Call for Partners | FermFinder: genome-guided screening of fermentation traits for healthy and tasty plant-based foods

Fermentation is a powerful tool to improve the sensory and nutritional qualities of (dairy or plant-based) foods. It can enhance desirable traits such as flavor and availably of beneficial compounds while reducing unwanted components. At Wageningen Food & Biobased Research, we have explored this potential through extensive screening efforts, resulting in large databases of flavor volatiles from fermented plant-based substrates. We have also studied the positive effects of fermentation on gut health and nutritional value. However, the key challenge that remains is to determine which microorganisms to use, on which substrates, and under what cultivation conditions to yield the fermentation process that results in tastier and healthier foods. Current approaches rely on high-throughput more trail-and-error lab-based screening, which is resource-intensive and still leaves much of the available genetic information unexplored. 

To address this, the FermFinder initiative aims to enable more targeted R&D in food fermentation by leveraging genome data. By identifying health- and flavor-enhancing molecules produced via microbial fermentation, we aim to systematically select target compounds relevant to food quality. We will build a curated library of enzymes and metabolic pathways that are responsible for microbial production of these compounds. Using in silico metabolic mapping, we will screen food-grade microorganisms—such as lactic acid bacteria and yeasts—for their biosynthetic potential. Candidate strains are then further assessed on key criteria like regulatory status, optimal cultivation conditions, and intellectual property considerations. Top candidates are selected for high-throughput lab validation of the identified traits, and the results are fed back into the screening model to refine its predictive power. 

This integrated approach will help unlock the full potential of microbial fermentation in plant-based foods by enabling faster, more efficient, and scalable development of strains that improve taste, health benefits, and sustainability.