Fermentation
All substrate is present from the start and the culture grows until it is exhausted. Fast and simple, but growth at the maximum rate drives overflow metabolism, and oxygen demand rises with the biomass formed, so batch cultures are usually kept to modest substrate concentrations.
Our ruleSimulations prepare you for the bench but don't replace hands-on practice.
Batch
All substrate is present from the start and the culture grows until it is exhausted. Fast and simple, but growth at the maximum rate drives overflow metabolism, and oxygen demand rises with the biomass formed, so batch cultures are usually kept to modest substrate concentrations.
How it differs from the standard method
- Induce expression in mid-exponential phase, while glucose remains.
- Lower temperature reduces uptake rate and overflow, and improves folding.
- Acetate formed early may be reconsumed once glucose runs out.
1Growing microbes on purpose
In bioprocessing, fermentation means growing bacteria, yeast or fungi in a controlled vessel to make biomass, a metabolite or a recombinant protein (it need not be anaerobic, despite the word's older meaning). A fermenter holds temperature, pH and dissolved oxygen at set points while the culture grows from a small inoculum to tens of grams of dry cells per litre.
Everything at the start
All the substrate is added at once and the culture grows until it runs out. Simple and quick, but growth runs at maximum rate, which in E. coli and yeast spills substrate as by-product, and oxygen demand peaks just as the culture is densest.
Feed what they can use
A short batch, then a concentrated feed delivered at the rate the cells can respire. The feed rate sets the growth rate, which keeps by-products away and lets the culture reach very high density.
Chemostat
Fresh medium flows in and culture flows out at the same rate. At steady state the growth rate equals the dilution rate, so the cells can be held in one physiological state for days.
2Overflow: why fast growth wastes sugar
Cells take up glucose faster than respiration can oxidise it once the growth rate passes a critical value, about 0.3–0.4 h⁻¹ for E. coli and about 0.3 h⁻¹ for baker's yeast. The excess is excreted: acetate by E. coli, ethanol by yeast (the Crabtree effect), even with plenty of oxygen.
3Oxygen, the other limit
A dense E. coli culture can use more than 200 mmol of oxygen per litre per hour, far more than any mammalian cell culture. Supply is kLa·(C* − C), raised by agitation and gas flow and, at the limit, by blending pure oxygen into the inlet gas.
4Chemostats: steady state and washout
In a chemostat the dilution rate D sets the growth rate. Residual substrate settles at the concentration that lets the cells grow at exactly D, and biomass at the yield times the substrate consumed.
Key terms
Practise these as flashcards →Rate of biomass increase per unit biomass, per hour; ln 2 divided by the doubling time.
Grams of biomass made per gram of substrate consumed; about 0.5 g/g for glucose respired by E. coli or yeast.
μ = μmax·S/(Ks + S): growth rate saturating with substrate concentration.
Excretion of acetate (E. coli) or ethanol (yeast) when glucose uptake exceeds respiratory capacity.
Ethanol formation by aerobic yeast at high glucose uptake rates, even with oxygen in excess.
Increasing the feed rate exponentially so that the culture grows at a chosen, constant μ.
Medium flow divided by culture volume; equals μ at chemostat steady state.
Loss of the culture from a chemostat when D exceeds the maximum growth rate.
The sequence a dissolved-oxygen controller uses: agitation, then gas flow, then oxygen enrichment.
Switching on expression of a recombinant gene, for example with IPTG for a T7 or lac promoter.
When to use it
- Producing recombinant proteins, enzymes or metabolites from bacteria or yeast at litre scale or above, where shake flasks cannot supply the oxygen or control the pH.
- Reaching high cell density for intracellular products, with a fed-batch feed holding growth below the overflow threshold.
- Studying physiology at a defined growth rate in a chemostat, or running a long, steady continuous production.
Compared with alternatives
Shake-flask expression is the screening step; move to a fermenter when you need more product, density or control.
Plate-reader or flask growth curves give μmax and lag to plan the batch phase.
The mammalian-cell counterpart: slower growth, lower oxygen demand, and shear-sensitive cells.
Harvest, cell disruption and purification take the product from the broth.
Sub-techniques
Choosing one here switches the whole page, including the protocol and the lab, to it.
All substrate is present from the start and the culture grows until it is exhausted. Fast and simple, but growth at the maximum rate drives overflow metabolism, and oxygen demand rises with the biomass formed, so batch cultures are usually kept to modest substrate concentrations.
- Induce expression in mid-exponential phase, while glucose remains.
- Lower temperature reduces uptake rate and overflow, and improves folding.
- Acetate formed early may be reconsumed once glucose runs out.