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Rumen Bacterial Community of Young and Adult of Reindeer Open Agriculture. 2020; 5: 10-20 Research Article Kasim A. Laishev, Larisa A. Ilina, Valentina A. Filippova, Timur P. Dunyashev, Georgiy Yu. Laptev, Evgeny V. Abakumov* Rumen bacterial community of young and adult of reindeer (rangifer tarandus) from Yamalo-Nenets Autonomous District of Russia https://doi.org/10.1515/opag-2020-0001 that the presence of the phylum Verrucomicrobia, and the received June 15, 2019; accepted December 3, 2019 genera Stenotrophomonas, Pseudomonas, etc., may be specific to Nenets breed reindeer and have a pattern with Abstract: The aim of the work was to compare the taxo- their presence on various plants and lichens that are part nomic composition of the rumen procariotic community of the reindeer diet. This is partially confirmed by data on in young and adult individuals of Nenets breed rein- plants microbiome taxonomy. deer (Rangifer tarandus ) from the central part of the Yamal region by using the NGS method (next generation Keywords: Reindeer; Rumen; Microbiome; Polar environ- sequencing) and compare the microbiome composition ments; Vegetation materials; Metagenomics; taxonomy of reindeer with the microbiome of their initial vegetation food material. The obtained data showed that the domi- nant position in microbial communities, like that of other ruminants, was occupied by representatives of phylum 1 Introduction Firmicutes and Bacteroidetes, whose total share between observed groups did not differ significantly. The compo- Currently, agriculture in the Russian Arctic is an inten- sition of the microbiome of the rumen of the investigated sively developing part of the local economic. Strong group of animals was completely different from the micro- localization of industrial and agricultural activity in biome structure of the initial vegetation cover. Digestion polar environments results in an increased consump- of vegetation by reindeers resulted in complex transfor- tion of local production by inhabitants of highly urban- mation in the initial plant microbiome and an increase of ized areas (Russian Arctic is the most urbanized part of biological diversity which was expressed in operational the country). The microbiome of agricultural ecosystems taxonomic unit (OTU) numbers increasing and changes in polar environments is under investigation and only a in indexes of alpha-diversity parameters. According to the few data are known about the taxonomy and functional results of alpha- and beta- diversity of the rumen micro- composition of the microbiome in compartments of arctic bial communities, the greatest uniqueness was revealed ecosystems environments. The stable state of the popula- for the microbiomes of the adults in comparison with tion of reindeer in current conditions is faced with a dev- calves and young. The presence of changes in the biodi- astation process. The reindeer’s rumen microbiota plays versity indexes of the rumen microbiota in the reindeer, an important role in food digestion (Church 1993; Morgavi examined by us, confirm the opinion of the researchers et al. 2013) due to enzymes produced by symbiotic micro- that the microbial community may also reflect the physio- organisms. In this context, the study of living reindeers in logical state of the animals. It has also been demonstrated natural conditions and the formation of their adaptations is required for corrections of current agricultural practices. This special interest is connected with the possibility for *Corresponding author: E.V. Abakumov, Saint-Petersburg State the effective use of poor Arctic region plant resources for University, 199178, 16-lne 29 Vasilyevsky Island Saint-Petersburf, Russia, E-mail: [email protected], [email protected] feeding, which undoubtedly can exert significant selective K.A. Laishev, North-West Center for Interdisciplinary Research of pressure on the structural and functional organization of Food Scurity Problems, Federal Agency of Scientific Organizations, the ruminal microbiome (Tarakanov 2006; Mukhachev 7, sh. Podbel’skogo, St. Petersburg-Pushkin, 196608 Russia and Layshev 2007). This problem became more urgent in L.A. Ilina, V.A. Filippova, T.P. Dunyashev, G.Yu. Laptev, «Biotrof+» Ltd, 19 korp. 1, Zagrebskii bulv., St. Petersburg, 192284 Russia Open Access. © 2020 K.A. Laishev et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution 4.0 Public License. Reindeers rumen microbial communmity dynamics 11 the context of increasing over pasturing of tundra’s in the represented by green plants, mosses, twigs, and various Yamalo-Nents autonomous region. impurities (Borozdin et al. 1990, Mukhachev, Layshev Reindeer (Rangifer tarandus) take a special place 2007). Among the important functions of reindeer rumen among other herbivorous