To determine the specificity of amplification, analysis of the product melting curve was performed after the last cycle of each amplification.

Data was captured using Stratagene MxPro Mx3005P QPCR software. Table 1 Primers employed for Real-Time PCR Target gene Sequence (5′ to 3′) Reference or GenBank accession no. E. coli 16S rDNA F GCAGGCCTAACACATGCAAGTC [30]   R TGCTGCCTCCCGTAGGAGT   traD F ACGCCTCCTGTTCTGTTTCA [DQ401103.1]   R ATCAGCCCGGTCAGATTGT   virB11 F GGATCAACTCAGCCACAAAAA [DQ401103.1] EPZ004777 mw   R CACCGTTCCGCTGTTCTATT   virD4 F GTTGTCCAGGGTAGCAGCAG [DQ401103.1]   R TGGACAACCAGGAACAAGC   dfr16 F GACCTCATCCTCCGATGG [AJ517790.2]   R TGGTCGGAGATATGGGTATAGAA   C3 F CGGACGCTGACATCTACCAA [25]   R TCCAGGTCTGCTCTCCCAAG   IL-1β F ATCAAACCCCAATCCACAGAGT [25]   R GGCACTGAAGACACCACGTT   IL-8 F TGTTTTCCTGGCATTTCTGACC [24]   R TTTACAGTGTGGGCTTGGAGGG   TNF α F ACCAGGCCTTTTCTTCAGGT [10]   R TGCCCAGTCTGTCTCCTTCT   ef1α F TGCCTTCGTCCCAATTTCAG [24]   R TACCCTCCTTGCGCTCAATC   Amplification efficiencies were measured with the formula of E = 10(-1/slope)

by two-fold dilutions of cDNA as described by Bogerd et al. [31]. Expression of the plasmid target genes was normalized to dfr16, estimated to be the most stable endogenous reference gene on the plasmid for our in vivo experiment. The function describing the relationship between C t (threshold cycle) and x (log copy number) for dfr16 ALK inhibitor was: C t = -3.45x + 13.98; R 2 = 0.99. The comparative CT method [2ΔCT method] was used to determine the expression level of analyzed genes [30]. The resultant fold units were calculated by dividing the normalized expression values with the placebo treated controls. Expression of the zebrafish inflammatory and immune response related target genes was normalized against expression of the housekeeping gene elongation MycoClean Mycoplasma Removal Kit factor 1 alpha (ef1α) [24] in challenged fish relative

to sterile physiological saline solution intubated and placebo treated controls. For absolute quantification of the total bacterial population of the gut, standard curves of 16S rDNA copy number were constructed using a PCR product of the 16S rRNA gene of Escherichia coli. The Cyclosporin A functions describing the relationship between C t (threshold cycle) and x (log copy number) for total bacteria was: C t = -3.19x + 53.66; R 2 = 0.99, as used by Castillo et al. [32]. To better address the activity of the innate immune response in zebrafish during the A. hydrophila infection, the transcription levels of the immune mediators: TNF α, IL-1β and IL-8 (pro-inflammatory cytokines) and C3 (complement system, acute phase protein) were evaluated. Fold changes in mRNA levels post-challenge and treatment were calculated in relation to the average mRNA levels of placebo treated fish. Statistical analysis The effect of treatment on selected gene expression level was analyzed with Student’s t-test as described by [33].