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Ilina L.A., Filippova V.A., Layshev K.A., Yildirim E.A., Dunyashev T.P., Brazhnik E.A., Dubrovin A.V., Sobolev D.V., Tiurina D.G., Novikova N.I., Laptev G.Yu., Yuzhakov A.A., Romanenko T.M., Vylko Yu.P. Variation in the russian arctic reindeer (Rangifer tarandus) rumen microbiome related to season change. Sel'skokhozyaistvennaya Biologiya [Agricultural Biology], 2020, Vol. 55, № 4, p. 697-713.
(how to cite this article)

doi: 10.15389/agrobiology.2020.4.697eng

UDC: 636.294:579.62:577.2

Acknowledgements:
Supported financially by Russian Science Foundation for project No. 17-76-20026 “Rumen microbiocenosis in Rangifer tarandus of the Russian Arctic as a fundamentals for promising animal biotechnologies”

 

VARIATION IN THE RUSSIAN ARCTIC REINDEER (Rangifer tarandus) RUMEN MICROBIOME RELATED TO SEASON CHANGE

L.A. Ilina1, V.A. Filippova1, K.A. Layshev2, E.A. Yildirim1,
T.P. Dunyashev1, E.A. Brazhnik1, A.V. Dubrovin1, D.V. Sobolev1,
D.G. Tiurina1, N.I. Novikova1, G.Yu. Laptev1, A.A. Yuzhakov2,
T.M. Romanenko3, Yu.P. Vylko3

1JSC Biotrof+, 19, korp. 1, Zagrebskii bulv., St. Petersburg, 192284 Russia, e-mail ilina@biotrof.ru (✉ corresponding author), deniz@biotrof.ru, filippova@biotrof.ru, timur@biotrof.ru, dubrowin.a.v@yandex.ru, sdv@biotrof.ru, natalia-iv-nov@rambler.ru, georg-laptev@rambler.ru;
2Northwest Center for Interdisciplinary Research of Food Security Problems, 7, sh. Podbel’skogo, St. Petersburg—Pushkin, 196608 Russia, e-mail layshev@mail.ru, alyuzhakov@mail.ru;
3Laverov Federal Center for Integrated Arctic Research (FCIARctic) RAS, Naryan-Mar Agro-Experimental Station, 1a, ul. Rybnikov, Naryan-Mar, Nenets AO, 166004 Russia, e-mail nmshos@atnet.ru, vylcko.yury@yandex.ru

ORCID:
Ilina L.A. orcid.org/0000-0003-2789-4844
Sobolev D.V. orcid.org/0000-0002-3238-979X
Laishev K.A. orcid.org/0000-0003-2490-6942
Novikova N.I. orcid.org/0000-0002-9647-4184
Yildirim E.A. orcid.org/0000-0002-5846-5105
Laptev G.Yu. orcid.org/0000-0002-8795-6659
Filippova V.A. orcid.org/0000-0001-8789-9837
Yuzhakov A.A. orcid.org/0000-0002-0633-4074
Dunyashev T.P. orcid.org/0000-0002-3918-0948
Romanenko Т.М. orcid.org/0000-0003-0034-7453
Dubrovin A.V. orcid.org/0000-0001-8424-4114
Vylko Yu.P. orcid.org/0000-0002-6168-8262

Received April 15, 2020

Reindeer (Rangifer tarandus) is a large Holarctic herbivore animal, the habitat of which, including its existence at low temperatures and poor diets, has led to the evolutionary development of their unique rumen microbiota, which is necessary for the efficient assimilation of the Arctic flora. In winter, lichens rich in secondary metabolites which can influence the representatives of the microbial consortium of the digestive tract, make up a large proportion of reindeer fodder plants. The toxic effects of certain lichen metabolites (e.g., usnic acid) on a number of microorganisms (Clostridiales, Enterococcus, Staphylococcus aureus, Escherichia coli, etc.) as well as ruminants (elk) were previously reported. However, little is known about the effect of lichen consumption on the reindeer rumen microbiome. Using molecular analysis, we were the first to study the seasonal patterns of the formation of the microbial communities of the rumen of the reindeer Rangifer tarandus, living in the Russian Arctic. The purpose of the study was to compare the composition of the bacterial community of the reindeer rumen in the summer-autumn and winter-spring periods using the method of NGS-sequencing. In the analysis of microbial communities, biodiversity, taxonomic structure, and the relationship of these indicators with the characteristics of reindeer nutrition in connection with seasonal changes were evaluated. Samples of the rumen content were collected in the summer-autumn and winter-spring periods in 2017-2018 from 20 Nenets reindeer (calves 4-8 months old and adult animals 3-6 years old, n = 3 per each age group) in the Nenets Autonomous District (AD). Seasonal differences, in contrast to gender and age, turned out to be the main factor influencing the reindeer rumen bacterial community, which, most likely, is due to differences in the composition of the pasture diet. In the summer-autumn period, a significant increase in the α-biodiversity of the rumen microbiome was noted compared to the winter-spring time for the number of OTUs, Chao1 and Shannon indices. A comparison of the β-diversity of the reindeer rumen microbiota composition has demonstrated the presence of pronounced cluster formation for samples collected in different seasons of the year. Despite the fact that in the winter period the diet of reindeer was mainly represented by lichens which are not typical food for other ruminants (such as cattle, sheep, etc.), it was interesting to note that, on the whole, the obtained microbiome profiles correspond to modern ideas about the ruminant rumen microbiota. Nevertheless, during different seasonal periods, significant changes in the representation of a number of taxa were noted, the clearest of which were detected for microorganisms associated with feed polysaccharide fermentation. So, in the winter-spring season, a significant increase in microorganisms that decompose polysaccharides of lichens, including hemicellulose (Butyrivibrio, Ruminococcus), and lichenin (Succiniclasticum, Paraprevotellaceae,and Prevotella). In the summer-autumn period, a significant increase in the proportion of cellulolytic bacteria (Clostridium, Blautia, Clostridiales, Christensenellaceae Mogibacteriaceae,and Prevotellaceae) is noted. In addition, it has been shown that in the summer period a whole spectrum of microorganisms that belong to bacterial pathogens, including Erysipelotrichaceae, Coriobacteriaceae, Mycoplasmataceae,and Rickettsiales, proliferate in the reindeer rumen. On the whole, the results obtained allow us to conclude that the reindeer rumen microbiome is quite clearly associated with nutritional characteristics during various seasonal periods, which determine adaptation to environmental conditions.

Keywords: Rangifer tarandus, reindeer, rumen, microbiome, seasonal changes, NGS, Russian Arctic.

 

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