The development of genomics technologies for guiding the predictive modeling of microorganism behavior to make food preservation treatments effective, are discussed. A fully genomewide description of cellular response to environmental conditions lies in the combination of a transcriptome and proteome/metabolome analysis. The predictive models based on mechanistics insight will have to make use of various levels of information and include physical parameters pertaining to the heat capacity and heat transfer during processing, and biochemical and nutritional parameters pertaining of the food. The developments also facilitate the construction of tools which allow tracking and tracing of microorganisms through whole food chain.