Genome-scale metabolic reconstructions of Escherichia coli highlight strain-specific adaptations to environmental niches

The number of complete genome sequences for E. coli strains continues to accumulate rapidly. We used 47 of these sequences and 152 draft sequences to generate strain-specific metabolic models using homology mapping of the content from the most recent metabolic model for E. coli K-12 MG1655 (iJO1366) as well as metabolic models of closely related species (Salmonella typhimurium LT2 (STMv1.0), Klebsiella pneumoniae MGH78578 (iYL1228) and Yersinia pestis CO95 (iPC815)). These new strain-specific models predict differences in strain phenotypes and allow for the generation of testable hypotheses for growth substrates and strain-specific auxotrophies. The models can further be used to improve genome annotations, transplant metabolic pathways of interest and predict gene essentiality in pathogenic strains to fight infection.