Comprehensive gene expression profiling in Japanese flounder kidney after injection with two different formalin-killed pathogenic bacteria

•Oligomicroarray for Japanese flounder was developed.•A number of differentially regulated genes in the kidney after 2 types formalin-killed bacteria cells (FKC) were identified.•Edwardsiella tarda FKC differentially regulated much more genes than Streptococcus iniae FKC.

Pathogenic bacteria possess some components, that are recognized by the host immune receptors. Different components are recognized by distinct receptors, and thus it is speculated that these components may regulate different gene sets. To investigate the gene expression profiles regulated by different bacterial components in Japanese flounder Paralichthys olivaceus, Japanese flounder were intraperitoneally injected with formalin-killed bacterial cells (FKC) of Edwardsiella tarda and Streptococcus iniae. The numbers of differentially regulated genes were much larger in the fish injected with E. tarda than those with S. iniae. Comprehensive gene expression profiling showed that almost all of the genes differentially regulated by injections of E. tarda FKC were also differentially regulated by injections of S. iniae FKC. mRNA levels of inflammatory cytokines, including interleukin (IL)-1β, IL-8, interferon γ and tumor necrosis factor were upregulated in both of the injected groups. Each of these mRNAs except for IL-8 mRNA were also much higher in the E. tarda FKC injected group than in the S. iniae FKC injected group. Furthermore, mRNA levels of IL-6 were strongly up-regulated in the E. tarda FKC injected group. The E. tarda FKC might induce higher inflammatory responses than S. iniae FKC.