In food production, colour shapes how consumers perceive taste and quality. Although synthetic colourings have dominated, a shift towards natural alternatives is growing. A new method uses the yeast Yarrowia lipolytica to produce betanin, a red pigment from beetroots. This sustainable approach improves purity and reduces resource use compared with traditional methods. Despite challenges in scaling and regulatory approval, this innovation could transform the food colouring industry and expand the palette of natural food colourings.
Colour has a pivotal role in shaping how consumers perceive taste and quality. Synthetic colourings have traditionally dominated the market, but growing consumer demand for natural alternatives is causing a significant shift within the industry. One promising development involves using the oleaginous yeast, Y. lipolytica, to produce betanin – a natural red colouring typically extracted from red beetroots. This approach could significantly alter the landscape of food colouring.
“What is truly revolutionary about our process is not just its sustainability and potentially lower cost but also obtaining a product with higher purity. Beetroot extract contains high concentrations of sugar, whereas our fermented product can be made sugar-free and thus more concentrated,” explains Irina Borodina, Professor, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby.
The first crucial step
The traditional method of extracting betanin from beetroot is notoriously inefficient and resource-intensive, given the pigment’s low natural concentration of about 0.2% wet weight. The biotechnological process developed by the researchers harnesses metabolic engineering and optimises fermentation to produce betanin and its chemical isomer twin, isobetanin, directly from glucose.
“This method not only simplifies the production process but also enhances its efficiency dramatically. We engineered Y. lipolytica as a new production host because of its capacity to produce high levels of lipids and organic acids, indicating potential for other valuable compounds such as betanin,” Irina Borodina explains.
Oleaginous yeast Y. lipolytica is an attractive cell factory that has been engineered to produce omega-3-fatty acids (DuPont), stevia glucosides and carotenoids (DSM), lipids (Novogy), Lepidoptera pheromones (BioPhero), and other products at industrial scale. It is a yeast species that commonly occurs in food, such as cheese or sausages.
"In contrast to baker’s or brewer’s yeast, Y. lipolytica does not produce ethanol, which simplifies large-scale manufacturing. The first crucial step was inserting genes for betanin biosynthesis from beetroots into the yeast’s genome. We did not just add these genes; we had to ensure that they were expressed correctly and at the right levels,” she elaborates.
Much higher than previous attempts
To do this, the team used CRISPR-Cas9 technology to precisely edit the yeast’s DNA, enhancing the pathways leading to betanin. They increased the supply of an amino acid precursor, l-tyrosine, essential for betanin, by modifying the yeast’s metabolic processes to boost its production.
“This involved deactivating genes that divert resources from l-tyrosine and deleting those that degrade betanin once it forms, such as the 4-HPPD gene that provides competing pathways and specific glucosidases that break down the pigment,” adds another main author, Philip Tinggaard Thomsen, Research Assistant, Novo Nordisk Foundation Center for Biosustainability.
The results were substantial. In controlled fermentation using a simple glucose source, the researchers achieved 1,271 mg of betanin per litre and 55 mg of isobetanin per litre within 51 hours.
“These are much higher than previous attempts with other organisms. Scaling up demonstrated that this process could transition from the laboratory to industrial applications effectively,” Philip Tinggaard Thomsen points out.
Finally, life-cycle assessment and techno-economic analysis verified the method’s environmental and economic viability.
“These assessments show that our method could significantly reduce the use of land and resources compared with traditional extraction methods while remaining cost-effective,” he explains.
Extends beyond betanin
The project showcases how targeted genetic tweaks and advanced fermentation can lead to more sustainable practices in producing food colouring.
“By engineering Y. lipolytica, we produced betanin at concentrations about 42 times higher than previously with other yeasts such as Saccharomyces cerevisiae,” Philip Tinggaard Thomsen notes.
This advancement in microbial fermentation technology provides substantial environmental benefits, according to comprehensive life-cycle assessment.
“If we fully harness the potential of this fermentation-based colouring production, we can satisfy the world’s demand with just one-tenth of the equivalent land area. The shift from land-dependent extraction processes to bioreactor-based production significantly improves both sustainability and scalability,” highlights Irina Borodina.
The application of the technology extends beyond merely producing betanin. The structural diversity of betalains, the pigment family to which betanin belongs, offers numerous opportunities for creating a variety of colours and hues.
“The current process presents a platform from which we can expand to making other betalain-type colours, which are currently too expensive to be extracted from plants. This could open up new avenues for producing a broader palette of natural food colourings, enhancing both the sustainability and economic feasibility of their production,” says Irina Borodina.
Scaling up from laboratory experiments to large-scale
As the global market for natural food colourings continues to grow, driven by consumer preference for safer and more sustainable products, this new work by the team is setting a new standard. Their development not only meets the market’s demands but also addresses broader environmental concerns associated with traditional agricultural practices.
“This work underscores the potential of metabolic engineering in creating more sustainable solutions. Several challenges must be overcome to bring this new yeast-based food colouring to market,” Irina Borodina emphasises.
First, scientists have to fine-tune the fermentation process to ensure efficiency and cost–effectiveness.
"Scaling up from laboratory experiments to large-scale production while maintaining quality is another major hurdle. Ensuring economic viability is critical, since the process needs to be affordable compared with traditional methods."
