Microbial Characterisation
A key objective of HealthFerm is to identify and understand microorganisms that can improve the nutritional quality, functionality and sustainability of fermented plant-based foods. To achieve this, researchers combined functional screening with advanced genome sequencing and bioinformatics to characterise microorganisms with promising technological and health-promoting properties. The resulting genomic resource provides an essential foundation for developing next-generation starter cultures tailored to cereal- and pulse-based fermentations.
HealthFerm successfully generated and annotated high-quality genomes for 102 microbial strains isolated from a wide range of fermented foods across Europe, including sourdough, borş, water kefir, kombucha and other traditional fermented products. Many of these strains originated from partner culture collections, while others were identified through the project's citizen science campaign, linking community participation directly with cutting-edge genomic research.
The selected microorganisms were chosen because of their potential to deliver important functional benefits during fermentation, including the production of short-chain fatty acids, exopolysaccharides and vitamin B12, as well as their ability to degrade dietary fibres, proteins and antinutritional compounds. By combining genome sequencing with phenotypic data generated elsewhere in the project, HealthFerm is creating a comprehensive understanding of how microbial genetics translates into fermentation performance and health-related functions.
These genomic data represent far more than a catalogue of microorganisms. They provide the basis for comparative genomics, genome mining, genotype-phenotype association studies and metabolic modelling, enabling researchers to predict microbial functionality before laboratory validation. This knowledge will support the rational design of starter cultures that enhance nutritional quality, improve fermentation efficiency and contribute to healthier, more sustainable fermented foods.
By creating one of the most comprehensive genomic resources for plant-based fermentation microorganisms, HealthFerm is helping to close important knowledge gaps and accelerating the development of innovative fermented foods that benefit both consumers and the food industry.