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. 2020 Aug 2;47(11):913–927. doi: 10.1007/s10295-020-02295-3

Table 1.

A non-exhaustive list of measurements and standard calculations that may be performed on each sample during a fermentation characterization experiment

Goal Measurement Calculation Description
Understand growth profiles Biomass (OD, DCW, cytometry) Growth rates Calculation of maximum specific growth rates (μmax) during exponential phase, doubling time (td), timing of exponential growth within the fermentation, number of cell doublings within the fermentation (both main fermentation alone and including entire seed train)
Understand production rates and profiles Product concentration, cell concentration Production rates Calculation of the rate of product formation (qp), both over the course of the fermentation and during specific intervals
Quantify residual substrate and substrate uptake rates and profiles Substrate concentration, cell concentration Substrate consumption rates Calculation of the rate of substrate consumption (qs), both over the course of the fermentation and during specific intervals
Understand production efficiency Product and substrate concentration

Production yields

Carbon balances

Yield coefficients for different substrates

Calculation of the efficiency of product formation (YSP = qp/qs), both over the course of the fermentation and during specific intervals

Account for all the carbon substrate added to the fermentation in biomass, product, pathway intermediates and byproducts (including CO2)

Calculation of the mass of cells produced per unit mass of substrate consumed—Yx/s during exponential growth

Identify and quantify pathway bottlenecks Concentration of Pathway intermediates and byproducts Byproduct formation Calculation of the amounts of different byproducts/pathway intermediates formed during specific phases of the fermentation
Identify potentially limiting nutrients and substrates Quantification of trace elements, Vitamins, AA, OA, Alcohols, N, P, S Yield coefficients Correlation of exhaustion of essential nutrients and decrease in growth rate or cessation of growth
Monitor cellular metabolism during fermentation Offgas (CO2, O2 Ethanol) Analysis of offgas and online measurements Calculation of Oxygen Uptake Rates (OUR), Carbon Dioxide Evolution Rates (CER) and Respiratory Quotient (RQ) throughout the fermentation. Interpret OUR, CER, RQ, DO and pH trends in the context of identifying growth phases, metabolic shifts and loss of metabolic activity
Monitor the process and measure substrate uptake rates Online measurements (pH, DO, feed rates, agitation, temperature)
Quantify viability loss during fermentation Viability (cytometry, CFUs) Viability Quantification of viability loss during fermentation
Monitor cellular morphology and broth viscosity during fermentation

Microscopy

Viscosity

Morphology

Viscosity

Documentation of cellular morphology and viscosity during the fermentation

OD optical density, DCW dry cell weight, AA amino acids, OA organic acids, N nitrogen, P phosphate, S sulfate, DO dissolved oxygen, CFU colony forming units)