Individuals within natural populations are highly diverse. They can vary regarding their physiological states and thus contribute differently to the performance of the whole community [1]. Hence, the characterization of microbial physiology on the single cell level is crucial for optimization and understanding of biotechnological processes.

Here a protocol is presented for detecting and monitoring the functional heterogeneity in a given yeast population, on both the cellular and molecular levels, using flow cytometry and microarray analysis (first published in Nature Protocols by Achilles et al. [2]). The protocol includes staining of living S. cerevisiae cells with three different fluorescent dyes, flow cytometric analysis, sorting of live cells and stabilization of their status, the subsequent isolation of RNA from small amounts of separated cells, and finally the quantification and integrity check of this RNA. Owing to the high quality and quantity of the isolated RNA from sorted cells, gene expression analysis can be performed by using microarrays, for example.