Serial adaptive laboratory evolution enhances mixed carbon metabolic capacity of Escherichia coli.

Microbes have inherent capacities for utilizing various carbon sources, however they often exhibit sub-par fitness due to low metabolic efficiency. To test whether a bacterial strain can optimally utilize multiple carbon sources, Escherichia coli was serially evolved in lactate and glycerol. This yielded two end-point strains that evolved first in lactate then in glycerol, and vice versa. The end-point strains displayed a universal growth advantage on single and a mixture of adaptive carbon sources, enabled by a concerted action of carbon source-specialists and generalist mutants. In addition, deconvolution of transcriptome profiles revealed coordinated activity of transcriptional regulators impart condition-specific regulation of gene expressions. The effectiveness of the serial ALE scheme in bioproduction applications was assessed under single and mixed-carbon culture conditions, in which serial ALE strain exhibited superior productivity of a commodity chemical compared to ancestral strains, highlighting the potential utility of serial ALE in bioproduction applications.