Human gastrointestinal (GI) tract inhabits huge amount of microorganisms which contribute to the immune response in the gut. An immune system disorder disease inflammatory bowel disease (IBD) was believed to be associated with several factors including gut bacteria, immunological responses, and genetic characteristic. Yet, the etiology of the IBD is not clear. Experiments on animal models and human samples had supported that commensal bacteria play an important role in the IBD pathogenesis. To better understand the pathogenesis of IBD, in this dissertation, bacteria rRNA gene populations were examined and associations related to the disease were analyzed in mouse model and human samples.

Evidences showed that several bacteria inculding Lachnospiraceae and Clostridium Ramosum were significant related to the colitis. It was not sure that those bacteria were the causal agents of the disorder in the immune system or their populations changed were the result of being targeted by the immune response disorder. Predominant bacteria in human mucosal tissue were examined in the disease sample comparing the healthy controls to address that the bacteria shift in the mucosal layer related to the IBD. Ruminococcus, also a member of Lachnospiraceae, was significant in the mucosal sample reduce in the disease subjects. A mucin-degrading bacteria Akkermansia was first found in this study related to the IBD. Faecalibacterium was only reduced specifically in Crohn's disease while keep similar lever in healthy control and Ulcerative colitis. Bacteria community two mouse model with different genetic background were investigate and different bacteria were presented in fecal and tissue samples.

Overall, consistent evidence in this study indicated bacteria levels of several species were reduced in the disease because of an immune response toward bacteria in this niche. This study provided a better clue to lead a greater understanding of the etiology of the IBD.