Alterations to the normal composition of our gut microbiota can result in disturbance of gut homeostasis. Opportunistic pathogens such as Clostridium difficile can profit from this environment, leading to colonisation of the gut. Clostridium difficile infection (CDI) is the most common healthcare associated disease in Ireland and with the incidence of occurrence on the rise. CDI represents a major health and economic burden to society. The primary pathogenesis of C.difficile has been attributed to its toxins; however the mechanisms that promote the initial colonisation and adherence of the pathogen still remain unclear. Glycosylation is an important factor affecting host-pathogen interactions in the gastrointestinal (GI) tract. We have, however discovered that the Surface Layer Proteins (SLPs) of C.difficile are not glycosylated and therefore do not contribute to host-pathogen interactions in this context. Subsequently, we examined the glycosylation profile on the surface of the colonic epithelium. To mimic the immunocompromised state of CDI patients, we used an in vivo model of antibiotic treatment to induce a susceptibility state in mice. Antibiotic treatment, and presumably the disturbance in microbiota composition, induced a protective state. This was evidenced by the glycan profile on the surface of the epithelium which was rich in fucose, a sugar known to promote the recovery of commensals, and depleted of sialic acid, an essential sugar used by C. difficile as an energy source. This protective state was further confirmed by the increased expression of anti-inflammatory cytokines IL-10 and TGFβ, and the increase in mucin and tight junction protein expression. We also observed decreased IL-22 expression, an essential cytokine for maintaining the integrity of the epithelium. For these reasons we propose that susceptibility to CDI is a result of compromised expression of IL-22 and the immunosuppressive environment induced by IL-10 and TGFβ that may delay the initial immune response to the pathogen. These findings are further supported by our observations of C. difficile infection in vivo where the increased sialic acid correlated with increased pathogen load and decreased IL-22 expression correlated with the excessive damage to the epithelial barrier. In this project we have identified novel mechanisms with an important role in CDI. These mechanisms may provide attractive targets for therapeutic intervention. Specifically, modulation of the fucose and sialic acid balance in the gut of immunocompromised patients may aid in commensal recovery and prevent C.difficile from thriving. Furthermore, enhancing IL-22 signaling may reinforce the integrity of the mucosal barrier in susceptibility state and infection.