Strain Matters: Host Responses Reflect Symbiont Origin in the Squid-Vibrio Symbiosis

Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses. Overall design: Juvenile squid from the same clutch where exposed to 1 of 5 bacterial strains used in this study. Squid were considered part of the same clutch if their eggs were laid by the same parental pair at the same time and the hatchlings emerged synchronously. Clutch identity was tracked to account for genetic background in downstream analyses.