NIZO Industry Insights: Food Fermentation

Fermentation may be an ancient technique, but it continues to create new opportunities in food production. Whether providing new sources of protein or health-enhancing ingredients or improving the taste, texture and safety of food products, fermentation adds value to the entire food industry.

René Floris, Food Research Division Manager at NIZO and member of the FoodNavigator Advisory Panel, asks Janneke Ouwerkerk, microbiome and fermentation expert at NIZO, to explain how.

René Floris: Why is food fermentation such a hot topic in the food industry right now?

Janneke Ouwerkerk: Food fermentation refers to any process in which the activity of microbes causes a desirable change in a food. People have used fermentation in food production since Neolithic times, creating a wide range of traditional foods from beer and alcoholic beverages to a variety of pickles, kombucha, and yogurt. Recently, trends such as protein transition and clean label products have encouraged the food industry to take a fresh look at this ancient technique and explore many new applications.

RF: What types of new applications are being explored?

JO: Traditionally, fermentation has been used to create beneficial changes in food, for example to create alcohol, leaven bread or preserve food. And this kind of application is still common in the world of protein transition, healthy food and clean label products. For example, fermentation is often used to add a pleasant depth of flavor to low-fat cheeses and plant-based cheese alternatives. Additionally, our own research at NIZO suggests that fermentation can remove volatile organic compounds that cause off-flavors often associated with plant-based protein ingredients, such as the hexanal responsible for the “vivacity” of pulse-based proteins. . We have also used fermentation to successfully acidify plant-based cream cheeses, providing better protection against mold growth than standard chemical acidification. In all these cases, fermentation makes it possible to obtain a desired result using a natural treatment, without resorting to chemical additives.

But fermentation is also increasingly used to directly manufacture food ingredients and components. Perhaps the most obvious application here is in the use of fermentation to grow a biomass of microbes that themselves act as food, either as a probiotic to promote consumer health benefits, or as an alternative source of proteins like Quorn. Even more recently, we have seen interest in “precision fermentation” where microorganisms are modified to produce a protein with an identical amino acid sequence to a target animal protein such as caseins and egg albumen.

RF: Do these new applications also use new fermentation approaches?

JO: Absolutely. For example, plant-based ingredients and products contain different sugars and fats as well as different dairy proteins, so you can’t just translate familiar fermentation processes. Meanwhile, when creating microbial proteins, the goal is to grow the biomass as quickly as possible, which is a very different goal from previous fermentation approaches.

In fact, many of these new applications are based on “new” microbes. For probiotics, this often means identifying new microbial species or strains that have specific desired traits and do not have undesirable traits like antibiotic resistance. Here, siliconeScreening is a valuable tool for quickly reducing the number of candidates. In contrast, precision fermentation involves microbes creating proteins that they would not naturally make. These microbes must therefore be genetically modified. This currently means that proteins from precision fermentation cannot be marketed in certain territories, such as the European Union, unless legislation changes.

As I mentioned, plant-based products provide a very different environment than animal-based ones. It is therefore often necessary, here too, to adapt the known cultures to this new environment. To avoid market entry problems around GMOs, it is possible to use accelerated evolution instead. It involves identifying a promising strain, then repeating the inoculation on the desired substrate, possibly guided by genome sequencing to follow the evolution of metabolic capacities, in order to create a new strain better adapted to the environment. (vegetal).

Serial transfer enhanced the acidifying potential of Lactococcus in soymilk. After about 200 generations (green), phenotype changes resulted in a faster rate of acidification and a lower final pH than the original population (red). Image source: NIZO

RF: What are the challenges of working with new microbes?

JO: There are many challenges on the road between the right microorganism and a commercial fermentation process. And it’s important to consider them early in the development journey to reduce the risk of longer delays later.

One of the main ones is manufacturability: can you grow your chosen microbe fast enough to support volume manufacturing with high stability and ensure food-grade production? In fact, you should start addressing this issue at the discovery stage when you identify the right microbe. High-throughput screening allows you to exclude microbes that grow too slowly or die too quickly, while silicone Genome analysis can highlight potential food safety issues such as genes associated with antimicrobial resistance, toxin production or pathogenicity

When using any form of new microorganism, it is important to note that even if there are no viable organisms in the final application, DNA may still be present. Thus, there is a possibility of transfer of new genes to microorganisms in the environment and precautions should be taken. This could involve using computer modeling and bioinformatics to assess the risks posed by new genes or even reverting to using (less optimized) organisms from regulator-approved lists of safe microbes, such as EFSA’s Qualified Presumptions of Safety (QPS) list.

RF: Once you have identified the right microorganism, what happens next?

JO: The next step is to design a fermentation process based on your microbe that will work effectively on a commercial scale. This must be done in a controlled, step-wise progression: from lab scale to small prototyping and pilot production before final transfer to volume production. Remember that microbes are living organisms that react to their environment, so it is important to understand how each step in this progression impacts the conditions for microbe growth during fermentation.

To maximize growth rates, culture medium and conditions must be optimized, which requires investigation of the interaction effects of various medium components, pHs, and cryoprotectants. Data science helps provide insight into in vitro experiments, distilling data from different equipment and tests into clear guidance on the best culture conditions.

Picture2 culture medium
Optimization of culture medium for maximum growth of a candidate microbe using optical density measurements and viable cell counts. Image source: NIZO

This optimization of the medium is generally carried out on a laboratory scale where the fermentation volumes are of the order of magnitude of microliters to liters. Production is then scaled up to tens and then hundreds of liters to explore downstream options (such as centrifugation and cross-flow filtration). Once all these conditions have been optimized, the fermentation can move into the pilot phase with fermentation volumes of several thousand liters, allowing formulations of food products. This step-by-step scaling is essential, because even small changes can have a big impact on how the microbe responds.