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

Escherichia coli usually represent less than 1% of the human intestinal microbiome, whereas in cystic fibrosis (CF) greater than 50% relative abundance is common and correlates with intestinal inflammation and fecal fat malabsorption. We show that E. coli isolated from fecal samples of young children with CF have adapted to growth on glycerol, a major component of fecal fat. E. coli isolates from different CF patients demonstrate increased growth rate in the presence of glycerol compared to E. coli from healthy controls, and unrelated CF E. coli strains have independently acquired this growth trait. Furthermore, 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. Our results indicate that there is selection of unique characteristics within the microbiome of individuals with CF, which could contribute to individual disease outcomes.