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Our Research Vision

Adopting an integrated interdisciplinary approach, we investigate the role of the intestinal microbiota in the maintenance of health and in the expression of diseases within and beyond the gastrointestinal tract. Our goal is to develop microbiota-directed therapies for the optimization of health and treatment of chronic diseases within and beyond the intestinal tract, and in so doing, to train the next generation of scientists.


Research Foci


Ongoing Clinical Studies

Expandable List

Funder: Canadian Institutes of Health Research

Description: This study aims to evaluate the benefit of low-level laser therapy for patients with chronic refractory constipation or fecal incontinence related to symptoms and autonomic dysfunction Contact info: Principal investigator: Dr. Jihong Chen (

Coordinator: Lijun Liu / 905-5259140 x 22585

Site: McMaster University Medical Centre, room HSC-3N5C

Study Funding Source:

Canadian Institutes of Health Research (CIHR) IMAGINE SPOR-Network Incubator Research Grant

Description: Most patients suffering from irritable bowel syndrome (IBS) report that ingestion of certain foods is a major trigger of symptoms, but the reason is unclear. Previous studies have shown that foods containing poorly absorbed carbohydrates (FODMAPs) are fermented by the bacteria in our bowels and these cause symptoms in some, but not all patients. Gut bacteria are capable of producing various products, such as histamine, that may be related to IBS symptoms. Our recent data suggest that consumption of FODMAPs promotes production of bacterial histamine.

What the study involves:

  • 6 weeks on a low-FODMAP diet
  • 3 interventions consisting of High- or Low-FODMAP drinks along with probiotics or placebo capsules.
  • Food diary
  • 6 stool samples
  • 6 urine samples

 Eligible participant descriptors:

  • Age 18-75
  • IBS diagnosis (as diagnosed by your physician)
  • Previous improvement of IBS symptoms when excluding certain foods


You will be compensated for your time at each study visit.

What are the challenges?

The challenges consist of 5 days of probiotics or placebo and 3 days of high- or low-FODMAP drinks along with L-histidine amino acid supplements.

How long are each of the visits?

30 – 60min

How will my samples be used?

  • Questionnaires: To assess any changes in your physical and psychological symptoms
  • Food Diary: To quantify FODMAP intake.
  • Blood Samples: To assess circulating chemicals in the blood which change the behavior of the gut.
  • Urine Samples:  To assess the chemicals in the urine.
  • Stool Samples: To assess the nature of the bacteria, present in the stool, which change the behavior of the gut.


Dr. Premysl Bercik, Caroline Seiler (PhD Candidate),

This study was approved by the Hamilton Integrated Research Ethics Board (#8342).

Title: Application of new technology for real-time tracking of dietary intake, physical activity, sleep and symptoms in IBD patients: a feasibility study

Funder: Farncombe Innovation Grant

Description: This is a feasibility study to test new remote tracking technologies in patients with Inflammatory Bowel Disease. Dietary intake and real-time symptoms will be tracked using the mobile applications Keenoa and Zamplo, respectively. Moreover, we will test the wearable Oura ring to track the patient’s physical activity, sleep patterns and heart health parameters. The study will last 3 months, and the outcomes of interest are related to the quality of the data collected and the overall participant’s experience using the tools.

Contact: PI – Dr. David Armstrong, Study Coordinator – Pedro Miranda (

Funding: Hamilton Health Sciences New Investigator Fund, Hamilton Academic Health Sciences Organization (HAHSO) AFP Innovation Grant

Collaborators: Kelly Grzywacz (CHU-Ste Justine)


Status: Recruitment Closed

Description: Multicentre randomized-controlled trial of the role of oral and colonic/rectal delivery of fecal microbiota transplant over a 6-week period in patients with active pediatric Crohn’s disease. Biweekly delivery of FMT or methylcellulose oral capsules / normal saline rectal irrigation/ enemas, followed by observation period up to 24 weeks.

Funding: Canadian Institutes of Health Research (CIHR) Project Grant

Collaborators: Katherine Morrison, Gregory Steinberg, Gita Wahi, Zubin Punthakee, et al

Design: Randomized Controlled Trial

Status: Actively Enrolling

Anticipated Project End Date: July, 2027


Funding: Hamilton Health Sciences Foundation

Collaborators: Paul Moayyedi, Michael Surette

Status: Recruitment (pediatric stool donors) ongoing


Anticipated Project End Date: n/a

Description: First Canadian pediatric FMT stool bank providing access to pediatric patients with recurrent C. difficile infection to healthy donor FMT. All FMT donors are <18yo, and recipients/donors are age-matched. Children across Canada are eligible to receive therapy, and only children with Health Canada approved indications (recurrent/refractory C. difficile infection) are eligible for participation. At this time, this program is not being used to support any research-based activities.

