Electronic Thesis and Dissertation Repository

Thesis Format

Monograph

Degree

Master of Science

Program

Microbiology and Immunology

Supervisor

Burton, Jeremy P.

Affiliation

Lawson Health Research Institute, St. Joseph's Hospital, Canadian Centre for Human Microbiome and Probiotics

2nd Supervisor

Silverman, Michael S.

Affiliation

London Health Science Center, St. Joseph's Hospital

Abstract

Historically used to treat Clostridioides difficile infection, fecal microbiota transplants (FMT) are now being tested to treat gut and systemic diseases, including (but not limited to) autoimmune, liver, and cardiovascular. Successful FMT relies on components within the donor sample, which may have specific conserved properties that vary greatly between individuals. Screening donors for potentially transmittable conditions is a well-established practice, however, screening material for the likeliness of a successful clinical outcome or finding the best match of material for patients has not been undertaken. We hypothesized an optimal donor may be selected by high-throughput in vitro screening of fecal microbiota. The objective was to (1) develop a high-throughput in vitro approach to assess the microbiome of a FMT population; and (2) to utilize a test population to demonstrate the developed approach using five protected FMT donors and five atherosclerosis patients. 16S rRNA gene microbiota sequencing was undertaken on samples before and after treatment with toxic compounds [trimethylamine, p-cresol] or their precursors. An intestinal barrier integrity model assessed how toxin components impacted permeability. The modelling represents a reproducible, straightforward approach for assessing a large sample population given treatment under controlled conditions. This is important because pinpointing successful attributes is difficult, given the influence of lengthy experimental times, small sample volume or the influence of confounding factors. Considering donors individually, results revealed specific characteristics towards less trimethylamine-producing capabilities and potential barrier-promoting qualities in two of the protected donors. This high-throughput approach may be useful to optimize the efficacy of future FMT therapy.

Summary for Lay Audience

Fecal microbiota transplant (FMT) is a term given to the transfer of stool material from one person to another. This material can be delivered via tubes into the stomach or colon or by putting the material in a capsule that is then swallowed. FMT has been shown to cure some chronic intestinal infections and is being tested for other ailments. The goal is to repopulate the diseased gut with microbes in a healthy donor’s feces. While screening donors for potentially transmittable conditions has become a well-established practice, the screening of material for the likeliness of a successful clinical outcome or finding the best match of material for patients with other diseases is not undertaken. Overwhelming evidence suggests that the key to a successful FMT relies on the components (i.e., microbes and compounds in the stool). However, it is difficult and time-consuming to take samples from donors and test them to see if they are a potential “good fit” for the target patient’s illness. The aim of this thesis was to develop and test a high-throughput approach to evaluate the suitability of donor stool when they were challenged with toxic dietary precursors. For this, stool from five healthy donors or atherosclerosis patients was exposed to well-known dietary factors and grown for 24 hours in 96-well plate format. The composition of the resulting microbial community was assessed with DNA sequencing, and ability of the bacteria and compounds to affect intestinal barrier cells was tested with microscopic imaging. This high-throughput model could potentially improve patient outcomes by allowing many stools to be screened over a short experimental period to determine the optimal choice for recipient health.

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