We used the binary squid-vibrio light-organ symbiosis as a natural model to study the hour-by-hour dialogue between bacterial cells and animal epithelia during the establishment of a persistent association. Although Vibrio fischeri cells represent less than 0.1% of the bacterioplankton, this bacterium in the only species able to efficiently colonize the light organ of the Hawaiian bobtail squid Euprymna scolopes (Nyholm & McFall-Ngai, 2004). Recent analyses of the process have provided evidence that, at 3 h, the animal is responding to only ~3-4 symbiont cells adhering to the superficial ciliated epithelium (Altura et al., 2013), where V. fischeri cells gather during their initial harvesting from the seawater. In this study, we deciphered early molecular events in the host response by monitoring the light-organ transcriptome. Using next-generation sequencing (454 technology, Life Sciences, Brandford, USA), we compared whole light-organ gene expression of squid just after hatching, squid exposed for 3 h to 106 environmental bacteria with (symbiotic) or without (aposymbiotic) the addition of ~5,000 V. fischeri cells.