Funding: In-Kind


Status: Recruitment Closed

Collaborators: Philip Britz-McKibbin

Description: We have conducted a cohort study of patients with pediatric Crohn’s disease, ulcerative colitis, and functional gastrointestinal disorders (controls) to assess unique urine metabolomics changes associated with each pediatric IBD phenotype and non-colitis controls. This study follows from earlier studies that showed robust urine metabolomics signatures that accurately differentiate between pediatric CD, UC, and may enable monitoring of adherence to nutritional therapies

PI: Dr Neeraj Narula
Dr. Paul Moayyedi, McMaster University
Dr. John Marshall, McMaster University
Dr. Dina Kao, University of Alberta
Dr. Charles Bernstein, University of Manitoba
Dr. Jeffrey McCurdy, University of Ottawa

Description: The study objectives are to learn about a) if alteration of the microbiota through fecal microbiota transplantation in pouchitis helps improve disease symptoms and improve endoscopic inflammation; and b) understand the changes that occur in the gut bacteria during fecal transplantation.  This is a randomized placebo-controlled trial involving multiple centres recruiting patients to evaluate whether fecal microbiota transplantation once weekly for six weeks increases the remission rate compared to placebo in patients with active pouchitis. After participating in the six-week trial of FMT or placebo intervention once weekly, all patients are offered open-label FMT weekly by enema for six weeks.  Targets:Anticipated sample size: 50
Anticipated end: December 1, 2024
Contact: Additional sites are welcome!

PI: Dr. Neeraj Narula, McMaster University
Dr. Paul Moayyedi, McMaster University
Dr. John Marshall, McMaster University
Description:The study objective is to learn whether alteration of the microbiota through fecal microbiota transplantation in ulcerative colitis helps improve disease symptoms and improve endoscopic inflammation more often and quicker when used in combination with vedolizumab as expected with vedolizumab alone.This is an open label trial of patients with prior biologic failure who are initiating vedolizumab treatment for UC.  Fecal microbiota transplantation once weekly for six weeks is offered concurrently for induction therapy when initiating vedolizumab. Participating SitesMcMaster University Medical Centre/Hamilton Health Sciences Centre, ON. Anticipated sample size: 10
Start: April 1, 2019.

Anticipated end: December 1, 2023
Contact: :

PI:  Dr. Smita Halder

Funder:  Index Pharmaceuticals

Contact Study Nurse:  Mitzi Lawrence,  905-525-9140 ext 20601

Angela Wesley

Description: The study will compare the safety and efficacy of an investigational medication, called cobitolimod, with a placebo in patients with moderate to severe active left-sided UC. Eligible participants will be randomly assigned in a 1:1:1 allocation to receive either cobitolimod or placebo via rectal enema every third week. The study will last up to 52 weeks (excluding screening) and involve 440 participants in around 200 study centers across the world. As an Investigator of the CONCLUDE Study, I invite you to consider referring patients who may qualify for participation. We are currently recruiting patients who:

Are ?18 years of age
Have been diagnosed with UC for ?3 months  Have moderately to severely active left-sided UC, as determined by a Modified Mayo score of 6 to 9
Have demonstrated an inadequate response, loss of response, or intolerance to at least one of the following treatments: oral GCS, AZA/6-MP, Biologics, JAK-inhibitors, or other approved advanced therapies for UC.

PI:  Dr. Smita Halder

Investigator Initiated Study

Contact Study Nurse:  Mitzi Lawrence  905-525-9140 ext 20601

Angela Wesley

Description: The primary objective of this trial is to determine whether, in subjects with moderately to severely active UC, treating to achieve a target of corticosteroid-free symptomatic + endoscopic + histological remission is superior to a treatment target of corticosteroid-free symptomatic remission, with regards to a primary endpoint of time to UC-related complication within up to 80 weeks of follow-up after achieving target. Treatment algorithms will feature the use of Vedolizumab after certain key assessment points.  A key premise is that vedolizumab has a favorable safety profile and can be safely and effectively used to treat subjects who are in symptomatic remission but who have not attained endoscopic or histological remission. They will receive IV Vedo for up to a year and if they are doing well will have the option for a second year on IV or s/c Vedo.

Title: Application of new technology for real-time tracking of dietary intake, physical activity, sleep and symptoms in IBD patients: a feasibility study

Funder: Farncombe Innovation Grant

Description: This is a feasibility study to test new remote tracking technologies in patients with Inflammatory Bowel Disease. Dietary intake and real-time symptoms will be tracked using the mobile applications Keenoa and Zamplo, respectively. Moreover, we will test the wearable Oura ring to track the patient’s physical activity, sleep patterns and heart health parameters. The study will last 3 months, and the outcomes of interest are related to the quality of the data collected and the overall participant’s experience using the tools.
Contact: PI – Dr. David Armstrong, Study Coordinator – Pedro Miranda (

 Title – A Phase 2b, Randomized, Double-Blind, Placebo-Controlled, Parallel- Group Study to Evaluate the Efficacy and Safety of PRV-015 in Adult Patients with Non-Responsive Celiac Disease as an Adjunct to a Gluten-free Diet

Funder – Provention Bio, Inc.

