All animals exist in lifelong relations with a complement of bacteria. Because of the ubiquity of these symbioses as well as the derived biomedical applications, the study of both beneficial and pathogenic host-microbe associations has long been established. The monospecific light organ association between the Hawaiian sepiolid squid Euprymnascolopes and the marine luminous bacterium Vibrio fischeri has been used as a experimental model for the study of the most common type of animal-bacterial interaction, i.e., the association of coevolved Gram-negative bacteria with the extracellular apical surfaces of polarized epithelia. A fundamental step for understanding the mechanisms of host-symbiont associations lies in defining the genetic components involved; specifically defining changes in host gene expression. The studies presented in this dissertation identify and characterize V. fischeri-induced changes in host gene expression at both the transcript and protein level.