Immunological dysregulation is the cause of many non-infectious human diseases such
as autoimmunity, allergy and cancer. The gastrointestinal tract is the primary site
of interaction between the host immune system and microorganisms, both symbiotic and
pathogenic. In this Review we discuss findings indicating that developmental aspects
of the adaptive immune system are influenced by bacterial colonization of the gut.
We also highlight the molecular pathways that mediate host-symbiont interactions that
regulate proper immune function. Finally, we present recent evidence to support that
disturbances in the bacterial microbiota result in dysregulation of adaptive immune
cells, and this may underlie disorders such as inflammatory bowel disease. This raises
the possibility that the mammalian immune system, which seems to be designed to control
microorganisms, is in fact controlled by microorganisms.