Description– A subset of patients with Celiac Disease displays persistent symptoms and laboratory abnormalities, despite following a strict gluten-free diet – the only available treatment for the disease. The causes for non-responsive celiac disease (NRCD) are unknown, and the lack of therapeutical alternatives makes this group of patients highly vulnerable. A new drug called PRV-015 – a monoclonal antibody that blocks interleukin 15 (IL-15) – has been shown to reduce intestinal inflammation and improve clinical symptoms induced by gluten consumption in celiac disease. This study aims to learn about the safety and effectiveness of PRV-015 as a treatment for NRCD patients.

Contact info:

PI – Dr. Maria Ines Pinto-Sanchez

Study Coordinator – Mark Khaouli (Postdoctoral Fellow)

Lab Website –


Title: A randomized controlled trial to evaluate the effect of late versus early introduction of gluten-free oats on symptomatic, serologic and disease activity in patients with newly diagnosed celiac disease.
Funder:  TBD
Description: Currently the only treatment for celiac disease is a gluten-free diet. Oats are safe for most people with celiac disease, provided they are pure, uncontaminated by gluten. Oats are often contaminated with gluten through cross-contamination with wheat, rye, barley due to agricultural practices, even some brands labelled as gluten-free. Furthermore, many patients remain symptomatic despite adhering to a gluten-free diet for different reasons, and concerns have been raised over whether introduction of oats to a gluten-free diet may contribute to persistent symptoms. Therefore, some experts recommend delaying introduction of gluten-free oats at the moment of diagnosis despite their highly nutritious composition.

Contact info:

Dr. Maria Ines Pinto-Sanchez (PI)

Jedid-Jah Blom, RD (Coordinator)

Shilpa Tandon:

Title: Zinc Supplementation Compared to a Zinc Diet to Treat Zinc Deficiency in Celiac Disease: A Pilot Study

Description: Zinc deficiency is highly prevalent in the celiac population and there is a need for exploring dietary treatment to improve this nutritional deficiency. Currently, the only treatment for zinc deficiency is through zinc supplementation which may have gastrointestinal side effects and inhibit the absorption of other minerals. This study aims to explore the feasibility of implementing zinc supplementation vs. a zinc-optimized gluten-free diet to treat low zinc. This six-month trial is open to adult patients with celiac disease, who have been on a gluten-free diet for at least 6 months and have low zinc.


Hamilton Academic Health Sciences Organization (HAHSO) Innovation Grants, Canadian Institue of Health Research (CIHR).

Contact Information:

Principle Investigator: Maria Ines Pinto-Sanchez

Coordinator: Shilpa Tandon (

Site: McMaster University Medical Center


Study Title: Restoration of impaired microbiota-mediated aryl hydrocarbon receptor signaling in celiac disease by oral tryptophan supplementation: an exploratory study, HiREB #14582, #NCT05576038.

Funder: Weston Family Foundation

Study Description:

Celiac disease has a significant health, social and economic burden, highlighting the need for adjuvant therapies to a gluten free diet (GFD). This study is a double-blind randomized, placebo-controlled study which aims to access the efficacy of tryptophan supplementation in improving celiac symptoms, modifying the gut microbiota composition, and increasing Aryl Hydrocarbon Receptor (AhR) activity in active celiac patients who are non-responsive to a gluten free diet.

The study involves: 

  • 3 weeks intervention involving tryptophan or placebo capsules
  • 3 physical visits at McMaster University
  • Urine, stool, and blood samples at baseline & post intervention
  • Endoscopy procedure at baseline & post-intervention
  • Symptom questionnaires
  • Food diary

Study Eligibility Criteria:

  • Biopsy and serology diagnosed celiac disease
  • Persistent celiac disease symptoms despite being on a GFD for at least 12 months.
  • Aged between 18 and 75 years old.
  • No other GI conditions (e.g., IBD)


Each study participant will be compensated for participation (total $250 + parking)

Contact Information:

Principal Investigators: Dr. David Armstrong, Dr. Elena Verdu

Study Co-ordinators: Utkarshini Kirtikar (PhD Candidate) , Gaston Rueda


Site: McMaster University

Lab Website:

Funder: HAHSO AFP Innovation Grant

Description: FiNCH is a pilot study to assess the feasibility of undertaking a prospective cohort study to answer the research question of the impact of cannabis exposure in utero on neurodevelopmental outcomes in babies and toddlers. FiNCH aims to investigate the components of a prospective cohort study, including recruitment, enrollment, follow-up, engagement, and data completion, as well as any notable developmental differences in babies exposed and not exposed to cannabis in utero.

