Optimization of a bioassay to evaluate Escherichia coli stress responses

During the genomics era, great emphasis was placed on sequencing microbial genomes and understanding their global gene expression. Later in the post-genomic era, focus shifted towards building on said information, mainly towards deeper knowledge on the relationship of genomics and transcriptomics with the biomolecular composition of microbes, and ultimately their metabolism. To that end, exploring microbial adaptation, e.g. to adverse conditions, is an integral part of current research, for which Escherichia coli is a favored model organism, as its metabolic pathways share pronounced similarities to mainstream pathways across other microorganisms. As such, E. coli has been extensively studied regarding general stress and specific metabolic responses, inclusively for establishing bioassays for detecting and characterizing the mode of action of antibacterial agents. For that, as an example, the global responses of E. coli to diverse stress conditions has been previously compared by transcriptomic and Fourier-transform infrared (FTIR) spectroscopy analysis, highlighting the importance of combining multiple techniques to profoundly understand the holistic cell response. In this work, a high-throughput FTIR spectroscopy based bioassay was developed for E. coli, and optimized regarding multiple parameters as inoculum growth phase, growth media composition and stress agent exposure time. The approach described allowed to identify the impact of each parameter on the metabolic resolution of the biomolecular fingerprint acquired with FTIR spectroscopy, and consequently the optimized bioassay maximizes the ability of FTIR spectroscopy to specifically characterize the impact of diverse stress agents on the E. coli metabolism.