The development of multi-parameter flow cytometric techniques in our laboratories has led to a functional classification of the physiological state of single celled micro-organisms, including both yeast and bacteria. This classification is based on the presence or absence of an intact fully polarized cytoplasmic membrane and the transport systems across it. Using these techniques it is possible to resolve a cells physiological state, beyond culturability to include metabolic activity enabling assessment of population heterogeneity. Importantly results are available in real-time, 1-2 min after a sample is taken, enabling informed decisions to be taken about a process. These techniques have been extensively applied by us for monitoring the stress responses of micro-organisms in such diverse areas as brewing, bio-remediation, bio-transformation, food processing and pharmaceutical fermentation, some of which are discussed here.