or lightheadedness. Rarely there could be an 
infection or fainting. The person drawing your blood will be trained to do that procedure and use 
techniques to minimize these risks. 

Risks of Colonoscopy: 
If you choose to participate in the optional sub-study for collection of tissue from your colon, there are 
potential risks, including bleeding, infection, or causing a hole in your intestines. However, biopsy 
samples are commonly taken during a colonoscopy, and is known to be safe and rarely lead to 
complications. 
Rare side effects in less than 1%

Risk to your privacy 

Worsening of your symptoms

Emotional distress from completing questionnaires
The researchers will try to minimize these risks by:
In order to minimize risk from the glucose hydrogen breath test, you are free to stop at any point you 
experience significant pain or discomfort. You can take medications, such as simethicone or Tylenol, if you 
develop significant bloating or discomfort. In order to minimize risk, procedures or blood tests already being 
performed for diagnostic or treatment purposes will be used for this research.  We will use every effort to 
maintain your privacy including keeping all records from this study in a secure, locked location and will only 
share information with other members of the study team. For the questionnaires, you may skip any question 
that you feel uncomfortable answering. You are free to withdraw from the study at any time.
Additionally, there may be a risk of loss to confidentiality or privacy.  See Section 9 of this document for more 
information on how the study team will protect your confidentiality and privacy.
As with any research study, there may be additional risks that are unknown or unexpected.
5.2 What happens if I get hurt, become sick, or have other problems as a result of this research?
The researchers have taken steps to minimize the risks of this study.  Even so, you may still have problems or 
side effects, even when the researchers are careful to avoid them. Please tell the researchers listed in Section 
10 about any injuries, side effects, or other problems that you have during this study.  You should also tell your 
regular doctors.
5.3 If I take part in this study, can I also participate in other studies?
Being in more than one research study at the same time, or even at different times, may increase the risks to 
you.  It may also affect the results of the studies.  You should not take part in more than one study without 
approval from the researchers involved in each study.  
5.4 How could I benefit if I take part in this study?  How could others benefit?  
You may not receive any personal benefits from being in this study. However, others may benefit from the 
knowledge gained from this study. However, some subjects with IBS will demonstrate improvement in their 
symptoms after being on rifaximin or a low FODMAP diet.  Frequent and comprehensive assessment provided 
as part of participating in this study may allow for closer monitoring of disease course.  In addition, this study 
may help us learn more about the possible causes and treatments for IBS.
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5.5 Will the researchers tell me if they learn of new information that could change my willingness to stay in 
this study?
Yes, the researchers will tell you if they learn of important new information that may change your willingness 
to stay in this study. If new information is provided to you after you have joined the study, it is possible that 
you may be asked to sign a new consent form that includes the new information.
6.  ALTERNATIVES TO PARTICIPATING IN THE STUDY
6.1 If I decide not to take part in this study, what other options do I have?
You are free to decline participation in this study.  We will continue to treat your IBS if you do not want to 
participate in this study.  There may be other ways of treating your condition including anti-spasmodics, anti-
depressants, antibiotics, and dietary modification.  However, any alternative treatment option should be 
undertaken with appropriate continued medical supervision.
7.  ENDING THE STUDY
7.1 If I want to stop participating in the study, what should I do?
You are free to leave the study at any time.  If you leave the study before it is finished, there will be no penalty 
to you. You will not lose any benefits to which you may otherwise be entitled.  If you choose to tell the 
researchers why you are leaving the study, your reasons for leaving may be kept as part of the study record. If 
you decide to leave the study before it is finished, please tell one of the persons listed in Section 10 “Contact 
Information”.
7.2 Could there be any harm to me if I decide to leave the study before it is finished? 
There is no harm if you decide to leave early.  However, if your symptoms were improving on rifaximin or a low 
FODMAP diet, you may experience worsening of your symptoms again.
7.3 Could the researchers take me out of the study even if I want to continue to participate?
Yes. There are many reasons why the researchers may need to end your participation in the study.  Some 
examples are:

The researcher believes that it is not in your best interest to stay in the study.

You become ineligible to participate.

Your condition changes and you need treatment that is not allowed while you are taking part in the 
study.

You do not follow instructions from the researchers.

The study is suspended or canceled.
8.  FINANCIAL INFORMATION
8.1 Who will pay for the costs of the study?  Will I or my health plan be billed for any costs of the study?  
The study will pay for research-related items or services that are provided only because you are in the study.  If 
you are not sure what these are, see Section 4.1 above or ask the researchers for a list.  If you get a bill you 
think is wrong, call the researcher’s telephone number listed in Section 10.1.
You or your health plan will pay for all the things you would have paid for even if you were not in the study, 
like:

Health care given during the study as part of your regular care

Items or services needed to give you study drugs or devices

Monitoring for side effects or other problems

Deductibles or co-pays for these items or services.
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If you do not have a health plan, or if you think your health plan may not cover these costs during the study, 
please talk to the researchers listed in Section 10 below or call your health plan’s medical reviewer.
If you are injured or in the event of a medical emergency, dial 911 or visit your nearest Emergency Room. If 
you believe the study has made you sick or caused you injury, contact one of the people listed in section 10 of 
this document (Contact Information). If taking part in the study makes you sick or causes you injury, you will 
have to arrange for treatment on your own, as the study will not provide medical treatment or provide any 
compensation to you. You or your insurance provider will be billed for all costs of treatment for sickness or 
injury caused by the study. It is possible that your insurance will not cover these costs.
By signing this form, you do not give up your right to seek payment if you are harmed as a result of being in 
this study.
8.2 Will I be paid or given anything for taking part in this study?
You will receive all treatments, glucose hydrogen breath testing and/or two dietary consultations free of 
charge for taking part in this study. 
You will be paid $20 for the baseline stool samples, $10 for additional samples taken at visit 3,4, and 5 for a 
total of $50. These will be sent to you as HSIP payments via checks in the mail.
8.3 Who could profit or financially benefit from the study results?
No one will benefit financially. 
Research can lead to new discoveries, such as new tests, drugs, or devices. Researchers, their organizations, 
and other entities, including companies, may potentially benefit from the use of the data or discoveries. You 
will not have rights to these discoveries or any proceeds from them.
9. CONFIDENTIALITY OF SUBJECT RECORDS AND AUTHORIZATION TO RELEASE YOUR PROTECTED HEALTH 
INFORMATION
The information below describes how the confidentiality of your research records will be protected in this 
study, and any sub-studies described in this document.  
9.1 How will the researchers protect my information? 
Your research information will be stored in a locked cabinet and will not be made a part of your regular 
medical record.  However, if the researcher orders any tests, the order and results may become part of your 
regular medical record.
A description of this clinical trial will be available on http://www.clinicaltrials.gov/, as required by U.S. Law. 
This Web site will not include information that can identify you. At most, the Web site will include a summary 
of the results. You can search this Web site at any time.
9.2 What protected health information (PHI) about me could be seen by the researchers or by other people?  
Why?  Who might see it?
Signing this form gives the researchers your permission to obtain, use, and share information about you for 
this study, and is required in order for you to take part in the study.  
Medical information and billing records are protected by the privacy regulations of the federal Health 
Insurance Portability and Accountability Act of 1996 (HIPAA).  This type of information is called protected 
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health information (PHI).  PHI about you may be obtained from any hospital, doctor, and other health care 
provider involved in your care, including:

Hospital/doctor's office records, including test results (X-rays, blood tests, urine tests, etc.)

Mental health care records (except psychotherapy notes not kept with your medical records)

Alcohol/substance abuse treatment records

HIV/AIDS status

All records relating to your condition, the treatment you have received, and your response to the 
treatment

Billing information

Demographic information

Personal identifiers
There are many reasons why information about you may be used or seen by the researchers or others during 
or after this study.  Examples include:

The researchers may need the information to make sure you can take part in the study.  

The researchers may need the information to check your test results or look for side effects.  

University, Food and Drug Administration (FDA) and/or other government officials, auditors, and/or 
the IRB may need the information to make sure that the study is done in a safe and proper manner.   

Study sponsors or funders, or safety monitors or committees, may need the information to: 
o
Make sure the study is done safely and properly
o
Learn more about side effects 
o
Analyze the results of the study 

Insurance companies or other organizations may need the information in order to pay your medical 
bills or other costs of your participation in the study.

The researchers may need to use the information to create a databank of information about your 
condition or its treatment.

Information about your study participation may be included in your regular UMHS medical record.

If you receive any payments for taking part in this study, the University of Michigan accounting 
department may need your name, address, Social Security number, payment amount, and related 
information for tax reporting purposes.

