EpiFerm

"EpiFerm– Epigenetics in Fermentation: Unlocking Methylation Maps of Starter Cultures."

The EpiFerm project aims to better understand how bacteria behave during fermentation, particularly in the production of plant-based foods such as fermented legumes or dairy alternatives. While scientists can already read the DNA of these bacteria and identify their genetic potential, it has been observed that strains with nearly identical genetic content can behave very differently. Some produce better flavors, others grow more efficiently, and some are more robust in industrial processes. This suggests that genetics alone cannot fully explain bacterial performance.

⌐ The project has been granted 2.999.440 DKK in funding.  
⌐ The project starts on 1 March 2026 and will end on 31 December 2027.

Introducing the EpiFerm project

Background for the project:

EpiFerm focuses on an additional layer of biological regulation known as epigenetics. In bacteria, this mainly involves chemical modifications of DNA, such as methylation, which can influence how genes are activated or silenced. These modifications do not change the genetic code itself but affect how it is used, acting as regulatory switches that can alter bacterial behavior.

This project is a top-up to the ongoing Plant2Food project MiCoP, which is developing a data-driven framework for designing microbial communities for plant-based fermentation. MiCoP has already generated a large collection of bacterial genomes and fermentation data, and aims at linking genetic features to functional outcomes. EpiFerm builds directly on this foundation by adding epigenetic information, thereby extending the understanding from gene content to gene regulation. By combining genetic and epigenetic data, the project aims to provide a more complete explanation of why bacterial strains differ in performance.

The activities 

The project will reanalyze existing long-read sequencing data from approximately 140 bacterial strains to recover high-resolution maps of DNA methylation. These epigenetic patterns will be linked to fermentation characteristics and tested experimentally in both controlled laboratory conditions and real-life production environments. This approach allows the project to extract new insights without the need for additional data generation, making it both efficient and innovative.

Outcomes

The expected outcomes include new knowledge about the role of epigenetics in bacterial function, improved methods for selecting and optimizing starter cultures, and openly available datasets and analytical tools for the scientific and industrial communities. Ultimately, EpiFerm aims to support the development of more reliable, high-quality, and sustainable plant-based fermented foods by enabling a deeper understanding of microbial behavior.