Animal-microbe symbioses are fundamental to animal physiology but the precise nature of molecular exchange between partners remains largely elusive. The mutualistic association between the Hawaiian bobtail squid, Euprymna scolopes and its luminous bacterium Vibrio fischeri is a powerful model to investigate interactions between the host and its microbial symbiont. In this system, bacteria are acquired via horizontal transmission within hours of hatching and colonize the crypt epithelium in the light organ as an extracellular partnership. Here, we study the transfer and localization of V. fischeri products into squid host cells during the initiation of symbiosis. To address this question, we exposed juvenile squids to either 106 CFU/ml of 15N-enriched wild-type V. fischeri strain ES114 or to 50 µg/ml 15N-labeled outer membrane vesicles (OMVs) extracted from the bacteria, as the latter are known to play a key role in signaling between symbiotic partners. Thin sections of host tissues were then analyzed with state of the art correlative transmission electron microscopy and quantitative ion microprobe isotopic imaging (NanoSIMS; nano-scale secondary ion mass spectrometry) techniques to visualize and quantify the incorporation and accumulation of 15N-isotopically labeled bacterial products within the squid host tissue at cellular and subcellular levels. All nuclei of epithelial cells in the light organ were heterogeneously enriched in 15N with hotspots localized in the nucleolus as early as 1 and 2 h following inoculation with either OMVs or intact bacteria, respectively. Accumulation of 15N was also observed in distant epithelial tissues of the light organ, where symbionts do not occur. Closer examination revealed labeling was concentrated in the euchromatin regions of the nucleus, where DNA is often under active transcription. We further analyzed other tissue types of the squid host and found that nuclear 15N-enrichment was not restricted to the epithelial cells of the light organ. Taken together, our results show that V. fischeri-derived molecules target the host nucleus, a strategy well known for many pathogenic bacteria. We are now exploring the species-specificity of these labeling patterns using other bacterial species. The unique link between spatial and functional information provided by the NanoSIMS technology has the potential to open a new frontier for the study of communication between host and symbiont.