Federal or State law may require the study team to give information to government agencies. For 
example, to prevent harm to you or others, or for public health reasons. 
The results of this study could be published in an article, but would not include any information that would let 
others know who you are. 
If you choose to participate in the sub-study involving saliva samples:
The federal Genetic Information Nondiscrimination Act (GINA) generally makes it illegal for health 
insurance companies, group health plans, and most employers to discriminate against you based on your 
genetic information.  This law does not protect you against genetic discrimination by companies that sell 
life insurance, disability insurance, or long-term care insurance.  Under this law:

Health insurance companies and group health plans may not request your genetic information that we 
obtain from this research

Health insurance companies and group health plans may not use your genetic information when 
making decisions regarding your eligibility or premiums
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
Employers with 15 or more employees may not use your genetic information that we obtain from this 
research when making a decision to hire, promote, or fire you or when setting the terms of your 
employment
GINA does not apply to the following groups; however, these groups have policies in place that provide 
similar protections against discrimination:

Members of the US Military receiving care through Tricare

Veterans receiving care through the Veteran’s Administration (VA)

The Indian Health Service

Federal employees receiving care through the Federal Employees Health Benefits Plans
In addition, these samples will be sent to the Karolinska Institute in Stockholm, Sweden and the IKMB Kiel in 
Kiel, Germany for genetic analysis of a metabolic enzyme in the small intestine. The samples will be de-
identified of patient information before being sent to the Karolinska Institute and the IKMB Kiel. After their 
analysis the samples will be destroyed. 
9.3 What happens to information about me after the study is over or if I cancel my permission to use my 
PHI?
As a rule, the researchers will not continue to use or disclose information about you, but will keep it secure 
until it is destroyed.  Sometimes, it may be necessary for information about you to continue to be used or 
disclosed, even after you have canceled your permission or the study is over.  
Examples of reasons for this include:

To avoid losing study results that have already included your information 

To provide limited information for research, education, or other activities. (This information would not 
include your name, social security number, or anything else that could let others know who you are.) 

To help University and government officials make sure that the study was conducted properly
As long as your information is kept within the University of Michigan Health System, it is protected by the 
Health System’s privacy policies.  For more information about these policies, ask for a copy of the University of 
Michigan “Notice of Privacy Practices”.  This information is also available on the web at 
http://www.uofmhealth.org/patient+and+visitor+guide/hipaa.  Note that once your information has been 
shared with others as described under Question 9.2, it may no longer be protected by the privacy regulations 
of the federal Health Insurance Portability and Accountability Act of 1996 (HIPAA).  
9.4 When does my permission to use my PHI expire?  
Your permission expires at the end of the study, unless you cancel it sooner. You may cancel your permission 
at any time by writing to the researchers listed in Section 10 "Contact Information" (below).  If you withdraw 
your permission, you may no longer be eligible to participate in this study.
10. CONTACT INFORMATION
10.1 Who can I contact about this study?
Please contact the researchers listed below to:

Obtain more information about the study

Ask a question about the study procedures or treatments

Talk about study-related costs to you or your health plan 

Report an illness, injury, or other problem (you may also need to tell your regular doctors)

Leave the study before it is finished
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
Express a concern about the study
Principal Investigator: Allen Lee, MD
Mailing Address:  
3912 Taubman Center
                 
1500 E. Medical Center Dr., SPC 5362
               
Ann Arbor, MI 48109 
Telephone:
(734) 936-9454
Study Coordinator:  
Almo Regazi
Mailing Address:    
52 Simpson Memorial Institute
102 Observatory Dr
                  
Ann Arbor, MI 48109
Study Coordinator: 
Jared Fehlman
Mailing Address:   
200 Simpson Memorial Institute
102 Observatory Dr
                
Ann Arbor, MI 48109
Telephone: 
(734) 647-3635
You may also express a question or concern about a study by contacting the Institutional Review Board 
listed below:
University of Michigan Medical School Institutional Review Board (IRBMED)
2800 Plymouth Road
Building 520, Room 3214
Ann Arbor, MI 48109-2800
Telephone: 734-763-4768  (For International Studies, include the appropriate calling codes.)
Fax: 734-763-1234
e-mail: irbmed@umich.edu 
If you are concerned about a possible violation of your privacy or concerned about a study you may contact 
the University of Michigan Health System Compliance Help Line at 1-866-990-0111.
When you call or write about a concern, please provide as much information as possible, including the name of 
the researcher, the IRBMED number (at the top of this form), and details about the problem.  This will help 
University officials to look into your concern.  When reporting a concern, you do not have to give your name 
unless you want to.
11.  RECORD OF INFORMATION PROVIDED
11.1 What documents will be given to me?
Your signature in the next section means that you have received copies of all of the following documents:

This "Consent to be Part of a Research Study" document.  (Note: In addition to the copy you receive, 
copies of this document will be stored in a separate confidential research file and may be entered into 
your regular University of Michigan medical record.)
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12.  SIGNATURES
Sig-A
Consent/Assent to Participate in the Research Study
I understand the information printed on this form.  I have discussed this study, its risks and potential benefits, 
and my other choices with ______________________.  My questions so far have been answered.  I understand 
that if I have more questions or concerns about the study or my participation as a research subject, I may 
contact one of the people listed in Section 10 (above).  I understand that I will receive a copy of this form at the 
time I sign it and later upon request.  I understand that if my ability to consent or assent for myself changes, 
either I or my legal representative may be asked to re-consent prior to my continued participation in this study.
Print Legal Name: ___________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ________________________
Sig-B
Consent/Assent for Participating in an Optional Sub-Study #1:
This project involves optional participation in a sub-study looking to analyze metabolomics differences from the 
stool samples. This sub-study aims to learn about the physical processes that lead to microbiome changes seen 
in IBS patients.  I understand that it is my choice whether or not to take part in the sub-study.  I understand that 
if my ability to consent or assent for myself changes, either I or my legal representative may be asked to re-
consent prior to my continued participation in this study.
_____ Yes, I agree to take part in the optional sub-study.
_____ No, I do not agree to take part in the optional sub-study.
Print Legal Name: ___________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ______________________________
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Sig-C
Consent/Assent for Participating in an Optional Sub-Study #2:
This project involves optional participation in a sub-study that would collect a saliva sample looking to 
understand enzymes that may potentially be involved with Irritable Bowel Syndrome with Diarrhea. I understand 
that it is my choice whether or not to take part in the sub-study.  I understand that if my ability to consent or 
assent for myself changes, either I or my legal representative may be asked to re-consent prior to my continued 
participation in this study.
_____ Yes, I agree to take part in the optional sub-study.
_____ No, I do not agree to take part in the optional sub-study.
Print Legal Name: ___________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ______________________________
Sig-D
Consent/Assent for Participating in an Optional Sub-Study #3:
This project involves optional participation in a sub-study collecting blood looking to understand immune 
markers that may potentially be involved with Irritable Bowel Syndrome with Diarrhea. I understand that it is my 
choice whether or not to take part in the sub-study.  I understand that if my ability to consent or assent for 
myself changes, either I or my legal representative may be asked to re-consent prior to my continued 
participation in this study.
_____ Yes, I agree to take part in the optional sub-study.
_____ No, I do not agree to take part in the optional sub-study.
Print Legal Name: ___________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ______________________________
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Sig-E
Consent/Assent for Participating in an Optional Sub-Study #4:
This project involves optional participation in a sub-study that would collect 12 colonic biopsies of normal 
looking mucosa from the ileum and colon. I understand that it is my choice whether or not to take part in the 
sub-study.  I understand that if my ability to consent or assent for myself changes, either I or my legal 
representative may be asked to re-consent prior to my continued participation in this study.
_____ Yes, I agree to take part in the optional sub-study.
_____ No, I do not agree to take part in the optional sub-study.
Print Legal Name: ___________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ______________________________
Sig-F
Principal Investigator or Designee
I have provided this participant and/or his/her legally authorized representative(s) with information about this 
study that I believe to be accurate and complete.  The participant and/or his/her legally authorized 
representative(s) indicated that he or she understands the nature of the study, including risks and benefits of 
participating.
Printed Legal Name: __________________________________________________________________
Title: ______________________________________________________________________________
Signature: _________________________________________________________________________
Date of Signature (mm/dd/yy): ________________________
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Prot_SAP_000.pdf: 
 ____________________________________________________________________________________________ 
1 
A Longitudinal Study to Identify IBS Phenotypes Using Fecal 
Microbiota and Hydrogen Breath Testing 
 
NCT03219528 
 
Date of IRB Approval: May 6, 2023 
 
 
 


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Title 
A Longitudinal Study to Identify IBS Phenotypes Using Fecal Microbiota and Hydrogen 
Breath Testing 
Principal Investigator: 
Allen Lee, MD 
Clinical Lecturer 
University of Michigan 
 
Co-Investigators: 
William Chey, MD 
Shanti Eswaran, MD 
Krishna Rao, MD 
Vincent Young, MD 
 
Funding Mechanism: (e.g., grant or cooperative agreement #) 
Michigan Institute for Clinical and Health Research KL2  
Institution(s):  University of Michigan 
Other Identifying Numbers: (e.g., Institution-assigned number, HUM 
HUM00129427 
 
Protocol Amendments: 
(Any modifications to the protocol should be annotated on the coversheet or in an 
appendix.  The annotation should note the exact words that are changed, the location in 
the protocol the date the modification was approved, and the date it became effective.) 
 
Draft or Version Number: 12.0 
Day Month Year: 16 Feb 2022 


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 TABLE OF CONTENTS 
Page 
Title Page…………………………………………………………………………………………1 
Table of Contents ............................................................................................................ 2 
Signature Page ............................................................................................................... 3 
List of Abbreviations ........................................................................................................ 4 
1 
Background/Scientific Rationale .............................................................................. 5 
2 
Objectives ............................................................................................................... 7 
3 
Expected Risks/Benefits.......................................................................................... 8 
4 
Eligibility ................................................................................................................ 11 
5 
Subject Enrollment ................................................................................................ 12 
6 
Study Design and Procedures ............................................................................... 12 
7 
Data Collection and Management Procedures ...................................................... 18 
8 
Data Analysis ........................................................................................................ 19 
9 
Quality Control and Quality Assurance.................................................................. 19 
10 
Statistical Considerations ...................................................................................... 19 
11 
Regulatory Requirements ...................................................................................... 21 
11.1 Informed Consent ....................................................................................... 21 
11.2 Subject Confidentiality ................................................................................ 21 
11.3 Data Safety Monitoring Plan ....................................................................... 21 
12 
References ............................................................................................................ 25 
Appendices ................................................................................................................... 32 
 
 
 
 
 


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SIGNATURE PAGE 
The signature below constitutes the approval of this protocol and the attachments, and 
provides the necessary assurances that this study will be conducted according to all 
stipulations of the protocol, including all statements regarding confidentiality, and 
according to local legal and regulatory requirements and applicable US federal 
regulations. 
Site Investigator: * 
 
Signed: 
 
Date: 
 
 
Allen Lee 
 MD 
 
 
 
* The protocol should be signed by the clinical site investigator who is responsible for 
the day to day study implementation at his/her specific clinical site.


