Transcriptome analysis of the opportunist pathogenic bacterium Clostridium perfringens ATCC 13124 grown in the presence of host polysaccharide hyaluronic acid and mucin

Purpose: The purpose of this study is to clarify the response of Clostridium perfringens ATCC 13124 to host polysaccharide. Methods: Clostridium perfringens ATCC 13124 cells were cultured anaerobically in a medium containing Minimal medium-like condition Poor + medium, medium in which hyaluronic acid or mucin was added to Poor + medium. Total RNA was extracted from bacterial cells by the Hot-Phenol method. Samples for RNA-seq were prepared according to the Illmina protocol available from the manufacturer. Array leads passed through quality filters were analyzed at the transcript isoform level using bowtie v 1.1.2. Results: Using the optimized data analysis workflow, we mapped about 50 million sequence leads per sample to the whole genome of Clostridium perfringens ATCC 13124. In addition, 2735 transcripts in C. perfringens ATCC 13124 were identified using a Bowtie aligner. Lead counts per genome were extracted from known gene annotations using the HTSeq program. RNA profile of Clostridium perfringens ATCC 13124 grown under different conditions: Minimal medium-like condition Poor + medium, medium supplemented with hyaluronic acid in Poor + medium, or medium supplemented with mucin.