An Integrated Multi-Omics and Computational Characterization of Seven Unique Escherichia coli Production Chassis Commonly-Used in Industrial Biotechnology

A major challenge in industrial biotechnology is the selection of an appropriate platform organism to be engineered in order to maximize the production of the desired chemical in as little time as possible. Often times, researchers resort to their in-house favorite strain due to a lack of a standardized and functional comparison across strains within a species. In this study, we set out to clarify some of the strain-specific differences in the most common laboratory organism and production chassis, Escherichia coli.  Specifically, we performed an integrated functional characterization of seven commonly used industrial Escherichia coli strains (BL21 (DE3), C, Crooks, DH5α, MG1655, W and W3110) through phenomics, transcriptomics, and genome-scale modelling under both aerobic and anaerobic conditions. Genome-scale metabolic models were generated for each of the strains and integrated with the phenomic data to determine reactions that carry high flux in each of the strains.  High-flux reactions and their encoding genes were compared to differentially expressed genes in each of the strains, as well as across the strains, to characterize shared and strain-specific behaviour.  Furthermore, the wild-type phenotypes of each of the strains were compared to production phenotypes for a variety of industrial compounds to make a prediction on what strains are inherently better suited to produce a given compound or class of compounds. The result of the study is a classification that can be used to guide selection of a given strain for the biosynthesis of a desired product.