Inflammatory bowel disease (IBD), a chronic and relapsing intestinal inflammation, affects about 3.6 million individuals in the United States and Europe. However, the etiology of IBD is still unknown and likely involves complex interactions among genetic susceptibility, gut bacteria flora and host immune system. The characterization of mucosal gene expression profiles in different IBD animal models will potentially provide molecular insights into the mechanisms that initiate, perpetuate or ameliorate IBD development. In this dissertation, alteration of mucosal gene expression profiles induced by different agents including a mild bacterial pathogen, Helicobacter bilis or an anti-inflammatory drug, hypoxoside were characterized. The association between differential mucosal gene expression and modulation of colitis development was studied.;Using microarray analysis, changes in mucosal gene expression potentially contributing to an increased susceptibility to colitis were evaluated in gnotobiotic C3H mice at 15, 30 and 45 days following H. bilis colonization. Our results showed that H. bilis colonization induced marked upregulation of genes associated with protein metabolism, immune responses, and downregulation of genes associated with fatty acid metabolism and detoxification In addition to the immune response-associated genes (e.g., interferon-inducible genes), genes associated with mucosal homeostasis, such as glycoprotein synthesis and detoxification, might potentially lead to the increased susceptibility to colitis induced by H. bilis colonization of gnotobiotic mice.;To directly determine if H. bilis colonization increased the susceptibility to DSS-induced colitis, mice were colonized with H. bilis for 6 weeks and then treated with a low dose of dextran sodium sulfate (DSS, 1.5 %) for five days followed by a four day restitution period. Our results demonstrated that H. bilis colonization increased the severity of colitis induced by DSS. Mucosal gene expression profiles showed that mice colonized with H. bilis plus treated with DSS had significant increases in the expression levels of genes associated with activation of immune cells (e.g., Cd28, Tnfsf13b/Baff) and recruitment of immune cell including the adhesive molecules(e.g., Itgb2/Cd18, Itgam/Cd11b and ItagL/Cd11a), chemokines/chemokine receptors(e.g., Ccl8, Ccr5 and Ccr10). Consistently, increased infiltration and/or proliferation of T cells, B cells and macrophages in the intestine mucosa and/or MLN were observed in mice treated with H. bilis + DSS in comparison to mice treated with DSS alone. The upregulation of the cell activation markers (e.g., Cd28, Tnfsf13b/BAFF ), pro-inflammatory cytokines IL17, and significant increased antibody responses to H. bilis and altered Schadler's flora (ASF) suggest the T cell and B cell were activated. Surprisingly, neutrophil infiltration was not observed. In addition, the detoxification-associated genes Cyp4b1 and Ugt8a were found to be downregulated in mice treated with H. bilis + DSS in comparison to mice treated with DSS alone.;Lastly, another IBD model, Brachyspira hyodysenteriae - induced colitis was used to assess effects of a plant extract hypoxoside on the colitis development. Our results showed that oral treatment of hypoxoside could ameliorate the colitis induced by B. hyodysenteriae infection, which was demonstrated by the reduced gross and histological lesions, reversed weight loss. The anti-inflammatory effects of hypoxoside were suggested to be associated with the reduction of neutrophil infiltration, downregulation of genes involved in NF-kappaB signaling pathways and decrease in mucosal active NF-kappaB subunit p65 protein levels and epithelial cell proliferation, but not anti-microbial activity.;In summary, the studies in this dissertation identified some promising genes and signaling targets for IBD such as genes associated with detoxification, activation/recruitment of immune cells and activation of NF-kappaB pathways and might potentially contribute to the therapeutic intervention of IBD patients.