The project addresses design, development and use of physical methods for research of microbial pathogens and their interactions with the environment. The metabolic processes of these microorganisms are regulated by various influences, such as oxygen availability, temperature, culture age, the presence of biofilm, other bacterial species, bacteriophages, or antimicrobial drugs. These interactions remain largely unexplored due to lack of techniques that would allow long-term non-destructive chemical analysis of individual cells under strictly regulated conditions.