We are colonized by trillions of microorganisms, including bacteria and fungi, which inhabit the external and internal surfaces of our bodies. It is becoming increasingly evident that these microbes play an important role in regulating many aspects of host physiology, including the immune system. For example, the bacteria in the gut are critical for the development and function of the immune system, as germ-free mice have an underdeveloped intestinal immune system. In addition, perturbations to the populations of commensal bacteria have been linked to autoimmunity and chronic inflammatory conditions, such as inflammatory bowel diseases and metabolic syndrome.
