On the basis of anatomical and physiological similarities between animals and humans, animal models are used for research and testing in biology and medicine. Giving rise to new drugs, vaccines, and treatments, whether for infectious or lifestyle diseases. Germ-free animals are animal models which do not carry any microorganisms (bacteria, viruses, fungi, protozoa, and parasites included) during their entire life-span. Gnotobiotic animals have a precisely defined microflora. These models help us understand not only the interactions between single microorganisms, but also between the microflora and different chemical substances. In our study, we have observed the intestine metabolism in germ-free animals, contaminated by Bacillus licheniformis, and in gnotobiotic animals contaminated by the bacteria Bacillus licheniformis with a continual application of the probiotic strain of Lactobacillus reuteri CCM 8617. The concentration of all observed organic acids in the droppings of the germ-free animals (group K1) was very low with a maximum value of 8,0 mmol/l. The concentrations of the observed organic acids in gnotobiotic mice with the monoculture Bacillus licheniformis were also comparably low. However, compared to the germ-free specimen, the concentrations reached a level of 12 mmol/l. In contrast to the animal group (K2, Bacillus licheniformis), the dixenic mice contaminated with Bacillus licheniformis and a continual application of Lactobacillus reuteri CCM 8617 (group L) have demonstrated a significantly higher concentrations of a majority of the observed acids, mainly: lactic acid on the 2nd day ( p < 0,01), on the 5th and 10th day (p < 0,05) of the experiment, propionic acid on the 2nd day of the experiment ( p < 0,01), succinic acid on the 10th day of applying the probiotic strain ( p < 0,05), and valeric acid on the 5th day of the experiment (p < 0,01). A higher production of organic acids has been confirmed in the section of cecum of the animal group with the monoculture Bacillus licheniformis. The applied probiotic strain Lactobacillus reuteri CCM 8617 was maintained in a range from 8,7 – 7,7 log KTJ/g. The results obtained indicate a positive effect of a continual application of the probiotic bacteria Lactobacillus reuteri CCM8617 on intestinal metabolism manifested by an increased concentration of organic acids in mice droppings, particularly in acetic acid, lactic acid, acetoacetic acid, succinic acid and propionic acid. Key words: germ-free animals, probiotic microorganisms, isotachophoresis, microflora