E-MTAB-9762
RNAseq of uropathogenic E. coli strain EO399, grown in conditions resembling passage through the gut; coli was grown in the presence or absence of 1 of 3 organic acids (acetic, butyric or propionic) at pH5.5 or pH7 and in aerobic or anaerobic conditions
Overview  Several methods are available to probe responses to external stresses at the whole genome level.  RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism's ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions. These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converged on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short chain fatty acids (SCFA) produced by fermentation of carbon compounds, and E. coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We therefore generated RNAseq and TraDIS data on the uropathogenic E. coli strain EO399 grown at either pH 7 or pH 5.5, in the presence or absence of one of three SCFAs (acetic, butyric or propionic acid), both aerobically and anaerobically.  Our analysis identifies both known and novel pathways as likely important under these conditions.
Overview  Several methods are available to probe responses to external stresses at the whole genome level.  RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism's ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions. These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converged on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short chain fatty acids (SCFA) produced by fermentation of carbon compounds, and E. coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We therefore generated RNAseq and TraDIS data on the uropathogenic E. coli strain EO399 grown at either pH 7 or pH 5.5, in the presence or absence of one of three SCFAs (acetic, butyric or propionic acid), both aerobically and anaerobically.  Our analysis identifies both known and novel pathways as likely important under these conditions.