The microbiota plays an important role in human health. Disturbance in microbiota composition can be compensated by administration of probiotic microorganisms. However, their application is associated with some constraints. Probiotics are commonly used in disease prevention, whereas they play only a supportive role in disease therapy. Moreover, probiotics during technological processes and gastrointestinal tract passage may lose their beneficial properties. These constraints can be overcome by genetic modification of bacteria. The current research shows that genetically modified bacteria can have new biological properties and can be used in diagnostics and therapy.