Electronic Thesis and Dissertation Repository

Thesis Format

Integrated Article


Doctor of Philosophy


Microbiology and Immunology


Burton, Jeremy P.

2nd Supervisor

Silverman, Michael



Fecal microbiota transplantation (FMT) is an emerging and effective therapy for the treatment of recurrent Clostridioides difficile infection. Members of the gut microbiome have been implicated in other diseases and FMT has been considered as a potential therapy. Two such conditions include non-alcoholic fatty liver disease (NAFLD) and multiple sclerosis (MS), both of which involve increased small intestinal permeability believed to contribute to the development and disease progression. One of the aims of this project was to determine if FMT could be safely used in patients with NAFLD and MS to improve health outcomes. Before starting the clinical studies, optimal ways of storing and preparing stool for FMT were investigated with a goal of reducing loss of viable bacteria due to sample collection, handling, and storage. Bacterial culture and next-generation sequencing techniques were utilized to assess the impact of processing and storage. With optimal procedures in place, which included storing samples as whole stool at -80 °C for up to 3 months, FMT donor screening was expanded to extend beyond transmissible diseases to include lifestyle factors, and personal/family history of disease. From this, only 5 of 46 healthy potential donors qualified, and they provided stool for patients with NAFLD (n=21) and MS (n=10). All FMT recipients with elevated small intestinal permeability, determined using the lactulose:mannitol permeability assay, improved following FMT. Microbiota engraftment was detected in some patients. The treatment was safe and well tolerated in all recipients. With NAFLD being the second leading cause of liver transplant in North America and MS having no cure, the use of FMT could potentially contribute to the quality of life and reduction in comorbidities. Since current treatment options for both diseases are not particularly effective, and the rates are increasing, new approaches are needed. The current findings provide a basis for larger studies with earlier intervention and longer follow-up. In summary, the improvement in intestinal barrier function with FMT shows a novel mechanism for this therapy, and one that has implications for many conditions associated with abnormal intestinal permeability.

Summary for Lay Audience

Fecal microbiota transplantation (FMT) is the transfer of stool from a healthy donor into the intestine of a diseased recipient. This requires stool samples to be homogenized and filtered, and the end product results in the transfer of microorganisms, including bacteria, viruses, archaea, and fungi, plus undigested food and fibre, and host cells into the intestine of the recipient. FMT has effectively treated recurrent Clostridioides difficile infections that cause severe and prolonged diarrhea in patients, but a number of other conditions may also benefit from these transplants. The first goal of this thesis was to ensure that storage and handling of donor samples optimally retained the viability of bacteria, which are likely a necessary component of FMT to be effective. Selecting donors for FMT is not simple, as many healthy people may be carriers of infectious diseases and/or have a person/family history of disease that could be passed along by FMT. Surprisingly, only 1 in 10 healthy people qualified to be a stool donor using our criteria. Using fecal material from the selected donors, two clinical trials were undertaken, which was the second goal of this thesis. The purpose of these two studies was to treat patients with non-alcoholic fatty liver disease (NAFLD) and others with multiple sclerosis (MS). Both of these conditions share having a modified bacterial composition in the gut, compared to healthy people. In addition, both have abnormal gut barrier function or “leaky gut syndrome”, which means that the proteins that usually bind intestinal epithelial cells tightly together to stop microorganisms and small molecules from entering the bloodstream, are less prevalent and less effective. The administration of FMT restored gut barrier function in these studies. The diseases NAFLD and MS are examples of chronic illnesses that afflict people worldwide. While there are a number of therapies available for both diseases that seek to reduce the symptoms or treat disease, none are particularly efficient, and the rates of both these diseases are slowly increasing. As more successful FMT donors are characterized and FMT becomes more readily available, we may see expanded uses of this therapy for a variety of other conditions that have links to abnormal gut barrier function.