Upstream processing

A bioprocess has two stages: upstream processing, everything before the fermentation, and downstream processing, everything after it. Upstream processing means getting everything right before you start:

• Optimise the medium.
• Sterilise the medium, the bioreactor, and all the tools.
• Produce a pure, healthy inoculum (the starter culture).
• Optimise the growing conditions.

The medium. The raw material is made fermentable, and the medium is formulated to provide everything needed:

carbon/energy source + nitrogen source + other nutrients → biomass + products + CO₂ + water + heat

The yield coefficient, Y = dry weight of cells produced ÷ carbon substrate used, helps design a medium that gives enough of each nutrient without waste.

The inoculum, often grown first in a shake flask, should be: healthy and in the log phase; not show a long lag; enough in amount; in the right form; free of contamination; and still productive.

The conditions:

• Aeration: sterile air is bubbled in through the sparger, because water dissolves very little oxygen.
• Agitation must be gentle enough: animal cells are more easily damaged by shear than plant cells, and plant cells more than microbes. The speed of the shaker or agitator (rpm) controls it.
• Temperature and pH are optimised separately; the best values for growth may differ from those for making the product.

Contamination is avoided by sterilising the medium, the vessel and everything added later, working aseptically, and using a pure culture as the inoculum.