Ruminants are herbivores with remarkable ability to degrade complex structural plant polymers otherwise indigestible for invertebrates. In specialized stomach-rumen, ruminants harbor complex microbiota which produces various cellulolytic and hemicellulolytic enzymes through synergistic interactions in order to degrade plant polymers. Ruminants provide the environment rich in nutrients to microorganisms who in turn produce short-chain volatile fatty acids as fermentation end product that provide
70 % percent of the daily metabolizable energy for host animal. In order to better understand this system, we studied the diet of five free-living ruminants and taxonomic composition of the rumen microbiota of three groups of domesticated ruminants. With a simple method of determining differences in the size of the rDNA ITS regions of plants we determined the diet profiles of five animals and found that their diet mainly consists of four plants: Carex nigra, Anemone nemorosa, Juniperus alpine and Larix decidua. Diet composition is comparable to that found by other researchers. Dominant bacterial phyla are Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. Unlike other studies, we observed a much greater abundance of the Proteobacteria phyllum in two animal groups. Furthermore, the ratio of dominant phyla in those two groups is uncommon because Proteobacteria are generally more abundant than Firmicutes and Bacteroidetes. The latter are in the fourth place and Actinobacteria in third. We observed a surprisingly high abundance of the genera Bifidobacterium, Mitsuokella, and Paenibacillus and two genera, Acheoplasma and Geobacillus, which are not described as a part of rumen microbiota in other studies. The dominant archaeal phylum is Euryarchaeota and most abundant genus is Methanobrevibacter found in all samples and accounting for 22 % of all archaeal sequences. Finally, we confirm that the composition of the rumen microbiota largely depends on the host and that it varies between different animals.
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