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LIST OF ABBREVIATIONS  
IBS, Irritable Bowel Syndrome 
SIBO, Small intestinal bacterial overgrowth 
GHBT, Glucose hydrogen breath tests 
FODMAP, Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and 
Polyols 
IBS-D, Diarrhea-predominant irritable bowel syndrome 
VAS, Visual analog scale 
NRS, Numerical Rating Scale 
PHQ-9, Patient Health Questionnaire  
VSI, Visceral Sensitivity Index  
IBS-QOL, IBS-quality of life 
TpH-1, Tryptophan hydroxylase-1 
SNPs, Single nucleotide polymorphisms 
OTU, operational taxonomic units 
LEfSE, linear discriminant analysis effect size  
AMOVA, analysis of molecular variance  
eCRF, electronic Case Report Form 
PHI, Protected Health Information 
GCP, Good Clinical Practice  
AE, Adverse Event 
 
 
 
 
 
 
 
 
 
 
 
 
 


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1 
BACKGROUND/SCIENTIFIC RATIONALE 
Irritable bowel syndrome (IBS) is a common but incompletely understood condition that leads to 
significant morbidity and substantial health care expenditures (1,2).  IBS is likely a multifactorial 
disorder including disordered motility, immune activation, gut barrier dysfunction, visceral 
hypersensitivity, and altered brain-gut interactions (3–5).   
The role of the gut microbiota is increasingly being recognized for its potential role in the 
pathogenesis of IBS.  Humans are host to a diverse community of microbes collectively known 
as the human microbiota, of which the vast majority live in the gut (6).  The gut microbiota 
normally interacts closely with the intestinal epithelial cells as well as the enteric immune and 
nervous system, which comprises the microbiota-gut-brain axis (7).  There is a symbiotic 
relationship between the microbiota and host with the gut microbiome providing essential 
functions, including maintenance of the gut epithelial barrier and immune function (8).  However, 
alterations in the structure and community function of the fecal microbiota may have a 
significant role in the pathogenesis of human disease, including IBS.  Acute gastroenteritis leads 
to an increased risk for development of post-infectious IBS and is associated with altered gut 
microbiota, increased permeability and immune activation (9–11).  Further evidence of the role 
of gut microbiota in IBS is shown by experiments where transfer of microbiota from patients with 
IBS to germ-free mice leads to rapid GI transit, impaired gut barrier function, and visceral 
hypersensitivity (12,13). 
Several studies have reported an increase in the relative abundance of Firmicutes, a reduction 
in the relative abundance of Bacteroidetes, and decrease in microbial diversity (14–16).  
However, studies are often conflicting and a specific microbial signature has not been 
discovered to date in IBS (17–19).  Incomplete phenotypic characterization, small sample sizes, 
the cross-sectional nature of study design, and probable heterogeneity of the patient 
populations also limited prior studies.  In addition, previous studies have not taken differences in 
diet or stool consistency into consideration despite the fact that these factors heavily influence 
the composition of the gut microbiota (20,21).   
Small intestinal bacterial overgrowth (SIBO) has also been postulated to be an important 
pathophysiologic factor in the pathogenesis of IBS (22–24).  SIBO is defined as presence of 
bacteria in excess of 105 colony-forming units per milliliter on culture of small bowel aspirates 
[34].  Prevalence figures of SIBO in IBS range from 4-64% depending on the method of testing 
(26).  SIBO is characterized by symptoms of diarrhea, abdominal pain, bloating, and gas.  It has 
been proposed that SIBO may lead to immune activation, triggering low-grade inflammation, 
epithelial barrier dysfunction, and visceral hyperalgesia seen in IBS (27).  Meanwhile, antibiotics 
improve symptoms in IBS patients with SIBO while those patients who achieved bacterial 
eradication showed the greatest symptomatic response (23).  However, little is known about the 
specifics of the gut microbiota in SIBO and whether these conditions are separate or 
overlapping entities. 
Small bowel aspirate and culture is an accepted means of quantifying upper intestinal bacteria, 
but this approach is time consuming, invasive, and has a high false-negative rate (28).  As a 
consequence, hydrogen breath tests have largely supplanted intestinal cultures as measures of 
SIBO.  There is some controversy regarding the substrate that is utilized in hydrogen breath 


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7 
tests.  Lactulose has been advocated as a preferred substrate as it is not absorbed in the GI 
tract.  However, simultaneous testing using scintigraphy and lactulose hydrogen breath testing 
(LHBT) demonstrated that abnormal findings with LHBT represent rapid orocecal transit rather 
than SIBO (29).  Glucose is another substrate that is commonly employed in hydrogen breath 
testing.  Although glucose is primarily absorbed in the proximal small bowel and therefore may 
miss distal SIBO, this is still the most common and widely available non-invasive test to 
diagnose SIBO (30). 
Despite our advances in understanding the pathophysiology of IBS, there are still unmet needs 
in terms of treatment options.  Rifaximin is a non-absorbable antibiotic that has been shown to 
improve symptoms in the diarrhea-predominant subtype of IBS (IBS-D) (31,32).  However, 
mechanisms by which rifaximin leads to improvement in IBS-D are still unknown.  In vitro 
studies suggest that rifaximin may prevent changes in barrier dysfunction and reverse mucosal 
inflammation by modulating bacteria in the small intestine (33).  Conversely, prior studies have 
not demonstrated significant effects of rifaximin on fecal microbial composition (34,35).  This is 
likely because rifaximin is insoluble in the colon and has antimicrobial effects primarily in the 
small bowel (36).  Furthermore, rifaximin leads to improvement in symptoms in only 40% of IBS 
patients with a therapeutic gain of 9% over placebo.  Because of these observations, one could 
argue that rifaximin may be effective only in those IBS patients who have concomitant SIBO.  
Indeed, a recent study demonstrated that those IBS patients with SIBO had a significantly 
increased response to rifaximin compared with those IBS patients without SIBO (37). 
Dietary modification has also been advocated as a potential treatment option in IBS-D.  The 
vast majority of IBS patients believe certain foods trigger their IBS symptoms (38).  Fermentable 
oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) are short-chain, 
poorly absorbable carbohydrates.  Recently, a diet low in FODMAP has been shown to improve 
symptoms in up to 76% of IBS patients (39,40).  However, two recent randomized controlled 
trials failed to show a low FODMAP diet was superior to traditional IBS dietary advice in 
controlling symptoms (41,42).  Furthermore, improvement in symptoms was reported by only 
50% of patients on low FODMAP diets.  Moreover, the exact mechanism by which a low 
FODMAP diet improves symptoms in IBS is still unknown.  It is postulated that the gut 
microbiota are critical in generation of symptoms in the presence of dietary FODMAPs and lead 
to production of gases, including hydrogen, CO2, and methane.  This may generate symptoms 
in IBS particularly in the setting of visceral hypersensitivity (43).   
Identifying those subjects who are most likely to respond to a low FODMAP diet is clearly 
needed but has been a vexing problem. Hydrogen breath testing has been advocated as a 
potential tool to identify subjects that malabsorb FODMAPs (e.g. lactose, fructose, sorbitol, and 
mannitol) and thereby might have better response to dietary FODMAP restriction.  However, 
questions regarding the reproducibility of breath testing as well as standardization of the test in 
this setting are still unanswered (44).  Furthermore, it was recently shown that a lactulose breath 
test could not discriminate between responders and non-responders to low FODMAP diets (45).  
Interestingly, a recent study in pediatric IBS subjects demonstrated that responders to a low 
FODMAP diet had different fecal microbial composition at baseline compared with non-
responders (46).  As the gut microbiota is postulated to be one of the main mediators in the 
pathogenesis of symptoms in IBS and FODMAP intake, this suggests that alterations in the 
fecal microbiota may predict response to dietary restriction of FODMAP. Genetic variability in 


