There has been an increasing and intense interest in the role that gut bacteria play in maintaining the health of the host. Gut microbiota have an estimated mass of 1-2 kg, number 100 trillion and together possess 100 times the number of genes in the human genome. In addition to their well-established role in the postnatal maturation of the mammalian immune system, they are also responsible for an enormous array of metabolic activities that include effects on the digestion of food and the production of a host of biologically active substances. Moreover, it is also rapidly becoming apparent that the gut microbiome plays a major role in the development and regulation of neuroendocrine systems such as the hypothalamic-pituitary-adrenal axis, a central integrative system crucial for the successful physiological adaptation of the organism to stress. In fact, our previous study on gnotobiotic mice demonstrated that exposure to gut microbes is a postnatal environmental determinant that regulates the development of the hypothalamic-pituitary-adrenal axis stress response and also the set point for this axis.