In this work, a detailed analysis of productivity metrics for the optimization of fermentation systems producing intracellular products is presented. Productivity metrics for fermentation systems can be broadly classified into two catagories: instantaneous and cummulative. The instantaneous metrics are intended to characterize the productivity of the fermentation system at the current instant in time providing a real-time metric that is suitable for monitoring the fermentation system. The difficulty with these metrics for intracellular product fermentation, however, is the difficulty in obtaining a reliable and accurate real-time measurement of the intracellular product. These metrics can also be difficult to interpret when semi-batch and semi-continuous fermentation operation are considered. Cummulative metrics are intended to provide an overall productivity measure of the fermentation system. It is these metrics that are typically employed for fermentation system optimization. Any combination of batch, continuous, semi-batch, and semi-continuous operation can be easily addressed using metrics in this catagory. It is cummulative productivity metrics that will be emphasized in this work.

Cummulative productivity metrics range from overall cost and profit functions to scaled total product functions in which time and media consumed are the typical scaling factors. We will analyze these metrics for an E. coli bacterial fermentation used to produce an intracellular DNA plasmid product. Interest in DNA plasmid production stems from the fact that approximately 25% of the ongoing clinical trials for gene therapy products use DNA plasmids to carry the corrective gene. The production of DNA plasmids using E. coli fermentation provides a particularly challenging optimization problem due to the instability of the intracellular DNA plasmid product. Although continuous fermentation is very efficient at increasing the production of biomass, DNA plasmid production is not directly related to cell mass production. At high cell mass production rates, the production of plasmids actually decreases due to a shift in the growth-related production of DNA plasmids. The result is the production of cells that have a low plasmid copy number, or are plasmid free, with an overall drop in plasmid production by the fermentation system.

Semi-continuous fermentation operation will be considered in this study in which an intial batch fermentation beyond the exponential growth phase is followed by continuous and semi-continuous fermentation. The goal of the productivity optimization is to determine the optimal fermentation operation sequence. Experimental studies are presented using the Life Technologies DH5a E. coli strain which produces the intracellular DNA plasmid pUC 18. The results of this study indicate that drastic differences in the optimal fermentation sequence are obtained using different, but closely related, cummulative productivity metrics. The presentation closes with an analysis of the commercial application of these metrics.