Taxonomic analysis of metagenomes and variety of plant polymers serving as food source for microbial communities in rumen of wild ruminants

Prežvekovalci so rastlinojedci, ki so izjemno uspešni v razkroju kompleksnih strukturnih rastlinskih polimerov, ki so za vretenčarje neprebavljivi. V specializiranem želodcu – vampu prežvekovalci vzdržujejo kompleksno mikrobioto, ki s sinergijskim delovanjem proizvaja številne celulolitične in hemicelulolitične encime za razgradnjo težko razgradljivih rastlinskih polimerov. Prežvekovalci mikrobom zagotavljajo okolje, bogato s hranili, dokler jim mikrobi s hlapnimi maščobnimi kislinami, ki so končni produkt fermentacije, zadovoljijo 70 % dnevnih energetskih potreb. Z namenom, da bi bolje razumeli ta sistem, smo proučili prehrano petih prostoživečih prežvekovalcev in taksonomsko sestavo vampne mikrobiote treh udomačenih prežvekovalcev. Z enostavno metodo ugotavljanja razlik v dolžini ITS regij rDNA rastlin smo ugotovili prehranske profile petih prostoživečih prežvekovalcev in ugotovili, da je njihova prehrana v glavnem sestavljena iz štirih rastlin: Larix decidua, Anemone nemorosa, Juniperus alpine in Carex nigra. Sestava prehrane je podobna sestavi, ki so jo ugotovili drugi raziskovalci. Dominanta bakterijska debla so Firmicutes, Proteobacteria, Bacteroidetes in Actinobacteria. Za razliko od ostalih študij smo opazili veliko večjo udeležbo debla Proteobacteria pri dvema skupinama prežvekovalcev. Pri teh živalih je tudi razmerje dominantnih debel nenavadno, saj je deblo Proteobacteria pogosteje zastopano kot debli Firmicutes in Bacteroidetes, ki sta v naši raziskavi po številčnosti na četrtem mestu, na tretjem pa je deblo Actinobacteria. Opazili smo nenavadno visoko zastopanost rodov Bifidobacterium, Mitsuokella in Paenibacillus ter rodov Acheoplasma in Geobacillus, ki nista identificirana v ostalih raziskavah vampne mikrobiote. Sestava arhej je precej podobna sestavi iz prejšnjih raziskav. Dominantne so arheje iz debla Euryarchaeota in rodu Metanobrevibacter, ki predstavlja 22 % vseh arhejskih sekvenc in se nahaja v vseh vzorcih. Na koncu potrjujemo, da je sestava vampne mikrobiote v največji meri odvisna od gostitelja in da se med različnimi živalmi razlikuje.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