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8 
tryptophan hydroxylase-1 (TpH-1) and sucrase-isomaltase single nucleotide polymorphisms 
(SNPs) have been demonstrated in IBS patients (47,48).  Unpublished data suggest that 
differences in TpH-1 SNPs may also potentially identify responders vs. non-responders to 
treatments, such as low FODMAP diet, in IBS.  Finally, a recent study suggested that treatment 
with low FODMAP diet may lead to improvement in cytokine profiles (49). 
Taken collectively, our current therapeutic options are quite limited in IBS-D and improve 
symptoms in only ≤ 50% of subjects in the best-case scenarios, which we believe is a 
consequence of multiple pathogenic factors.  Given that IBS is a heterogeneous condition, there 
is a pressing need to stratify IBS patients into distinct subtypes to optimize responses to 
diverse therapies including antibiotics versus dietary measures.  In the investigations included in 
this proposal, we will test the hypotheses that: (i) distinct IBS-D phenotypes with characteristic 
clinical features can be generated by identifying the presence or absence of SIBO and by 
defining fecal microbial populations, and (ii) longitudinal analyses using microbiota-derived 
metrics as well as SIBO status may provide important details into how these treatments improve 
symptoms in IBS and may also provide clues on which patients may respond to different 
therapies.  
2 
OBJECTIVES 
Aim 1:  Randomize IBS-D subjects to receive either treatment with a nonabsorbable 
antibiotic rifaximin vs. low FODMAP dietary intervention.   
a) 200 IBS-D patients will be carefully phenotyped using validated questionnaires (IBS 
symptoms, stool form, psychological function, quality of life) and diet analysis. 
b) IBS-D subjects will undergo baseline testing including glucose hydrogen breath tests 
(GHBT) to define the presence of SIBO.  Fecal microbiota will also be characterized by α- 
and β-diversity and dominant phyla on 16S RNA analyses.  
c) IBS-D subjects will be randomized to receive either rifaximin 550 mg three times daily x 14 
days or low FODMAP diet x 4 weeks under direction of study bionutritionist. 
d) The primary outcome will be changes in mean daily pain or bloating by visual analog scale 
(VAS) after intervention compared with baseline.  Responders to intervention will be 
defined by ≥ 30% reductions in mean daily pain or bloating by VAS compared with 
baseline.  Secondary outcomes will be defined by reduction in IBS Symptom Severity Scale 
by ≥ 50 compared with baseline.  
e) Other secondary outcomes, including GI symptoms, stool form, psychological function, 
quality of life, and diet intake, will be compared to determine if subjects present differently.  
Aim 2: Determine using longitudinal analyses how SIBO status and fecal microbiota 
features associate with response to treatment with rifaximin or a low FODMAP dietary 
intervention. 
a) Fecal microbial analyses will be repeated at 2, 4 and 5 weeks while GHBT will be repeated 
at the end of the intervention.   


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b) The primary aim will be change in fecal microbial diversity after intervention compared with 
baseline.  We hypothesize that low FODMAP diet will result in a 10-15% increase in 
diversity in fecal microbiota compared with baseline. 
c) Secondary outcomes including response to treatment with rifaximin or low FODMAP diet 
will be related to the (i) presence of SIBO on initial testing, (ii) persistence of SIBO after 
intervention, (iii) abnormal α- and β-diversity on initial testing, (iv) changes in α- and β-
diversity as well as in dominant microbial phyla at 2, 4 and 5 weeks, and (v) changes in 
serum cytokine profiles, including TNF-α, IL-1β, IL-6, IL-8, and IL-10.   
d) Other outcomes that will be assessed include differences in tryptophan hydroxylase-1 
(TpH-1) and sucrase-isomaltase single nucleotide polymorphisms (SNPs) in different 
cohorts of IBS-D patients.  
Aim 3: Develop a predictive model to identify subsets of IBS-D patients responsive to 
treatment. 
a) We will develop and validate a predictive model of response to low FODMAP diet using 
data from the subjects randomized to a low FODMAP diet (Aim 1) combined with existing 
data from a separate cohort of IBS-D subjects previously treated with a low FODMAP diet 
(HUM 00053274).  
3 
EXPECTED RISKS/BENEFITS 
The data accumulated in this study will advance our understanding of the 
pathophysiology of IBS, including the role of the gut microbiota and SIBO in the 
pathogenesis of IBS, and may provide important information on which IBS subjects will 
most benefit from therapies including dietary modification and rifaximin.   
There are potential direct benefits for all IBS subjects in this study.  On study entry, 
glucose hydrogen breath tests (GHBT) as well as analysis of fecal microbiota will be 
performed that may provide new insight into causes of symptoms in patients with IBS.  
Furthermore, subjects with IBS will be treated with well accepted treatments for IBS, 
including a nonabsorbable antibiotic rifaximin or diets low in FODMAP.   IBS-D subjects 
treated with low FODMAP diet will be provided education on a low FODMAP diet from a 
trained bionutritionist.  IBS-D subjects will track their symptoms by completing 
questionnaires online including the Bristol Stool Form Scale as well as an 11-point NRS 
on abdominal pain and bloating daily.  IBS-D subjects will be asked to complete these 
questionnaires after their evening meal. They will also be instructed to track their diet for 
24 hours prior to each weekly or biweekly visit using a food questionnaire.  Finally, all 
IBS-D subjects will be seen or receive a phone call by the PI and/or study team every 
week or every two weeks during the study.  At each visit, survey information will be 
obtained using validated questionnaires including IBS-Symptom Severity Scale, 
Gastrointestinal Symptom Rating Scale-IBS, Patient Health Questionnaire (PHQ-9), 
Visceral Sensitivity Index (VSI), and IBS-quality of life (IBS-QOL).  The IBS-Symptom 
Severity Scale is a 10-item questionnaire that tracks severity of IBS symptoms and is a 


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valid way to monitor changes in IBS symptoms over time.  This will take approximately 5 
minutes to complete.  The Gastrointestinal Symptom Rating Scale-IBS is a 15-item 
questionnaires that tracks both upper and lower gastrointestinal symptoms.  This will 
take approximately 8 minutes to complete.   The PHQ-9 is a 9-item questionnaire that is 
a reliable and valid measure of depression severity.  This will take approximately 5 
minutes to complete.  The VSI is a 15-item questionnaire which is a reliable, valid 
measure of GI-specific anxiety.  This will take approximately 8 minutes to complete.  
The IBS-QOL is a 34-item questionnaire that is a reliable, valid quality of life measure 
specific for IBS.  This will take approximately 15 minutes to complete.  This frequent and 
comprehensive assessment provided as part of participating in this study may allow for 
closer monitoring of disease course. 
There are potential risks for subjects, including:  
1) Risk to privacy (rare): There is a potential risk to the IBS-D subject's privacy (<1% 
risk).  While every effort will be made to maintain privacy, it is possible that others 
may learn about information acquired from the medical records. 
 
For Aim 3, there are additional risks to privacy associated with secondary review of 
data from a separate database (HUM 00053274). However, we will follow standard 
procedures to minimize these risks. This includes use of data abstraction forms that 
will not contain any PHI. All subjects will be identified by a study ID number. The list 
linking the subject to his/her study ID number will be retained by the investigators in 
a secure location separate from the source documents. The list linking PHI to study 
ID numbers will be accessed only for verification of data abstraction if any 
inconsistency or incompleteness of study data requires review of a participant’s 
medical record. Once the data has been reviewed, analyzed, and verified, and the 
investigators are satisfied that no further review of the subject’s medical record is 
needed, the list of links to the identifiers for that subject population will be destroyed. 
This will ensure that no links to PHI persist beyond the duration of the study. No PHI 
will be sent outside of the institution. All presentations/publications will deal with data 
in aggregate form. Source documents created for study purposes will identify 
patients by study ID number only and will not contain PHI. 
2) Glucose hydrogen breath testing (likely): IBS-D subjects will be asked to drink 75 g 
of glucose dissolved in 250 ml of sterile water. IBS-D subjects may experience (10-
25%) bloating, abdominal cramping, and/or flatulence after consuming this drink. 
However, symptoms typically resolve quickly and may represent underlying 
physiologic abnormalities causing their symptoms.  Subjects will be allowed to take 
medications, such as simethicone or Tylenol, if they experience significant bloating 
or discomfort. IBS-D subjects may experience dizziness, faint spells, and/or nausea 
after the glucose hydrogen breath test. Subjects should bring a snack with them on 


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11 
days that the hydrogen breath test should be done to help with dizziness and 
lightheadedness.  
3) Risks of Blood Draw: If subjects decide to participate in optional sub-study, 10mL of 
blood will be drawn from a vein at Visits 1 and 5. There could be pain, bruising, or 
lightheadedness. Rarely there could be an infection or fainting. The person drawing 
blood will be trained to do that procedure and use techniques to minimize these 
risks.  
4) Risks of treatment (infrequent): There are theoretical concerns about treatment with 
rifaximin and low FODMAP diet.  Rifaximin is an antibiotic and theoretical concerns exist 
regarding potential for antibiotic resistance.  However, rifaximin is a minimally 
absorbable antibiotic with low risk of clinically relevant bacterial resistance (50,51).  
Randomized controlled trials with rifaximin in IBS have not demonstrated significant 
differences in adverse events between rifaximin and placebo (31,32,52).  General 
antibiotics side effects may occur, such as vomiting, nausea, diarrhea, etc. There are 
also theoretical concerns that prolonged therapy with a low FODMAP diet may have 
detrimental effects on gut microbial composition (53).  However, multiple studies 
examining low FODMAP diet in IBS have demonstrated the safety and tolerability of this 
dietary approach (40–42,45).  The effects of rifaximin in pregnancy and women who are 
breastfeeding are unknown and therefore pregnant women or women who are 
breastfeeding will be excluded from the study.  Finally, women of child bearing age will 
be warned that oral contraception may not be as effective when taken with rifaximin. 
5) General risks (infrequent): This is an interventional study.  IBS-D subjects' condition 
may worsen or improve while undergoing intervention with either rifaximin or a low 
FODMAP diet.  Participation in this study will not prevent normal clinical care of IBS or 
its consequences.  In addition, some prescribed medications may need to be stopped 
temporarily during the study.  This includes medications that may influence pain 
sensation, including narcotic pain medications.  IBS-D subjects will also be asked to 
discontinue antibiotics for at least 3 months and probiotics for at least 1 month prior to 
enrollment.  IBS-D subjects will be asked to avoid Pepto-Bismol for at least 2 weeks 
prior to GHBT.  IBS-D subjects will also be instructed to eat a low carbohydrate diet for 
at least 2 days prior to the GHBT to avoid inaccurate test results.  If IBS-D subjects are 
taking any of these medications, their symptoms may return or worsen when they are 
stopped.  However, the stopping of medications is temporary and is not felt to cause 
any undue hardship.  Finally, there is a risk that some of the questions in the surveys 
may produce emotional distress.  If the IBS-D subject desires, he/she can be referred to 


