Functional genomics and physiology

Research is focused on the functional genomics and eco-physiology of food-related micro-organisms, including food spoilage bacteria such as Lactobacillus spp. and thermophilic sporeformers and food-borne pathogens such as Salmonella Thyphimurium, Listeria monocytogenes and Bacillus cereus. Main research areas include microbial ecology and physiology, stress response, biofilm formation, sporulation and germination, combining molecular and physiological approaches. Results and insights obtained add to our understanding of microbial spoilage and pathogen behaviour in foods. An important and strategic element in this research includes analysis at the level of (sub)populations and/or single cells and spores using flow cytometry-assisted cell sorting (expert operator at FHM, M. Tempelaars; se also CAT-AgroFood website). This approach enables analysis of survival capacity and fitness of spoilage  microorganisms and pathogens at low numbers in different conditions including (model) foods. Based on this understanding more effective and/or novel combinations preservation treatments can be developed (see Fig. 1). Such information is also relevant for validation of minimal processing strategies developed at FBR, and joint projects (FBR contact Dr Masja Nierop Groot) aim to enhance mechanistic understanding of the impact of High Hydrostatic Pressure, Pulsed Electric Field and Cold Plasma treatments on adaptive stress response and survival capacity of selected target bacteria. Using genome sequenced model strains and environmental isolates further insight can be obtained about cellular targets and efficacy of these food preservation and surface disinfection treatments. Main results on microbial stress response, biofilm formation, bacterial spore resistance and germination have also been published in opinion and/or review papers such as Current Opinion in Biotechnology and Environmental Microbiology, next to a vision paper on bacteriophage applications in Microbial Biotechnology (see list of publications).

Functional genomics research on microbial spoilage and food-borne pathogens profits from cost effective and high throughput genome and RNA sequencing, that support genome comparisons and gene trait matching studies to identify key factors (and gene networks) contributing to robustness and fitness of evolved strains and variants (see figure 2). In cooperation with expert groups, virulence characteristics of evolved strains and variants will be assessed and data will be used to construct food chain models that support risk analysis and food safety management (together with den Besten and Zwietering).
 

Research and collaborations on (functional) genomics and eco-physiology of food-related micro-organisms, including food spoilage bacteria and food-borne pathogens may be extended to other relevant areas that are in line with current activities, and include, i. food system dynamics (joint action Food Science Cluster, in cooperation with den Besten and Zwietering) aiming at the development of new, safe and sustainable products and production processes, ii. identification and mechanistic understanding of novel antimicrobials targeting bacteria, yeasts and fungi, and iii. role of bacteriophages in pathogen ecology and their application in food quality and safety control (in cooperation with Smid).

For more information about functional genomics and physiology or education/graduation projects mail to Tjakko.abee@wur.nl or check the reader/page with projects for BSc and MSc projects.