L-rhamnose globally changes the transcriptome of planktonic and biofilm Escherichia coli cells and modulates biofilm growth
L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. Our results reveal that L-rhamnose significantly affects growth kinetics and biofilm formation, particularly reducing biofilm growth in rich media at 37 °C. Transcriptomic analysis through RNA-seq showed that L-rhamnose modulates gene expression differently depending on the temperature and media conditions, promoting a planktonic state by upregulating genes involved in rhamnose transport and metabolism and downregulating genes related to adhesion and biofilm formation. These findings highlight the nuanced role of L-rhamnose in bacterial adaptation and survival, providing insights for potential applications in controlling biofilm-associated infections and industrial biofilm management. Overall design: PHL628 E. coli cells were grown in rich (LB) or minimal (M9) media supplemented with either L-rhamnose at 0.5% (w/w), no sugar (0%, LB samples), or 0.5% (w/w) D-glucose (M9 samples).  Cells were grown at either 28 C or 37 C and three biological replicates of planktonic and biofilm samples of each experimental condition type were harvested (16 conditions, 48 samples total).