From microorganism to end product: fermentation as a technical chain

Fermentation is an age-old technique, but at the same time an important platform for modern industrial production. Microorganisms now produce not only ethanol, citric acid, and enzymes, but also insulin, vanillin, and alternative proteins. New applications range from bio-based asphalt and textile dyes to dairy products without cows.

During the WoTS 2026 seminar Fermentation in practice: from microorganism to end product[1] Jeroen Koendjbiharie from the Vrije Universiteit Amsterdam and Julia Keppler from Wageningen University & Research showed what is needed for that.

Evolution as a development tool

Every fermentation process involves a microorganism that must produce sufficiently quickly, stably, and efficiently under industrial conditions. To this end, researchers can use targeted genetic modification or random mutagenesis with screening. Both methods have limitations. Targeted modification requires knowledge of the organism and the underlying mechanism, while suitable screening is not always available.

Laboratory evolution offers an additional route. Researchers repeatedly subject microorganisms to conditions where a desired trait yields an advantage. Examples include faster growth, higher tolerance, or a different product yield. Variation, heredity, and selection pressure then do the work. This makes it possible to improve complex traits without fully understanding every biological mechanism beforehand.

Koendjbiharie illustrated this with a yeast strain that initially grew hardly at all in a medium without biotin. After evolution in bioreactors, the maximum growth rate increased sharply. Another study focused on yeast for wine with a lower alcohol content. Selection for osmotolerance led to more glycerol and less ethanol. At the same time, the examples highlight an important point of attention: microorganisms follow the imposed selection pressure, but do not necessarily choose the route the researcher expects beforehand.

From produced protein to food

A high-producing microorganism does not yet yield a usable foodstuff. Keppler distinguished between traditional fermentation, biomass fermentation, and precision fermentation. In traditional fermentation, the transformed foodstuff forms the end product. In biomass fermentation, the microbial cells themselves are used. Precision fermentation employs bacteria, yeasts, or molds as cell factories for specific ingredients, including milk and egg proteins.

After fermentation, separation, purification, protein analysis, formulation, and structuring follow. It is precisely in these steps that it must become apparent whether a protein can emulsify, foam, or gel. This ultimately determines whether it is suitable for, for example, milk, ice cream, or a cheese-like product. Small differences in protein structure or genetic variant can influence the functional properties. Accurate analysis of the produced protein is therefore essential.

The next step goes beyond copying existing animal proteins. Researchers can modify proteins, develop new building blocks, and reconstruct natural structures, such as casein micelles. Automation and predictive models must accelerate ingredient testing. In this way, the central question shifts from “Can we produce this protein?” Unpleasant “What functionality do we want to design?”

[1] seminar-fermentation-in-practice-from-micro-organism-to-end-product/ – FHI, Federation of Technology Branches