Contact info:

Co-PI: Dr. Elyanne Ratcliffe and Dr. Lucy Giglia

Research Coordinators: Leticia Hernandez-Galan (Clinical Project) and Rochelle Maurice (Participant Focus Groups)


Description: The purpose of this study is to assess the effect of probiotic bacterium Bifidobacterium longum NCC3001 on gastrointestinal and psychological symptoms of IBS. Beneficial effects of this probiotic bacterium on symptoms of depression and brain function was previously demonstrated in a small pilot study performed at McMaster University. This new study aims to validate and confirm these findings. Bifidobacterium longum NCC3001 will be provided in a powder form to be mixed with water or certain types of milk, and taken once a day for 6 weeks. In this trial, you will receive BL NCC3001or placebo. A placebo looks like the probiotic product, but it does not contain the bacteria. A placebo is used in some trials so that the trial investigator can see if the effects are due to the trial product.

Eligible participants:
age 18-70; IBS diagnosis (as diagnosed by your physician); Symptoms of anxiety and/or depression. Study Duration:14 weeks (Hospital visits: 4; phone call visit: 1). Compensation:for your time in the study visit and parking expenses in the hospital will be covered.

Researchers: Dr. Premysl Bercik (Principal Investigator), Dr. Andrea Nardelli (Study Coordinator), Dr. Gaston Rueda (study coordinator)
Study Funding Source:Nestlé Health Science,Vevey, Switzerland
Contact: Andrea Nardelli –

Description: This study is being conducted to understand the behavior and influence of intestinal microbiota in different gastrointestinal diseases, such as Celiac Disease, Irritable bowel syndrome (IBS), Crohn´s disease and Ulcerative colitis.

Eligibility criteria:

– Adult patients between 18-75 years old.

– Diagnosed with one of the following diseases:

– Celiac disease, with active symptoms and/or following a gluten containing diet

– Irritable bowel syndrome (IBS).

– Crohn’s disease or Ulcerative colitis with active symptoms.

-Healthy volunteers

What will the study measure?

  • Gastrointestinal symptoms, general health and wellbeing scores, using questionnaires.
  • If diagnosis of celiac disease: presence of celiac disease genes, assessed by a genetic test., as well as specific markers for celiac disease.

Samples collected:

-One stool sample

-Blood sample (optional)

-Biopsies (optional) if you are scheduled for endoscopy

Duration of the study:

This research study lasts the same time as your regular endoscopy appointment.

Will there be a compensation to participate?

We will offer compensation, as well as parking ticket for offering your time participating in the study.

Contact us to know further information about the study:

Gaston Rueda, MD – Research Fellow:

Utkarshini Kirtikar, PhD Candidate:

The study has been approved by Hamilton Integrated Research Ethics Board  – Study #:15311

Crohn’s Inflammation Microbial Proteolytic Activity: CIMPA)

Funder: Weston Family Foundation

Study description:

Crohn’s disease (CD), characterized by discontinuous intestinal injury and inflammation, has been associated with changes in the luminal microbiota and impaired barrier function. Our previous study showed that patients with active Crohn’s disease have different bacteria from patients with inactive Crohn’s disease (in remission) and healthy people. We also showed that inflamed areas are leaky and are associated with bacteria that appear to come into closer contact with the bowel lining. It is not clear why some areas are affected, and other areas are not. The patchy nature of Crohn’s disease could be due to bacteria or other factors such as digestive enzymes that break down proteins leading to intestinal damage or greater inflammation. We plan to explore further our previous results by identifying bacteria more precisely and studying whether or not they produce enzymes that can degrade the gut lining. We will conduct this study in patients with active Crohn’s disease, by collecting samples from the gut lining (biopsies and brushings) to compare the activity of the enzymes in inflamed areas and non-inflamed areas

The Study involves:

  • Clinically prescribed colonoscopy procedure
  • Clinical symptom questionnaires assessing disease activity
  • Brushing and biopsy samples
  • Stool sample

Study eligibility criteria:

  • Confirmed diagnosis of Crohn’s disease
  • Patients experiencing active symptoms of Crohn’s disease


-$50 Amazon gift card and parking pass on the day of colonoscopy procedure

Contact information 

Principal Investigators: Dr. David Armstrong, Dr. Elena Verdu

Study Coordinators: Janet Szeto (MSc. Student):; Dr. Gaston Rueda (research fellow):


McMaster University

Lab Website:


The study has been approved by Hamilton Integrated Research Ethics Board  – Study #: 7789