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12 
a mental health specialist within the UMHS or another provider outside the UMHS 
system. 
6)  Risks for sharing samples (rare):  If subjects decide to participate in an optional sub-
study, saliva samples will be shared with Karolinska Institute and IKMB Kiel to evaluate 
differences in sucrase-isomaltase SNPs. There are potential risks to the IBS-D subject’s 
privacy.  However, all samples will be de-identified and only investigators at UMHS will 
have access to the linkage code.   
4 
ELIGIBILITY CRITERIA 
IBS Patients: 
200 consecutive adult subjects ≥ 18 years of age at screening who meet the following 
inclusion and exclusion criteria will be eligible for enrollment: 
Inclusion criteria: 
• 
Rome IV criteria for IBS-D  
• 
Subjects will be asked to avoid Pepto-Bismol for 2 weeks prior to GHBT. 
• 
Subjects will be instructed to avoid eating or drinking for 8 hours and avoid smoking for 
6 hours prior to the test  
• 
Have colonoscopy or sigmoidoscopy with mucosal biopsy within the past 2 years prior to 
enrollment 
• 
Have an average score of 4 or higher over a 7-day pre-screen taking online symptom 
surveys assessing abdominal pain and bloating 
 
Exclusion criteria:  
• 
Underlying celiac disease 
• 
Inflammatory bowel disease 
• 
Other organic disease that could explain their symptoms.   
• 
History of GI tract surgery, except for appendectomy 
• 
Narcotics, antibiotics taken within 3 months or probiotics taken within one month prior 
to enrollment will not be permitted.  
• 
Previously received formal dietary education, including a low FODMAP diet, for 
treatment of IBS. 
• 
Previously received antibiotics, such as rifaximin, for treatment of IBS or SIBO. 
• 
Women who are pregnant 
• 
Women who are breastfeeding 
 
Additional IBS subjects and Healthy Controls: 
 


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50 consecutive adult subjects ≥ 18 years (25 IBS-D and 25 healthy controls) who are 
undergoing colonoscopy for clinical purposes (e.g. colon cancer screening) 
 
For IBS subjects: 
Inclusion criteria: 
• 
Rome IV criteria for IBS-D  
Exclusion criteria:  
• 
Underlying celiac disease 
• 
Inflammatory bowel disease 
• 
Other organic disease that could explain their symptoms.   
• 
History of GI tract surgery, except for appendectomy 
• 
Narcotics, antibiotics taken within 3 months or probiotics taken within one month prior 
to enrollment will not be permitted.  
• 
Women who are pregnant 
• 
Women who are breastfeeding 
For healthy controls: 
 
 
Exclusion Criteria: 
• 
History of chronic GI disorder, such as irritable bowel syndrome, inflammatory bowel 
disease, and small intestinal bacterial overgrowth 
• 
Narcotics, antibiotics taken within 3 months or probiotics taken within one month prior to 
enrollment will not be permitted 
• 
Women who are pregnant 
• 
Women who are breastfeeding 
5 
SUBJECT ENROLLMENT 
Most patients with irritable bowel syndrome are seen in gastroenterology or general 
medicine clinics.  IBS-D patients will be recruited from gastroenterology and general 
medicine clinics at Taubman Center and in the satellite clinics within the University of 
Michigan Health System. We will also be sending out letters to patients identified from 
DataDirect as eligible for the study. Eligible IBS-D subjects will be contacted and given 
material explaining the nature of the study and introduction to a low FODMAP diet.  
They will be given time to read the materials. If they choose to participate, they will 
undergo a one week pre-screening an 11-point numerical rating scale (NRS) for 
abdominal pain and bloating for 7 days. If the subjects qualify through the pre-screen, 
they will sign the consent document in the presence of the PI and/or Designee.  IBS-D 
subjects will be enrolled on a first come, first served basis.  This approach will ensure 
that IBS-D subjects are representative of the population of patients with IBS in 
Southeast Michigan.   


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14 
Emails to providers in the General Medicine and Gastroenterology clinics in the 
University of Michigan System, public advertisements, telephone calls, and web 
postings on UMClinicalStudies.org will also be utilized to recruit IBS-D subjects. 
 
IBS subjects who do not meet inclusion/exclusion criteria will not be enrolled in the 
study.  All data collected from IBS-D subjects who are screen failures will be saved for 
data analysis. 
 
IBS subjects and healthy controls who are undergoing colonoscopy will be approached 
in the Medical Procedures Unit to determine their interest in participating in the optional 
sub-study and to determine their eligibility. 
6 
STUDY DESIGN AND PROCEDURES 
Specific Aim 1: Randomize IBS-D subjects to receive either a nonabsorbable antibiotic 
rifaximin vs. low FODMAP dietary intervention.  
 
1A.  Research Approach: 
200 IBS-D subjects will be carefully phenotyped using validated questionnaires (IBS symptoms, 
stool form, psychological function, quality of life) and diet analysis.  IBS-D subjects will also 
undergo baseline testing including GHBT as well as fecal microbial analysis.  IBS-D subjects will 
then be randomized to receive either rifaximin or low FODMAP diet intervention at the initial 
screening visit.  Efficacy of therapies will be monitored with validated questionnaires to track 
symptomatic improvement.  The primary outcome will be changes in mean daily pain or bloating 
after intervention compared with baseline.  Responders to intervention will be defined as ≥ 30% 
reduction in mean daily pain or bloating by visual analog scale (VAS) compared with baseline.  
Secondary outcomes will monitor changes in IBS-Symptom Severity Score as well as 
differences in GI symptoms, stool form, psychological function, quality of life, and dietary intake 
before and after intervention. 
 
1B.  Experimental Methods: 
Subject Recruitment:  200 adult subjects ≥ 18 years of age who meet Rome IV criteria for IBS-D 
will be enrolled in the study. Women of childbearing age will undergo a urine pregnancy test to 
exclude the possibility of pregnancy.  Women who are breastfeeding will also be excluded. IBS-
D subjects will be excluded if they have underlying celiac disease, inflammatory bowel disease, 
or other organic disease that could explain their symptoms.  All IBS-D subjects will have prior 
sigmoidoscopy or colonoscopy with mucosal biopsies within the past 2 years to rule out 
microscopic colitis.  IBS-D subjects with a history of GI tract surgery, except for appendectomy, 
will also be excluded from the study.  Antibiotics taken within 3 months prior to enrollment will 
not be permitted (54).  IBS-D subjects on probiotics must discontinue their use at least 1 month 
prior to fecal collection.  IBS medications, including anti-depressants, will be allowed if the dose 
has been stable for at least 1 month before inclusion.  Medications will be carefully tracked to 
follow any potential confounding issues.  IBS-D subjects who have previously received formal 


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15 
dietary education for IBS, including a low FODMAP diet, or previously received antibiotics, 
including rifaximin, for treatment of IBS-D or SIBO will be excluded from the study.   
GI Symptom Assessment:  All IBS-D subjects will complete validated questionnaires to quantify 
severity of IBS symptoms, including IBS Symptom Severity Scale (IBS-SSS), Gastrointestinal 
Symptom Rating Scale-IBS (GSRS-IBS), an 11-point numerical rating scale (NRS) for 
abdominal pain and bloating, and Bristol Stool Form Scale (BSFS) at baseline (55–58). The 
NRS for abdominal pain and bloating and the BSFS will be completed online through the 
REDCap Survey Tool. 
Psychological and Quality of Life Assessment:  IBS-D subjects will also complete validated 
questionnaires to assess for presence of and to measure severity of psychological disorders, GI 
specific anxiety, and impairments in quality of life.  All IBS-D subjects will complete the Patient 
Health Questionnaire (PHQ-9), Visceral Sensitivity Index (VSI), and IBS-quality of life (IBS-
QOL) (59–61).  The PHQ-9 will be reviewed by the study team within 24 hours of completing the 
questionnaire.  If a subject answers affirmative to the question “Thoughts that you would be 
better off dead or of hurting yourself in some way,” they will be provided with the appropriate 
referral to mental health counseling and/or the subject’s PCP will be alerted. 
Dietary Assessment:  All IBS-D subjects will undergo initial consultation with the study team and 
will be instructed on how to monitor and record their dietary intake.  IBS-D subjects will then 
record daily their dietary intake for 3 days prior to fecal collection. 
Fecal Collection and Preparation:  Three fresh stool samples will be collected from all IBS-D 
subjects at baseline.  Each sample will be immediately placed into an OMNIgeneGUT 
collection tube (DNA Genotek, Inc., Ottawa, ON, Canada) which allows for self-collection and 
stabilization of fecal DNA samples for up to 60 days at ambient temperature (62).  Samples will 
then be mailed back or picked up by the study team and stored at -80oC in Vince Young’s Lab 
for long-term storage. If patients consent to the optional portion of the study, they will provide a 
stool sample in 95% ethanol at Visits 1, 3, 4, and 5. We will also collect a one-time stool sample 
and symptom questionnaires from healthy controls. Healthy controls will not have a history of 
gastrointestinal conditions and do not report any abnormal bowel movements or abdominal 
pain.  
Tryptophan hydroxylase-1 (TpH-1) and sucrase-isomaltase single nucleotide polymorphisms 
(SNPs): Buccal swabs will be collected from all IBS-D subjects at baseline.  Each sample will be 
immediately placed into an OrageneDISCOVER (DNA Genotek, Inc., Ottawa, ON, Canada) 
which allows for stabilization of salivary DNA samples for up to 5 years at ambient temperature.  
Samples will then be stored at -80oC for long-term storage. De-identified DNA samples will be 
shared with Karolinska Institute and IKMB Kiel to analyze differences in sucrase-isomaltase 
SNPs.  This portion of the study is optional and subjects have a choice to allow their saliva 
samples to be stored for this sub-study. 
Serum cytokine profiles: Serum cytokines, including TNF-α, IL-1β, IL-6, IL-8, and IL-10 will be 
measured at baseline and at week 5. Whole blood will be collected in a 10 ml SST tube.  SST 
tubes will be allowed to clot at room temperature for 30 minutes.  The serum will then be 
separated from the red blood cells by spinning for 15 min at 1300G at 4oC.  The serum will then 
be aliquoted from each blood collection tube into (3) 2-ml transfer tubes and stored at -80oC for 


