Strain-level heterogeneity in Vibrio parahaemolyticus limits the correspondence between planktonic gene expression and surface-associated phenotypes

Background Vibrio (V.) parahaemolyticus is a ubiquitous marine bacterium that persists in dynamic marine environments through adaptive behaviors including motility and biofilm formation. However, the extent to which phenotypic variability among strains relates to baseline transcriptional states under standardized laboratory conditions remains unclear. In this study, a strain-resolved analysis of 26 V. parahaemolyticus strains comprising clinical reference and seafood-associated environmental strains was conducted. Phenotypic assays were conducted at 25°C, 30°C, and 37°C, while targeted genetic screening and transcriptional profiling of 35 motility-, biofilm- and virulence-associated genes were performed during exponential growth at 30°C under standardized planktonic growth conditions. Results Motility increased with temperature and incubation time, while biofilm formation was primarily temperature dependent but showed substantial variability between individual strains. Mixed-effects modeling and intraclass correlation analysis demonstrated that a large proportion of phenotypic variance was attributable to strain identity rather than isolate origin. Gene-content screening revealed conserved core components alongside variable accessory loci across strains. Transcriptional profiling revealed extensive heterogeneity among strains and distinct expression tendencies between isolate origins, including elevated flgL , gbpA and oxyR expression in clinical reference strains and increased opaR , mfpA , vp0962 , tssL2 and scvE expression in several environmental isolates. However, these baseline transcriptional patterns did not consistently explain differences in mature biofilm biomass measured in the crystal-violet assay. Conclusions These results demonstrate that strain identity is a major determinant of both phenotypic and transcriptional variation in V. parahaemolyticus. Baseline transcriptional measurements obtained under standardized growth conditions captured regulatory diversity but were not sufficient to account for phenotypic variability across strains. These findings highlight the importance of strain-resolved analyses when interpreting functional traits within bacterial species.