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Irritable Bowel Syndrome (IBS) is the most common gastrointestinal disorder which affects approximately 4% of the population worldwide, according to the Rome IV criteria. It is characterized by abdominal pain and altered bowel movements in the absence of relevant structural abnormalities. The diagnosis of IBS is based on symptom profiles as no biomarkers exist to guide diagnosis or treatment stratification. Accumulating data suggests that altered gut microbiota and chronic low-grade inflammation play important roles in genesis of IBS. However, the mechanisms are unclear. My thesis first addresses the hypothesis that changes in fecal β-defensin secretion reflect compositional changes in the intestinal microbiota. This was driven by the understanding that compositional changes in the microbiota (“dysbiosis”) may play a role in the expression of IBS, and that a marker of these will identify those patients who might benefit from microbiota-directed therapies. I used a murine model in which I disrupted the microbiota using interventions relevant to the natural history of IBS i.e., antibiotics, stress, or dietary changes. I showed that experimentally induced compositional changes in the microbiota, with the exception of stress, altered the secretion of fecal β-defensin. My study indicates that monitoring fecal β-defensin over time identifies compositional changes in microbiota. I next investigated mechanisms and treatment options for a recently recognized variant of post-infectious IBS (PI-IBS) developed following antibiotic treatment in patients recovering from Clostridioides difficile infection (CDI). I refer to this variant as post-CDI gut dysfunction. I used a humanized mouse model in which germ-free mice were colonized with fecal microbiota from patients with post-CDI gut dysfunction, or age and sex matched healthy controls. I found that mice colonized with microbiota from a patient with severe slow transit constipation post-CDI reproduced the donor phenotype. Mice developed slow colonic transit due to macrophage mediated damage to the interstitial cells of Cajal (ICC) that maintain normal motility. These changes were reversed after fecal microbiota transplantation (FMT) from healthy donor mice thus confirming that the post-CDI gut dysfunction is microbiota driven. Similar results were obtained in a patient with slow transit constipation without a history of infection. My findings prompted me to next evaluate the therapeutic potential of microbiota-directed dietary therapies. I chose psyllium, the flavonoid quercetin, and pectin based on their demonstrated ability to alter microbiota composition. Psyllium and pectin each normalized colonic transit, and this was accompanied by an alteration in macrophages morphology, restoration of the disrupted ICC network and an increase in short chain fatty acids production. My results demonstrate the importance of a dysbiotic microbiota in this post infectious- IBS (PI-IBS) variant and, identify two potentially useful dietary based therapeutic approaches to improve gut dysfunction in these and similar patients. If findings from my thesis are confirmed in humans, it could offer novel approaches for identifying those IBS patients who might benefit from microbiota-directed therapeutics. / Thesis / Candidate in Philosophy