Gene expression and proteomic adaptation of food borne pathogens in response to environmental stress and natural antimicrobials in dairy traditional foods

Dairy products have been associated with several foodborne disease occurrences caused by bacteria. Several intrinsic factors, including the use of natural antimicrobial compounds, as well as extrinsic factors and a competitive microbiota represent stresses useful to hamper the growth and survival of microbial pathogens. Microbial cells have adopted defense systems to survive and to face adverse environmental and technological stresses. Adaptation systems work through a wide range of cellular pathways that can be differentially regulated due to different physiological states of cells and to genetic differences. In the last years the classical methodologies based on phenotypic characterization has been complemented with proteomics and other omics approaches to unravel the stress adaptation framework. Despite recent progress, details on the mechanisms of action of the more promising natural molecules against food-borne microorganisms and how they adapt and regulated the transcription and expression of their proteins during stresses exposure in traditional dairy products remains largely unclear.

Quantitative proteomics analysis to measure the overall protein expression changes of selected wild-type or mutant strains of foodborne pathogens after environmental stress and natural antimicrobial treatment in traditional dairy products will be performed. Subsequently, the identification of the microbial phenotypic and metabolites modifications after perturbation induced by stress will be carried out by phenotype microarray and MS spectroscopy.

Evaluation of the effects of the natural antimicrobials on specific target genes recognized to play an important role in the stress response mechanisms of bacteria and optimization of the protocols for the up-scaled use of natural preservatives in traditional dairy processing. 

Mutants by inactivating environmental adaptation key genes (e.g. oxidative stress response, biofilm) will be created to identify the role of these genetic elements in the stress adaptation. Experiments in dairy pilot plants mimicking industrial cheese manufacturing will be carried out.

The main aim is the evaluation of microbial molecular adaptation to stressful environment, providing the basis for the future development of suitable molecule mixtures in relation to the food shelf-life and safety requirements in traditional Italian foods. The omic approaches and the comparison of the transcriptomic and proteomic profiles of virulent strains, also harbouring mutations in specific genes coding for key features, will provide a better knowledge on the molecular mechanisms of adaptive and survival strategies to natural antimicrobial compounds and will reveal the key pathways and subcategories of differentially expressed proteins: on one side the progressive damages of the cells due to the application of stressful condition, on the other side strategies set up by the microorganisms to survive to them will be observed. The gene expression and proteomic shift associated with the stress exposure will be linked to microbial phenotypic and metabolic modifications, which are the final expressions of genomic information.