Nitrogen nutrition of E. coli in the mammalian intestine

Our focus of this study is to determine the differential expression of genes related to uptake and degradation of nitrogenous compounds in E. coli colonizing the mouse intestine as compared to E. coli grown in minimal medium in vitro. We colonized CD-1 male mice with E. coli MG1655 StrR wild type and extracted the total RNA from mouse cecal mucus (GSE217743). We also colonized CD-1 male mice with E. coli MG1655 ∆glnG StrR CamR and extracted the total RNA from mouse cecal mucus. We grew E. coli MG1655 StrR wild type in MOPS minimal medium containing high nitrogen (10 mM NH4Cl) and low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase and stationary phase culture. We also grew E. coli MG1655 ∆glnG StrR CamR in MOPS minimal medium containing low nitrogen (3 mM NH4Cl) and extracted the total RNA from exponential phase culture. The extracted RNA samples were sequenced, and differential expression analysis was done to determine the genes related to uptake and degradation of nitrogenous compounds that are important for E. coli colonization. Our results indication nitrogen is not limiting for E. coli in the intestine and genes related to uptake and degradation of several aminoacids, di- and tripeptides, aminosugars, ethanolamine, urea among others are upregualated in the mouse intestine as compared to invitro culture grown in high nitrogen conditions. E. coli MG1655 StrR and E. coli MG1655 ∆glnG StrR CamR were fed separately to CD-1 male mice and on the 9th day, the mice were euthanized, mucus from the cecum was obtained and total RNA was extracted and sequenced. E. coli MG1655 StrR and E. coli MG1655 ∆glnG StrR CamR were cultured in MOPS minimal medium containing high or low nitrogen, and the total transcriptome of exponential phase culture and/or stationary phase culture was sequenced.