Human organism consists of not only from numerous of eukaryotic cells but also from thousands of microorganisms. The most complicated is the microflora of gastrointestinal tract. Numerous studies indicates that the complex network of interactions between the host organism and its microbiome can have a very significant impact on the health condition of the host. These interactions can affect not only to gastrointestinal tract but can be related to different processes and organs. Disturbance of the homeostasis, e.g. after antibiotic course, can therefore have significant health implications Therefore, very important is the deepest exploring of the network of these interactions and dependencies.