In vivo RNA-sequencing of Vibrio cholerae during intestinal colonization of infant rabbits

To understand how cholera toxin (CT) produced by Vibrio cholerae modulates gene expression of this organism within the intestine, RNA-seq analysis was performed on two samples each of WT and the ?ctx mutant bacteria harvested from either the infant rabbit ileum or the cecum one-day post-intragastric infection. We found that 243 genes that were significantly up-regulated in the WT compared to the ?ctx mutant and these included 101 genes in ileum samples, 118 in the cecum samples, and 24 in both samples. We found that genes known to be induced under low-iron growth conditions were up-regulated in WT relative to the ?ctx mutant in both the ileum and in the cecum, with a marked up-regulation in the ileum relative to the cecum. We also found that genes involved in TCA cycle metabolism, L-Lactate utilization, and LCFA utilization were significantly up-regulated in the WT in the ileum relative to the ?ctx mutant during infection. We conclude that CT-induced disease creates an iron-depleted metabolic niche in the gut that modulates the transcriptional profile of this pathogen during infection. Overall design: RNA-seq analysis was performed on two samples each of WT and the ?ctx mutant V. cholerae harvested from either the infant rabbit ileum or the cecum one-day post-intragastric infection.