 ____________________________________________________________________________________________ 
16 
future analyses. This portion of the study is optional and subjects have a choice to allow their 
blood samples to be stored for this sub-study 
Glucose Hydrogen Breath Test (GHBT): SIBO will be diagnosed using the glucose H2/CH4 
breath test as previously described (63).  Briefly, H2/CH4 breath concentrations will be measured 
by gas chromatography (Quintron Instrument Company, Milwaukee, USA) in parts per million 
(ppm) after administration of an oral loading dose of glucose (75 g in 250 ml of sterile water).  
Breath samples will be collected every 15 minutes for a total of 120 minutes.  The test will be 
considered positive for SIBO when H2 and/or CH4 increase by ≥ 12 ppm above baseline. 
COVID-19 modifications: Patients will be given take home hydrogen test kits either in person or 
through the mail to conduct the test at home. Instructions will be given prior to test with the take 
home test kit. Patients could bring the test result back either in person or through mail and the 
lab will analyze the results. 
Trial Protocol: In order to minimize unequal allocation between arms, IBS-D subjects will be 
randomized using block randomization with random permuted sizes of 2 or 4 in a 1:1 ratio into 
two arms: one group will undergo treatment with rifaximin 550 mg three times daily for 14 days.  
The second group will be placed on a low FODMAP diet (≤ 9 grams per day as previously 
described) for 4 weeks (40,64,65).  IBS-D subjects undergoing dietary intervention will undergo 
consultation with a bionutritionist knowledgeable in low FODMAP diets.  A diet plan will be 
implemented and individualized to subjects based on information from their dietary history.  
Written information regarding allowable vs. non-allowable food items will be provided to IBS-D 
subjects and bionutritionists will be available during the study for further education.  IBS-D 
subjects randomized to the low FODMAP diet group will meet with the GI nutritionist at the 
completion of the 2nd week of dietary intervention to answer any potential questions regarding 
the diet.  IBS-D subjects will complete a 24-hour dietary recall each week or every two weeks 
during the 4-week dietary intervention to ensure compliance. 
Symptom Assessment:  IBS-D subjects will record stool frequency, BSFS, and symptom scores 
for abdominal pain and bloating daily on a diary card.  IBS-D subjects will complete 
questionnaires on a weekly basis during study visits to determine changes in symptoms.  
Responders to intervention arm (both rifaximin and low FODMAP diet) will be defined as ≥ 30% 
reductions in mean daily pain or bloating compared with baseline.  Secondary outcomes, 
including reduction in IBS Symptom Severity Scale by ≥ 50 compared with baseline at the end 
of the interventional arm, will also be monitored.  These are both considered to reflect clinically 
meaningful improvements in IBS (55,57).  IBS-D subjects will be seen on a weekly or biweekly 
basis and diary cards will be collected.  Adherence to medications or dietary intervention will 
also be assessed at that time.   
Specific Aim 2: Determine using longitudinal analyses how SIBO status and fecal 
microbiota-derived metrics associate with response to treatment with rifaximin or a low 
FODMAP dietary intervention. 
2A. Research Approach: 
We will prospectively follow the results of GHBT and fecal microbiota before and after treatment 
with rifaximin and low FODMAP dietary restriction.  We will collect fecal samples throughout the 
study period in IBS-D patients.  All IBS-D subjects will also undergo GHBT before and after 


 ____________________________________________________________________________________________ 
17 
intervention.  The primary aim will be change in fecal microbial diversity after intervention with 
rifaximin or low FODMAP diet compared with baseline.  Secondary outcomes will evaluate 
whether response to treatment with rifaximin or low FODMAP diet is associated with: (i) 
presence of SIBO on initial testing, (ii) persistence of SIBO after intervention, (iii) changes in α- 
and β- diversity as well as in dominant phyla. We will also utilize human intestinal enteroids to 
model how host-microbial interactions may influence response to treatment with rifaximin or low 
FODMAP diet in IBS. 
2B. Experimental Methods: 
Fecal Collection and Preparation: Stool samples will be collected from all IBS-D subjects at 
weeks 2, 4 and 5 as described in Aim 1. Stool samples will be stored for up to 5 years at the 
conclusion of the study for future analyses, including evaluating differences in metabolomics, 
such as histamine, p-hydroxybenzoic acid, azelaic acid, and H2 (45). This portion of the study is 
optional, and subjects have a choice to allow their stool samples to be stored for this sub-study. 
This may provide mechanistic descriptions of how changes in gut microbiota lead to changes 
seen in IBS. If patients consent to this optional portion of the study, they will provide a stool 
sample in 95% ethanol at weeks 0, 2, 4, and 5. Subjects will be compensated a nominal amount 
of $20 for stool samples returned at week 0 and $10 each for weeks 2, 4 and 5 to express our 
gratitude for their participation in the study. We will also provide mailers to mail back samples to 
minimize study burden on participants. 
GHBT: Glucose H2/CH4 test will be repeated at week 5 as described in Aim 1. 
Serum cytokine profiles: Serum cytokines will be repeated at week 5 as described in Aim 1. 
Handling and processing of the blood will be described in Appendix 1.  
Mucosal Samples: If subjects consent to participate in this optional sub-study, mucosal biopsies 
will be taken from eligible subjects who are scheduled to undergo a colonoscopy for clinical 
purposes (e.g. to rule out alternative causes of symptoms or screening for colon cancer). In 
addition to the IBS subjects recruited to participate in the clinical trial, we will recruit an 
additional 25 IBS subjects as well as 25 healthy controls undergoing colonoscopy for clinical 
purposes (e.g. colon cancer screening) to determine how host-microbial interactions may impact 
on IBS vs. healthy controls.  
Mucosal biopsies will be utilized to generate human intestinal enteroids to study host-microbial 
interactions determining response to treatment in IBS. Four mucosal biopsies will be obtained 
from normal appearing mucosa in the ileum, ascending and sigmoid colon (total of 12 mucosal 
biopsies per patient), placed in a sterile cryovial on ice, and immediately stored at -80°C for 
long-term storage. 
Sequencing and Data Analysis: 
(i) MiSeq Illumina Sequencing:  DNA samples will be submitted to the University of Michigan 
Host Microbiome Initiative under the Microbiome Explorers Program and will be processed 
using the MiSeq Illumina sequencing platform.  16S rRNA gene libraries will be constructed 
using primers specific to the V4 region.   
(ii) OTUs and Diversity Measurements:  The open-source software program, Mothur, will be 
used following the steps outlined in the Mothur MiSeq SOP (66,67).  The 16S rRNA gene 
sequencing profiles will be assessed using metrics for α diversity (such as Shannon or inverse-


 ____________________________________________________________________________________________ 
18 
Simpson indices) and β diversity-based distance measures between samples, such as θyc or 
Bray-Curtis (68,69).  Community types will be identified using unsupervised clustering 
algorithms, and individual operational taxonomic units (OTUs) will be identified and compared 
between/within patients (see Biostatistical analysis).   
(iii) Quantitative PCR Targeting the 16S rRNA Gene: qPCR will be used to quantify the total 
number of 16S rRNA gene copies/gram.  Reactions will be performed on a CFX Connect Real-
Time PCR detection system (Bio-Rad Laboratories; Hercules, CA) with universal 16S rRNA 
gene primers as previously described (33). 
Specific Aim 3: Develop a predictive model to identify subsets of IBS-D patients 
responsive to treatment. 
3A. Approach: 
We will develop and validate a predictive model of response to low FODMAP diet using data 
from the subjects randomized to a low FODMAP diet (Aim 1) combined with existing data from a 
separate cohort of IBS-D subjects previously treated with a low FODMAP diet (HUM 00053274).  
3B. Experimental Methods: 
We will use the combined cohort of patients treated with a low FODMAP diet (Aim 1 and HUM 
#00053274), which will be split into a training set from a random sample of 80% of the data 
while the remaining 20% of the data will serve as the test set. Using a random forest model, 5x2 
nested cross-validation (CV) will be performed within the training set for model selection and 
hyperparameter tuning. The candidate models will be compared by testing for overlap of 
confidence intervals for area under the curves (AUCs, two-sided test). Once a final model is 
selected, model performance will be evaluated on the test set.  
 
