Ruminants have evolved to digest diverse plant materials by a complex consortium of rumen microbes. Humans and other mammals produce only enzymes for digestion of animal and plant proteins, lipids, sugars and starches, they have no mechanism for digestion of the abundant plant structural polysaccharides: cellulose, hemicellulose and pectins. Herbivores on the other hand developed an ecto-symbiotic relationship with microorganisms, which provide the enzymes required to digest plant structural polysaccharides in the gastointestinal tract. Wild alpine ruminants forage on extremely complex plant polymers most of the year: poor quality vascular plants, mosses, lichens and fungi. This suggests that they are tolerant to fiber and tannin-rich plants and capable of digesting the recalcitrant plant polymers from their winter forage. Alpine wild ruminants therefore represent a very special microbial ecosystem with maximum degradation efficiency of recalcitrant plant material, but their rumen bacteria and dietary preferences have not been comprehensively studied yet.
The objective of our extensive metagenomic study is to identify the microbial key genes, involved in the degradation of complex plant polymers in the gastrointestinal tract of wild ruminants. First, we plan to characterize plant polymers representing the local Alpine flora consisting wild ruminant feed in the montane region of the mt. Košuta, which forms part of the State hunting reserve Kozorog Kamnik. This region is one of the largest, most preserved, and biodiverse hunting areas in Slovenia. Due to its high altitude gradient (2200 m), it is characterized by a mixture of continental and sub-polar (alpine) climates with occasional Mediterranean influences. Five species of wild ruminants can be found distributed in this area, depending on their natural preferences: roe deer, red deer, chamois, mouflon, capricorn.
We intend to perform deep sequencing of prokaryotic transcriptome to determine the extent and type of microbial transcripts with denovo assembly. This will serve as a basis for the identification of transcripts of functional genes in the mammalian gastrointestinal tract involved in the degradation of the plant cell wall polysaccharides, their nature and dynamics of the expression of key genes for the degradation of complex polysaccharides.