The human gut microbiota is a complex microbial ecosystem that contributes an important component towards the health of its host. This highly complex ecosystem has been underestimated in its importance until recently, when a realization of the enormous scope of gut microbiota function has been (and continues to be) revealed. One of the more striking of these discoveries is the finding that the gut microbiota and the brain are connected, and thus there is potential for the microbiota in the gut to influence behavior and mental health. In this short review, we outline the link between brain and gut microbiota and urge the reader to consider the gut microbiota as an ecosystem 'organ' rather than just as a collection of microbes filling a niche, using the hypothesized role of the gut microbiota in autism spectrum disorder to illustrate the concept.