Study Timeline: 
 
Figure 1 IBS Subject Timeline 
Schedule of Events - Low FODMAP Group 
Visit Number 
Pre-Visit 
Visit 1 
Visit 2 
Visit 3 
Visit 4 
Visit 5 
Visit Description 
Pre-
screening 
(Phone/in 
person) 
Baseline 
(Phone/in 
person) 
Monitoring 
(Phone/in 
person) 
Monitoring 
(Phone/in 
person) 
Monitoring 
(Phone/in 
person) 
Monitoring/ 
Outcomes 
(Phone/in 
person) 
Time point 
Eligibility 
Day 0 
Day 7±3 
days  
Day 14±3 
days 
Day 28±3 
days 
Day 35±3 
days 
7 day pre-screening questionnaire 
X 
 
 
 
 
 
Informed Consent 
X 
 
 
 
 
 
Medical History /Physical 
Examination 
 
X 
X 
X 
X 
X 
Urine pregnancy test (Females of 
childbearing age) 
 
X 
 
 
 
 
Washout  
X 
 
 
 
 
 
Questionnaires 
 
X 
 
X 
 
X 


 ____________________________________________________________________________________________ 
19 
*Female participants capable of bearing children will be required to attend visit 1 in person for the pregnancy test 
*During COVID-19 pandemic, all hydrogen breath tests will be conducted remotely 
Schedule of Events – Rifaximin Group 
*Female participants capable of bearing children will be required to attend visit 1 in person for the pregnancy test 
*During COVID-19 pandemic, all hydrogen breath tests will be conducted remotely 
3-day food diary 
 
X 
 
 
 
 
24-hour dietary recall 
 
 
X 
X 
X 
X 
GI nutrition consultation 
 
X 
 
X 
 
 
Colonoscopy with mucosal 
biopsies (optional) 
X 
 
 
 
 
 
Serum Cytokine Profiles (optional) 
 
X 
 
 
 
X 
Buccal swab collection (optional) 
 
X 
 
 
 
 
Glucose hydrogen breath testing 
 
X 
 
 
 
X 
Stool collection for fecal microbial 
analysis 
 
X (3 
baseline 
samples) 
 
X 
X 
X 
Randomization 
X 
 
 
 
 
 
Dietary Compliance 
 
 
X 
X 
X 
X 
Adverse Events Monitoring 
 
 
X 
X 
X 
X 
Visit Number 
Pre-Visit 
Visit 1 
Visit 2 
Visit 3 
Visit 4 
Visit 5 
Visit Description 
Pre-
screening 
(Phone/in 
person) 
Baseline 
(Phone/in 
person) 
Monitorin
g 
(Phone/in 
person) 
Monitorin
g 
(Phone/in 
person) 
Monitorin
g 
(Phone/in 
person) 
Monitoring/ 
Outcomes 
(Phone/in 
person) 
Time point 
Eligibility 
Day 0 
Day 7±3 
days 
Day 14±3 
days 
Day 28±3 
days 
Day 35±3 
days 
7 day pre-screening 
questionnaire 
X 
 
 
 
 
 
Informed Consent 
X 
 
 
 
 
 
Medical History /Physical 
Examination 
 
X 
X 
X 
X 
X 
Urine Pregnancy Test (Females 
of childbearing age) 
 
X 
 
 
 
 
Washout 
X 
 
 
 
 
 
Questionnaires  
 
X 
 
X 
 
X 
3-day food diary 
 
X 
 
 
 
 
24-hour diet recall 
 
 
X 
X 
X 
X 
Colonoscopy with mucosal 
biopsies (optional) 
X 
 
 
 
 
 
Serum cytokine profiles 
(optional) 
 
X 
 
 
 
X 
Buccal swab collection 
(optional) 
 
X 
 
 
 
 
Glucose hydrogen breath 
testing 
 
X 
 
 
 
X 
Stool collection for fecal 
microbial analysis 
 
X (3 
baseline 
samples) 
 
X 
X 
X 
Randomization 
X 
 
 
 
 
 
Medication Dispensing 
 
X 
 
 
 
 
Medication Compliance 
 
 
X 
X 
 
 
Adverse Events Monitoring 
 
 
X 
X 
X 
X 


 ____________________________________________________________________________________________ 
20 
7 
Data Collection and Management Procedures 
Data Handling and Entry:  All data including questionnaire results and physiologic 
testing will be recorded and reviewed by the study team.  Data will then be entered into 
an electronic case report form (eCRF) that complies with Title 21 of the Code of Federal 
Regulations (21 CFR Part 11).  All passwords will be strictly confidential to protect 
subject’s protected health information (PHI).  Only the Primary Investigator (PI) and 
Study Coordinator will have access to the data and subject identifiers.  Only the PI and 
Study Coordinator will be allowed to enter data onto the password-protected web-based 
server. 
Computer Systems:  Data entry will be entered into REDCAP which is validated and 
conforms to regulatory requirements.  Only the Primary Investigator (PI) and Study 
Coordinator will have access to the data and subject identifiers.  Only the PI and Study 
Coordinator will be allowed to enter data onto the password-protected web-based 
server. 
Phone Visits: All phone visits will be conducted with a University Health System phone 
to protect patient confidentiality. 
SignNow: a secure application that enables users to electronically prepare and send 
University business documents for the purpose of requesting and obtaining digital 
signatures to help protect confidentiality.  
Data Validation:  Validation checks will be programmed within the eCRF system as 
well as supplemental validation performed by review of the downloaded data, will be 
applied to the data in order to ensure accurate, consistent, and reliable data. 
Direct Access to Source Data:  A developed review procedure that complies with 
Good Clinical Practice (GCP) guidelines. 
Source Document/Case Report Form Completion:  Source documents and the 
eCRFs will be completed for each study patient.  It is the Investigator’s responsibility to 
ensure the accuracy, completeness, and timeliness of the data reported in the patient’s 
source document/eCRF.  The source document/eCRF should indicate the patient’s 
participation in the study and should document the dates and details of the study 
procedures, AEs, and patient status. 
Record Retention:  The Investigator will maintain all study records according to 
applicable regulatory requirement(s). 


 ____________________________________________________________________________________________ 
21 
8 
DATA ANALYSIS 
Procedure for Accounting for Missing, Unused, and Spurious Data:  The primary 
outcome measure in our study is changes in mean daily pain or bloating after 
intervention with rifaximin or low FODMAP diet compared with baseline.  We will use 
multiple imputation with 10 imputed datasets to replace missing values on outcome and 
predictor variables [77].  If 10 imputed datasets are not sufficient to ensure stability of 
estimates, we will use 20 imputed datasets.  This allows for maximal use of available 
data while maximizing statistical power.   
9 
QUALITY CONTROL AND QUALITY ASSURANCE 
The PI and Study Coordinator will be responsible for Quality Control and Quality 
Assurance and will be performed in accordance with Standard Operating Procedures at 
the University of Michigan. 
10 
STATISTICAL CONSIDERATIONS 
Aim 1: 
All of the interventional analyses will be analyzed on an intention-to-treat basis.  Each 
IBS-D subject will act as his/her own control for analysis of the effects of either rifaximin 
or low FODMAP diet intervention.  This paired design inherently eliminates a significant 
amount of bias/confounding and affords increased statistical power.  We will power our 
study to detect a ≥30% improvement in mean daily bloating or abdominal pain after 
intervention compared with baseline.  Using available data from a US study on low 
FODMAP diet in IBS patients (42), we conservatively estimate that we will require 14 
IBS-D subjects in each arm to have >90% power to detect a mean difference of 1.7 in 
abdominal bloating scores after intervention via paired t-tests with the expected 
standard deviation (SD) of ±1.8.  Thus, our expected enrollment of 32 IBS-D subjects in 
each arm will be more than sufficient for analyzing this aim (see biostatistical analysis 
for Aim 2), even if the SD is nearly two-fold larger than expected.  
Aim 2: 
We will examine both inter- and intra-individual variability in microbiota-derived metrics.  
We plan to use a paired design to eliminate a significant amount of bias/confounding 
and increase statistical power.  We anticipate that there will be some variability in the 
three samples collected prior to treatment, and various techniques will be employed to 
average these data so they are incorporated as the baseline.  For example, for α 
diversity (Shannon index) a simple average of the three time points will be sufficient to 


 ____________________________________________________________________________________________ 
22 
establish a baseline α diversity.  Similar techniques will be applied to other community 
structure metrics, to create “deltas” between post-treatment time points and the 
baseline. 
These microbe-derived metrics and accompanying clinical variables will be initially 
analyzed through descriptive statistics before/after intervention.  Histograms and 
measures of frequency or central tendency/spread will be used to optimize variable 
constructions.  Subsequently, initial bivariable longitudinal analyses in an inter-individual 
fashion (assessing group-wide trends before/after intervention) that also account for the 
paired nature of the data (intra-individual) will be employed for categorical data 
(McNemar’s test) and continuous data (paired t-test), or their non-parametric 
equivalents for data not normally distributed.  Multiple comparisons will be made for 
individual OTU abundance metrics, with a focus on the most abundant taxa.  However, 
we will avoid a high false discovery rate through use of linear discriminant analysis 
effect size (LEfSe) analysis (70).  Similar to Aim 1, we will power our study using a 
paired t-test based on the primary outcome to detect a change in diversity at the end of 
the intervention compared with baseline.  In addition, we will also examine intermediate 
endpoints or longitudinal trends over time to determine if these are important.  If this is 
the case, we will also use mixed model analyses with repeated measures.   
Although this work is exploratory, we wanted to ensure that we will have sufficient 
power to detect notable differences in microbial and functional characteristics with our 
planned recruitment base.  Based on prior studies with low FODMAP diet in IBS 
patients (42,45,71), we conservatively estimate that 60% of IBS-D subjects will respond 
to treatment.  We further expect that only those IBS-D subjects who respond to a low 
FODMAP diet will show changes in fecal microbial diversity. Given our sample size of 
32 subjects per arm, we will have >90% power to detect a mean difference ≥ 0.4 in θYC 
(a measure of β-diversity) between responders and non-responders. As we are already 
seeing differences in θYC of this magnitude or greater, this suggests we are 
appropriately powered to detect meaningful differences in the microbiota between 
groups even if our standard deviation is 2-fold greater than expected. 
 
