The wild ruminants which live in the high mountains feed on plants that have a very high lignin content. This represents an additional challenge for the intestinal microbiota. However, these wild ruminants are one of the most efficient animals in their digestion of this kind of plants. Due to the fact that they have basically an unlimited number of different plant species on which they can feed, their diet is poorly understood. The purpose of this master's thesis was to determine the doe's, deer's, roe deer's and chamois' diet, all of which live in the State hunting reserve with the special purpose Kozorog Kamnik. By using very simple and inexpensive methods we managed to establish a database consisting of 79 plant species and a platform for the routine analysis of ruminal and fecal samples. With the use of the PlantID platform, we have successfully identified the plant species found in the ruminal and fecal samples. Furthermore, we have made a comparison of the sheep's, bovine's and cow's metagenomes at the level of all genes and at the level of only those genes which are involved in the break down of carbohydrates. Additionally, we have identified the experimental parameters that had the greatest impact on the dispersion of these data and they were: the type of study, sequencing method, the type of the animal host and experimental replicates, respectively.