Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis

E. coli isolates from different CF patients demonstrate increased growth rate when grown with glycerol, a major component of fecal fat, as the sole carbon source compared to E. coli from healthy controls. CF and control E. coli isolates have differential gene expression when grown in minimal media with glycerol as the sole carbon source. While CF isolates display a growth promoting transcriptional profile, control isolates engage stress and stationary phase programs, which likely results in slower growth rates. RNA-seq analysis was performed to analyze the transcriptomes of CF and control E. coli when grown on glycerol (GlyMM) or glucose (GluMM) as the sole carbon source. Since the different isolates are not isogenic mutants, transcriptome analysis on GluMM served to establish baseline gene expression for each of these genetically distinct strains.