Transcriptomes of Streptococcus anginosus KH1 in artificial saliva medium and modified serum medium

The transcriptomes of S. anginosus KH1 under conditions mimicking either the oral cavity or the bloodstream were determined to identify loci that are highly regulated by culture media. Overall design: Total cellular RNA was isolated from KH1 cultures at OD600 = 0.3. Ribosomal RNA was removed from the RNA preparation using RiboMinus transcriptome isolation kits (Invitrogen). Transcriptome sequencing was performed by a commercial service (Welgene, Taiwan). Briefly, the RNA library was constructed using a SureSelect XT HS2 mRNA library preparation kit (Agilent, USA). The sequences were determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Reads were assessed through a Phred quality score (Q score of 20) and trimmed using Trimmomatic v0.36. The trimmed reads were mapped to the genome sequence of KH1 by using HISAT2. TPM (transcripts per million) was used to calculate the expression level of each gene. The significant difference in the expression level of each locus between the two growth conditions was analyzed using DESeq2 v1.28.1 with genome bias detection/correction and Welgene Biotech's in-house pipeline. For each condition, duplicate samples were analyzed. Genes exhibiting a fold change >2.0 and a p-value < 0.05 between the two culture conditions were considered significant.