Human digestive system is colonized by a large number of bacteria, estimated to 10(6) - 10(12) per one gram. Those bacteria through a network of interactions and interdependencies, are integrated superorganism. The intestinal flora is a very important element in host's defense against infections of the gastrointestinal tract, caused by for example Salmonella. Therefore, this bacteria have evolved a number of mechanisms, which adapt pathogen to the conditions of the gastrointestinal tract, and on the other hand to the change this environment, for easier colonization and internalization into host cells. One of elements of mentioned above interactions are antimicrobial peptides produced by host's Paneths cells, which have antimicrobial feature. Salmonella mostly are resistant for those peptides, moreover they can stimulate AMPs production for increasing their abilities in competition for ecological niche. In case of Salmonella quorum sensing mechanism was also identified. It allows for recognition of other bacteria presence, which stimulate Salmonella for higher expression of SPI-1, SPI-4 genes. These genes encoded proteins are involved in many host-pathogens interaction, inter alia inflammatory induction. Using of antibiotics in case of Salmonella infections always cause dramatic changes in intestinal flora compositions, which facilitate Salmonella internalizations to host's cells and sometimes could even stimulate to this process. Antibiotic treatment could also cause increase of antimicrobial resistance. Also antibiotics influence on Salmonella carriage was confirmed. Moreover antibiotics could cause super-shedder phenotype, what was detected on streptomycin-treated mice with Salmonella carriage.