Functional genomics and physiology

Our main research areas include microbial ecology and physiology, stress response, biofilm formation, sporulation and germination, combining molecular and physiological approaches. Through this work, we aim to improve understanding of microbial spoilage and pathogen behaviour in foods.

Survival capacity and fitness

A key and strategic element of our research is the analysis of (sub)populations and single cells or spores using flow cytometry-assisted cell sorting. This approach allows us to analyse the survival capacity and fitness of spoilage microorganisms and pathogens present in low numbers under various conditions, including in (model) foods. Based on these insights, we develop more effective or novel combinations of preservation treatments. 

In joint projects with colleagues at WUR, we aim to deepen mechanistic understanding of how High Hydrostatic Pressure, Pulsed Electric Field and Cold Plasma treatments affect the adaptive stress response and survival capacity of selected target bacteria. Using genome-sequenced model strains and environmental isolates, we further investigate the cellular targets and efficacy of food preservation and surface disinfection treatments.

Identification of key factors

Our functional genomics research on microbial spoilage and food-borne pathogens benefits from cost-effective, high-throughput genome and RNA sequencing. These techniques support genome comparisons and gene-trait matching studies to identify key factors and gene networks that contribute to the robustness and fitness of evolved strains and variants. In collaboration with expert groups, we assess the virulence characteristics of evolved strains and variants and use the resulting data to build food chain models that support risk analysis and food safety management (in cooperation with den Besten and Zwietering).

We aim to expand our research and collaborations on functional genomics and eco-physiology of food-related microorganisms into other relevant areas that align with our current activities. These include:

• food system dynamics (joint action within the Food Science Cluster, in cooperation with den Besten and Zwietering), aiming to develop new, safe and sustainable products and production processes;
• identification and mechanistic understanding of novel antimicrobials targeting bacteria, yeasts, and fungi; and
• Exploring the role of bacteriophages in pathogen ecology and their application in food quality and safety control (in cooperation with Smid).