Gene expression changes of Planococcus kocurii O516 in various culture conditions (with or without sulfamethoxazole)

The strain Planococcus kocurii O516 isolated from the marine culture environment was found to be stably and highly effective for the degradation of sulfamethoxazole. We investigated the expression behavior of functional genes related to this degradation ability in P. kocurii O516 under the culture conditions with or without sulfamethoxazole. Overall design: Five milliliters of bacterial resuspension (in each medium) were inoculated into 50 mL of respective test media and the cultures were shaken at 120 rpm at 30°C. As test media, Muller-Hinton Broth medium with and without sulfamethoxazole were used. After incubation at 24 h, 50 mL of each culture was taken and used for RNA-Seq. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequence data by HiSeq_4000 were assembled and analyzed using the CLC Genomics Workbench and the statistical software R with various packages (edgeR, and DEGSeq). HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Then, using DEGSeq R package (1.20.0), the gene expression values relative to the two different mediums were calculated to log2 values of fold change (log2FC) with FDR (false discovery rate) values under the four culture conditions.