Converging arguments suggest a role of micro-organisms in the pathogenesis of inflammatory bowel disease (IBD) in humans and in animal models (Table 1). This chapter critically reviews these arguments and their clinical implications. The role of micro-organisms has been experimentally studied by suppressing micro-organisms from the microbiota (using germfree or gnotoxenic animals or antibiotics), introducing in the intestine new microorganisms or microbial components (e.g. probiotics, CpG-DNA) or increasing the relative proportions of certain endogenous bacteria (using prebiotics for example). The problem has also been approached using knockout animals with modified receptors to microbial signals. The chapter discusses observations made in humans, and highlights some gaps in the present knowledge and theories.
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