Schematic figure illustrating the design and the principles of Flow-FISH protocol established in this study. (A) Single steps of optimized purification procedure 1-C2-S2-H1-F2. (B) The purified sample is used for Flow-FISH, a combination of fluorescence in situ hybridization (FISH) and a subsequent analysis by flow cytometry. During FISH the 16S rRNA molecules of target microorganisms are hybridized with fluorescence labeled oligonucleotides (FISH probes). Samples with fluorescence labeled microorganisms are analyzed by flow cytometer. In the flow cell fluorescently labeled particles are delivered in single file to pass a focused light beam. The fluorescence emission of labeled cells is detected simultaneously with the detection of the scattered light of particles in two directions representing the cell size and granularity. *SHMP = sodium hexametaphosphate.