ruminants. This is a unique anaerobic microflora is its ability to detoxify the second- animal species, which during the expansion of its habitat, ary phenolic metabolites of lichens, e.g. usnic acid (Orpin has acquired specific adaptations for life in the severe et al. 1985; Sundset et al. 2008). However, by examining northern conditions. Agriculture in the Arctic zone is 32 livestock species, Henderson et al. (2015) demonstrated mostly reindeer farming. Nowadays on the territory of that changes in the rumen microbiota were associated the Russian Federation there are more than 1.5 million with the identity of the host species, and not with the diet. domestic reindeers, and in the Yamalo-Nenets Autono- The reindeer rumen ​​microbiome is less studied (Aagnes et mous District – there are about 680 thousand individuals. al. 1995; Sundset et al. 2007) compared with other rumi- This results in over grazing and degradation of vegetation nants, such as sheep and cattle (Jami and Mizrahi 2012). resources, as well as land use redistribution. The quality Until the 1990s, studies of reindeer ruminal microor- of pastures is susceptible to intensive changes. That is why ganisms were based on observations of cultured strains investigation of reindeer food quality, with special refer- on artificial nutrient media (Hungate 1966). Certain ence to microbiological characteristics of their stomach, is strains of reindeer ruminal fungi were studied (Orpin et urgent for development of current agricultural practices in al. 1985; Mathiesen 2005; Sundset et al. 2007). The devel- the polar environments. opment of molecular-genetic methods for observing the The geographical isolation of reindeer from other microorganisms has significantly expanded the under- subspecies of the ruminant family Cervidae (Sundset et standing of microbiome composition of the rumen. An al. 2007) not only resulted in anatomical and morpholog- important feature of metagenomic studies is the absence ical differences in the structure of their digestive system, of the need to cultivate microorganisms, which is a fun- compared with other ruminants (Dubos 1966; Hofmann damental point, since up to 99% of microorganisms in 1973; Hackmann et al. 2010), but also in the formation of the biosphere cannot be cultivated on artificial nutrient specific microbial communities of the rumen. These dif- media. Moreover, in polar environments the presence of ferences could be the result of: microbiome composition cultivated forms of microorganisms are very low. That is of local vegetation resources and adaptation of reindeer why previous studies essentially under evaluation the tax- to severe environmental conditions in arctic ecosystems. onomic and functional diversity of gastrointestinal micro- There are some studies that suggest that there is a corre- biota. lation between the evolution of a host organism and its According to estimates, the diversity of ruminal micro- intestinal microbiota (Brooks et al. 2016; Groussin et al. organisms reaches several thousand species, of which less 2017). It is reasonable to suggest that the difference in the than 100 have been studied in detail. Most among them intestinal microbiota may be due to the divergence of their are strictly anaerobic uncultivated species, which cannot hosts in the process of evolution (Delsuc et al. 2014). be investigated without application of metagenomic The relation of host phylogeny and their dietary strat- techniques (Henderson et al. 2015). Therefore, the most egies, the connection between host genetic diversification informative way of studying the rumen microbial com- and the gastrointestinal microbiota is still under investi- munity is molecular genetic methods such as NGS (next gation (Ley et al. 2008; Muegge et al. 2011). It has been generation sequencing), which are not primarily aimed at shown that the microbial community of the rumen may studying its individual members, but the structure of the also reflect regional characteristics of the diet and the community as a whole. NGS is the most modern technique general physiological state of the animals. Also, the pecu- that allows analysis of several hundred thousand genetic liarities of vegetation used as a feed by reindeers, in terms sequences at once, determining the structure of the micro- of initial composition of microbiome, could be a factor bial community and assessing the influence of various which affects gastrointestinal microbiota quality. factors on it. The composition of reindeers’ food base varies sig- Few publications can be found about the ruminal nificantly with the season. During the summer-autumn microbiocenosis of reindeers in the territory of Norway. period, the basis of their diet is plants, including cereals, Zielińska et al. (2016) studied the microbial
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