There is a growing appreciation of the relationship between gut microbiota, and the host in maintaining homeostasis in health and predisposing to disease. Bacterial colonisation of the gut plays a major role in postnatal development and maturation of key systems that have the capacity to influence central nervous system (CNS) programming and signaling, including the immune and endocrine systems. Individually, these systems have been implicated in the neuropathology of many CNS disorders and collectively they form an important bidirectional pathway of communication between the microbiota and the brain in health and disease. Over the past 5 years substantial advances have been made in linking alterations in microbiota to brain development and even behaviour and the concept of a microbiota-gut brain axis has emerged. Animal models have been essential in moving forward this frontier research area. In order to assess such a role we use studies involving, germ free mice and early-life microbiota manipulations and finally probiotic administration in adulthood. We assess neurochemical, molecular and behavioural effects following these manipulations. Our data show that the gut microbiota is essential for normal stress, antidepressant and anxiety responses. Moreover, microbiota is essential for both social cognition and visceral pain. Finally, there are critical time-windows early in life when the effects of microbiota on brain and behaviour appear to be more potent. Our data also demonstrates that these effects may be mediated via the vagus nerve, spinal cord, or neuroendocrine systems. Such data offer the enticing proposition that specific modulation of the enteric microbiota by dietary means may be a useful "psychobiotic"-based strategy for stress-related neurodevelopmental disorders and possibly even neurodegenerative processes.