The understanding of both mucosal immune defenses and intestinal inflammation requires some consideration of the interactions between the host and the intestinal commensal microbiota. Humans live in a bacterial world as microbes from the environment are in constant contact with the skin and have access to the mucosal compartments of the body. The latter can remain sterile or, in contrast, become colonized. Whereas the distal respiratory tract is sterile under physiological conditions, the distal gastrointestinal (GI) tract is heavily colonized. It has been calculated that there are more bacterial cells in the indigenous microbiota of the gut than own eucaryotic cells in the body (1).