The gastrointestinal tract is a biologically diverse and complicated system which carries out essential physiological functions that support human health, while at the same time maintaining itself as an isolated environment to prevent infection and systemic disease. To maintain homeostasis in the gut, communication between the host and residing microbial communities must occur to identify and eliminate potential pathogens which could colonize and cause damage through aggressive pro-inflammatory responses by the mucosal immune system. To prevent such events, a number of host and bacterial-mediated mechanisms are utilized to monitor the environment and initiate appropriate immune responses to invading pathogens. An essential component of this communication process between gastrointestinal microflora and the host involves distinguishing indigenous species from pathogens through ligand-receptor interactions which lead to various signaling events in host cells. Such events generally result in the development of mucosal immunity and immunological tolerance. While these signaling pathways provide a highly effective means of communication between the gut microflora and the host, pathogens have developed mechanisms to manipulate these pathways to evade detection by the immune system to persist and cause disease. These adaptations include cell surface modifications and the expression of various virulence factors in response to different immunological and hormonal components produced by the host.