The exact mechanism of pathogenesis of inflammatory bowel disease (IBD) is not yet clear. However, a key role for intestinal bacteria in the development and maintenance of IBD is now well-accepted and has led to extensive efforts to characterize IBD patients’ gut microbiota composition. Nonetheless, few studies have examined intestinal microbial composition and host interactions in pediatric treatment-naïve IBD subjects. Using a multi-omic approach, we analyzed the gut microbiota-host interactions at the mucosal- luminal interface from two distinct colonic regions in a pediatric treatment-naïve cohort of Crohn’s disease (CD), ulcerative colitis (UC) and non-IBD control individuals. CD patients displayed a significant decrease in bacterial richness in the distal colon, as compared to controls. Significant changes in the microbial composition at different taxonomic levels were observed in IBD patients relative to controls, especially in the distal colon. IBD patients had an increased abundance of hydrogen sulfide (H2S) producers, including Veillonella (g), Streptococcus (g) and Fusobacterium (g), and a decreased abundance of butyrate producers such as Blautia (g), Lachnospiraceae (f) and Ruminococcus (g). IBD patients showed statistical differences in their metabolomic profile as compared to controls, with the majority of significant metabolites, such as pesticides, amino acids, bacterial-derived molecules and dipeptides, being increased in CD and UC subjects. An alteration of the gut microbiota composition was associated with an alteration of the host and bacteria metabolome in IBD subjects; notably, increase of taurine, mecarbam-f7 and oxazole positively correlated with H2S producers and negatively correlated with butyrate producers. Finally, microbial genes involved in oxidative stress response, virulence, iron uptake, storage and metabolism were upregulated in the proximal colon of IBD patients. Our findings provide information about the host-microbiota interactions in the context of IBD. Understanding the relationships between the host and his intestinal microbes could help to develop therapeutic strategies to treat IBD.

In the gastrointestinal (GI) tract, goblet cells are the major source of mucins, the main structural components of the mucus layer, which functions as the front line of innate defense. The GI tract contains trillions of commensal microbes, and these microbes can manipulate mucin production by activating different signalling cascades initiated by pattern recognition receptors (PRRs), including bacterial sensing Toll-like receptors (TLRs). In addition, sterile α motif pointed domain-containing ETS transcription factor (SPDEF) is a transcription factor that modulates goblet cell differentiation and positively regulates mucin production. During helminth infections, due to the co-existence of parasites and microbiota in close proximity of goblet cells in the gut, it is likely that helminth-microbiota interactions play an important role in mucin production. Indeed, goblet cell hyperplasia and increased mucin production are observed in many enteric helminth infections, including Trichuris muris, and these processes play key roles in host infection clearance. However, it should be noted that the role of microbiota within this axis is not yet understood. Here, we hypothesize T. muris-induced altered microbiota modulates goblet cell differentiation and mucin production via SPDEF-mediated transcriptional regulation and TLR2 signalling. C57BL/6 mice were gavaged with ~300 T. muris eggs. Mice were sacrificed 36 days post-infection. Microbiota from these T. muris-infected and non-infected mice were transferred into two groups of germ-free (GF) mice. Microbiota analysis revealed that treatments in both experiments (infection with T. muris and microbiota transfer from T. muris-infected mice into GF mice) significantly account for the among-sample variations in the composition of the gut microbiota between groups (p <= 0.001). In GF mice, transfer of T. muris-infected microbiota significantly increased goblet cell numbers and TLR2 expression as well as upregulated Muc2 expression compared to MSc Thesis –Yousefi Y; McMaster University – Medical Sciences v GF mice with non-infected microbiota. Antibiotic-treated (ABX-treated) TLR2 knockout (KO) mice after receiving microbiota from T. muris-infected mice showed significantly decreased expression of Muc2 and Muc5ac compared to ABX-treated wild-type (WT) mice receiving the same microbiota. To investigate whether SPDEF is a driving factor for Muc2 production in response to T. muris microbiota stimulation, we next transferred T. muris-infected microbiota into antibiotic-treated SPDEF KO and WT mice. We observed a slight, though not significant, the influence of SPDEF on the stimulation of mucin production by T. muris microbiota. These findings reveal important interactions among parasites, resident microbiota, and host in relation to goblet cell response in the gut. In addition, this study provides new information on TLR2-based innate signalling in the regulation of goblet cell biology and mucin productio / Thesis / Master of Science (MSc)