Method for detecting a microorganism in a sample, comprising the steps of: (a) providing the sample; (b) fixing the cells contained in the sample using a fixing agent and separating the resulting fixed cells from the sample in order to provide fixed cells; (c) bringing the fixed cells into contact with a chemical homogenising agent and drying the resulting homogenised cells in order to provide dried cells, wherein the chemical homogenising agent comprises (i) a monosaccharide or disaccharide, (ii) a polyol, and (iii) water; (d) bringing the dried cells into contact with a solution of a fluorescently tagged nucleic acid probe specific to the microorganism to be detected in order to provide a first reaction mixture; (e) incubating the first reaction mixture in order to cause binding of the fluorescently tagged nucleic acid probe to the corresponding target nucleic acid sequence in the cells of the microorganism to be detected; (f) following step (e), bringing the first reaction mixture into contact with a solution of a quencher-tagged nucleic acid probe in order to provide a second reaction mixture, wherein the quencher-tagged nucleic acid probe comprises a quencher which at least partially quenches the fluorescence of the fluorescently tagged nucleic acid probe and has a nucleic acid sequence which is substantially complementary to the nucleic acid sequence of the fluorescently tagged nucleic acid probe; (g) incubating the second reaction mixture in order to bring about binding of the molecules of the fluorescently tagged nucleic acid probe which are not bound to the target nucleic acid sequence in the cells of the microorganism to be detected to the quencher-tagged nucleic acid probe; and (h) following step (g), introducing the second reaction mixture into a flow cytometer, and detecting the fluorescence emitted by the cells of the microorganism to be detected which contain the fluorescently tagged nucleic acid probe. (a) providing the sample; (b) fixing the cells contained in the sample using a fixing agent and separating the resulting fixed cells from the sample in order to provide fixed cells; (c) bringing the fixed cells into contact with a chemical homogenising agent and drying the resulting homogenised cells in order to provide dried cells, wherein the chemical homogenising agent comprises (i) a monosaccharide or disaccharide, (ii) a polyol, and (iii) water; (d) bringing the dried cells into contact with a solution of a fluorescently tagged nucleic acid probe specific to the microorganism to be detected in order to provide a first reaction mixture; (e) incubating the first reaction mixture in order to cause binding of the fluorescently tagged nucleic acid probe to the corresponding target nucleic acid sequence in the cells of the microorganism to be detected; (f) following step (e), bringing the first reaction mixture into contact with a solution of a quencher-tagged nucleic acid probe in order to provide a second reaction mixture, wherein the quencher-tagged nucleic acid probe comprises a quencher which at least partially quenches the fluorescence of the fluorescently tagged nucleic acid probe and has a nucleic acid sequence which is substantially complementary to the nucleic acid sequence of the fluorescently tagged nucleic acid probe; (g) incubating the second reaction mixture in order to bring about binding of the molecules of the fluorescently tagged nucleic acid probe which are not bound to the target nucleic acid sequence in the cells of the microorganism to be detected to the quencher-tagged nucleic acid probe; and (h) following step (g), introducing the second reaction mixture into a flow cytometer, and detecting the fluorescence emitted by the cells of the microorganism to be detected which contain the fluorescently tagged nucleic acid probe.