Microbes as tomorrow’s production factories 

Johanna Sippo

19.12.2024

Photo by Studio Kari Liikonen, courtesy of The Research Council of Finland

Currently, the industrial production of dyes for the textile industry requires a significant amount of chemicals and burdens the environment. Natural dyes, on the other hand, have traditionally been extracted from fungi and plants. However, it’s not necessarily sustainable to use valuable farmland for cultivation of dye plants. Fungi that produce dyes grow scattered in forests mostly in the fall.

What if these issues could be solved? At VTT Technical Research Centre of Finland, researchers are pursuing an innovative project that harnesses genetically modified microbes to produce natural dyes derived from fungi and plants, offering a more environmentally friendly alternative to chemically produced dyes. Red and yellow shades are already achievable, but blue and green still require further development

Dyes produced by microbes are just one example of the biotechnological revolution expected in the coming years, explains research professor in biotechnology and Academician Merja Penttilä. 

“Industrial production has traditionally been seen as separate from living nature, but this is now changing,” says Penttilä.

A radical shift is underway as industrial production transitions to closed bioreactors capable of operating continuously throughout the year. Biological mechanisms found in nature can be used to produce everything from fuels and new materials to fine chemicals and food.

Many of these are already a reality. In another VTT project, microbes are creating leather-like materials. Finnish startup Solar Foods, originating from VTT, uses microbes to produce food protein from carbon dioxide and hydrogen produced using solar energy. 

Biotechnology as Part of the Bioeconomy  

Globally, investment in biotechnology is already significant. The UK’s national research funding body, UKRI, has allocated over € 950 biotechnology and bioengineering research over the coming decade. The EU considers biotechnology and bioproduction as critical technologies for Europe’s future competitiveness. Similarly, in the United States, biotechnology and biomanufacturing were elevated to a national research priority last year. China and South Korea have also expanded their biosciences research efforts. 

Compared to major nations, Finland is a small country, but relative to our size, we have been strong in biotechnology, Penttilä says. . 

“Our legacy in the forest industry has provided us with solid expertise in bio-based raw materials and bioproducts.”  Finland’s forests hold biomass, which could be developed for new uses now that global demand for paper has declined. Much can also be done with agricultural and food waste fractions. “When grain is harvested, straw can be used as a raw material in bioreactors,” Penttilä notes.

Biology-based Innovations offer endless possibilities  

Penttilä specializes in the molecular biology of microbes, yeasts and molds. Currently, she is coordinating research funded by a four-year grant from the Jane and Aatos Erkko Foundation. The focus is on how artificial intelligence can predict the behavior of proteins such as enzymes responsible for synthesis of the biochemical reactions in cells. This could lead to the design of new enzymes capable of performing reactions not found in nature. To produce these enzymes, corresponding new genes would also need to be designed. This could have immediate applications, such as the production of new biomaterials by microbes.

”Eri eliöiden biologiset prosessit muistuttavat hyvin paljon toisiaan. Jos opimme ennustamaan entsyymien toimintaa yhdessä eliössä ja sovelluskohteessa, nopeuttaa se kaikkea biotekniikan kehitystyötä”, Penttilä kertoo.  

Molekyylibiologian puolella tekoälyennusteet ovat jo todellisuutta. Proteiinien rakenteen ennustavan tekoälyn kehittäminen toi vuoden 2024 kemian Nobel-palkinnon Demis Hassabukselle ja John M. Jumperille. Palkittu kaksikko työskentelee Googlen tutkimuslaboratoriossa. Tämä on Penttilästä hyvin kuvaavaa. 

“The biological processes of different organisms are quite similar. If we learn to predict enzyme behavior in one organism and for one application, it will accelerate all biotechnological development,” Penttilä explains. The long-term applications are much broader, including for instance breeding of higher-yielding crops.

In molecular biology, AI-based predictions are already a reality. The development of AI that predicts protein structures won the 2024 Nobel Prize in Chemistry for Demis Hassabis and John M. Jumper. The award-winning duo works at Google’s research laboratory, which Penttilä finds very telling.

“The world is beginning to understand that biotechnology can impact everything in the future. For example, if we want to go to Mars, we need solutions for producing food on long journeys and on foreign planets”, she continues. 

It’s no surprise that biotechnology also interests IT giants.  

Bridging the funding cap

In Finland, Penttilä calls for more investment in the phase between basic research and applied research aimed at developing products and new services. 

“Projects funded by the Research Council of Finland are great for advancing understanding of basic biological mechanisms. On the other hand, Business Finland provides funding for setting up new companies or expanding the export potential of already established companies.”

However, there is a significant gap between these stages, which Penttilä believes needs suitable support instruments. This intermediate phase involves determining whether preliminary findings could be refined into industrial production. In biotechnology, much can be achieved at this stage by utilizing all available biological data and incorporating AI and robotics into the design of new cells, production processes, and products.  Existing industries often adapt to entirely new approaches somewhat sluggishly. Current models are rarely questioned until the industrial viability of new technologies is proven.

“That’s where funding from foundations, for instance, could step in,” Penttilä suggests.