 
11 
REGULATORY REQUIREMENTS 
11.1 Informed Consent 1 
 
 
1 The IRB may waive some or all elements of informed consent – consult 
the IRB for consenting requirements. 


 ____________________________________________________________________________________________ 
23 
Informed consent will be signed by subjects after the protocol is explained by either the 
PI, co-I or study coordinator. If an IBS-D subject is a patient of the PI or Co-I, the study 
coordinator will be responsible for obtaining informed consent to avoid potential issues 
of coercion. Before signing, IBS-D subjects will be given ample opportunity to ask 
questions about the protocol. Consent forms could be signed in the Taubman Center or 
in the GI Physiology Laboratory in the Medical Procedures Unit.  Please see Informed 
Consent attached as an appendix. 
 
11.2 Subject Confidentiality  
All study team members will make every effort to protect each IBS-D subject’s 
confidentiality.  Participants will have privacy in a closed exam room to be able to 
provide information to the PI and/or study coordinator regarding medical history, current 
condition, and any other relevant information pertaining to the study.  Research records, 
data, and/or specimens will be kept in a locked office and/or locked cabinet with access 
restricted only to study team members. Study members will also secure electronic data 
on computers by using password protection, installing and regularly updating security 
software, as well as encryption of data. Only the PI and the Study Coordinator will have 
access to the data and IBS-D subject identifiers. Subjects will receive REDCap 
encrypted and secure links to fill out the online questionnaires. Only the PI and the 
Study Coordinator will be allowed to enter data onto the password-protected web-based 
server. Patients will be called using University Health System phones to protect patient 
privacy. 
  
11.3 Data Safety Monitoring Plan 
 
11.3.1. Oversight Responsibilities  
Oversight of the trial is provided by the Principal Investigator (PI), Dr. Lee. Dr. Lee 
assures that informed consent is obtained prior to performing any research procedures, 
that all subjects meet eligibility criteria, and that the study is conducted according to the 
IRB-approved research plan.  
 
11.3.2 Unanticipated Problems, Adverse Events and Serious Adverse Event 
Collection and Reporting2 
 
 
 
2 The Office for Human Research Protections (OHRP) considers unanticipated problems involving risks to subjects or others to 
include, in general, any incident, experience, or outcome that meets all of the following criteria: 


 ____________________________________________________________________________________________ 
24 
There is minimal direct risk to study subjects as all interventions are well accepted 
treatments for IBS. All members of the study team will stay current with training in the 
protection of human research participants and HIPAA. The PI will regularly monitor the 
data in collaboration with the research team, with periodic review by the IRB at the 
University of Michigan. We will minimize risk by using rigorous data security protocols to 
protect protocol deviations (e.g. violation of human subject confidentiality or comprised 
data integrity) and will ensure expedient reporting to the IRB (see below). 
All adverse clinical experiences, whether observed by the investigator or reported 
by the subject, must be recorded, with details about the duration and intensity of each 
episode, any actions taken, and the subject’s outcome. The Principal Investigator must 
evaluate each adverse experience for its relationship to the study and for its 
seriousness. 
The Principal Investigator must appraise all abnormal laboratory results for their 
clinical significance. If any abnormal laboratory result is considered clinically significant, 
the Principal Investigator must provide details about the action taken and about the 
subject’s outcome. 
 
 
All AEs will be assessed by the Investigator(s) and will be recorded in the eCRF, 
including the date of onset and resolution, severity, relationship to study, outcome, and 
action taken. All AEs will be reported to the IRB that meet reporting criteria. Toxicity will 
be graded according to the Common Toxicity Criteria as follows: 
0 = No adverse event or within normal limits 
1 = Mild AE, not requiring treatment 
2 = Moderate AE, resolved with treatment 
3 = Severe AE, resulted in inability to carry on normal activities and required 
professional medical attention 
4 = Life threatening or disabling AE 
 
 
• 
unexpected (in terms of nature, severity, or frequency) given (a) the research procedures that are described in the protocol-
related documents, such as the IRB-approved research protocol and informed consent document; and (b) the characteristics 
of the subject population being studied; 
• 
related or possibly related to participation in the research (in the guidance document, possibly related means there is a 
reasonable possibility that the incident, experience, or outcome may have been caused by the procedures involved in the 
research); and 
• 
suggests that the research places subjects or others at a greater risk of harm (including physical, psychological, economic, or 
social harm) than was previously known or recognized. 
 
An incident, experience, or outcome that meets the three criteria above generally will warrant consideration of substantive 
changes in order to protect the safety, welfare, or rights of subjects or others.   


 ____________________________________________________________________________________________ 
25 
5 = Fatal AE 
Serious adverse event (SAE) is defined by the FDA as an AE resulting in any of 
the following outcomes: Death, a life-threatening adverse event, inpatient hospitalization 
or prolongation of existing hospitalization, a persistent or significant incapacity or 
substantial disruption of the ability to conduct normal life functions, or a congenital 
anomaly/birth defect. Important medical events that may not result in death, be life-
threatening, or require hospitalization may be considered serious when, based upon 
appropriate medical judgment, they may jeopardize the patient or subject and may 
require medical or surgical intervention to prevent one of the outcomes listed in this 
definition. Once an AE or SAE is known, research team members at the study site will 
ensure that participants receive appropriate care and all actions taken by the PI and/or 
co-investigator after observing the AE or SAE will be documented. 
 
11.3.2. Management of Risks to Subjects 
Expected AEs:  
Expected AEs associated with the interventions being used in the study and study 
procedures include:  
• Abdominal cramping, bloating, flatulence, lightheadedness or dizziness with the 
GHBT 
• Pain, bruising or lightheadedness with the blood draw 
AE Management: 
Subjects will be allowed to take medications, such as simethicone or Tylenol, if they 
experience significant bloating or discomfort with the GHBT. They will also be offered 
juice or other beverages if they experience dizziness or lightheadedness with the GHBT 
or with blood draws. 
 
11.3.3  Entity Responsible for Monitoring 
The Principal Investigator is responsible for complying with local and institutional 
requirements related to the reporting and documenting of SAEs.  These reports must 
include submission of all qualifying SAEs to the IRB and/or Independent Ethics 
Committee (or others).  The guidelines established in the Committees on Human 
Research “Adverse Event and Unanticipated Problems Reporting Policy” will be 
followed.   
 
11.3.3 Data Analysis Plans 


 ____________________________________________________________________________________________ 
26 
Study data are accessible at all times for the PI to review. The PI reviews study 
conduct, including accrual, drop-outs, and protocol deviations, on a monthly basis. The 
PI reviews AEs individually real-time and in aggregate on a quarterly basis. The PI 
reviews serious adverse events (SAEs) in real-time. The PI ensures all protocol 
deviations, AEs, and SAEs are reported to the IRB according to the applicable 
regulatory requirements. 
 
11.3.4 Stopping Rules 
This study will be stopped prior to its completion if: (1) the intervention is associated 
with adverse effects that call into question the safety of the intervention; (2) difficulty in 
study recruitment or retention will significantly impact the ability to evaluate the study 
endpoints; (3) any new information becomes available during the trial that necessitates 
stopping the trial; or (4) other situations occur that might warrant stopping the trial. 
 
 
 
 
11.3.5 Safety Review Plan 
Study progress and safety will be reviewed monthly (and more frequently if needed). An 
Annual Report will be compiled and will include a list and summary of AEs. In addition, 
the Annual Report will address (1) whether AE rates are consistent with pre-study 
assumptions; (2) reason for dropouts from the study; (3) whether all participants met 
entry criteria; (4) whether continuation of the study is justified on the basis that 
additional data are needed to accomplish the stated aims of the study; and 
(5) conditions whereby the study might be terminated prematurely. The Annual Report 
will be forwarded to the IRB. The IRB and other applicable recipients will review 
progress of this study on an annual basis. 


 ____________________________________________________________________________________________ 
27 
12 
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Appendix 1 
Cytokine Profile Collection: 
Visits 2 and 6 (if optional consent is obtained): 
1. 10 ml of blood will be drawn and placed into  2 SST tubes.  
2. Whole blood SST tubes will be transported at room temperature to the lab. 
3. Processing for SST tubes: 
a. SST tubes will be allowed to clot at room temperature for 30 minutes. 
b. Serum will be separated from the red blood cells by spinning for 15 min at 
1300G at 4oC.  
c. The serum will then be aliquoted from each blood collection tube into (3) 
2-ml transfer tubes and then the collection tube will be discarded into the 
red biohazard disposal bucket. 
d. Each collection tube will be labeled with the subject’s unique ID number 
and/or letters. 
e. Each collection tube will then be frozen at -80oC for future analyses.