Yildirim Elena, Ilina Larisa, Laptev Georgy, Filippova Valentina, Brazhnik Evgeni, Dunyashev Timur, Dubrovin Andrey, Novikova Natalia, Tiurina Daria, Tarlavin Nikolay, Laishev Kasim
Molecular Genetic laboratory, BIOTROF+ LTD, Saint-Petersburg, Russia.
Department of Animal Husbandry and Environmental Management of the Arctic, Federal Research Center of Russian Academy Sciences, Pushkin, Saint-Petersurg, Russia.
PeerJ. 2021 Nov 24;9:e12389. doi: 10.7717/peerj.12389. eCollection 2021.
The key natural area of Russian reindeer (, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter-spring (WS) and summer-autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.
The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).
The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% ( < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS ( = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold ( = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly ( < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.
The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.
俄罗斯驯鹿（涅涅茨品种）的关键自然区域是北极地带，气候条件恶劣，饲料资源稀缺，尤其是在寒冷的冬季。驯鹿对这些条件的适应不仅与动物自身的遗传潜力有关。瘤胃微生物群通过参与纤维消化，为动物适应困难条件提供了重要帮助。我们研究的目的是调查俄罗斯联邦亚马尔 - 涅涅茨自治区天然牧场中，冬季到春季（WS）和夏季到秋季（SA）季节期间，犊鹿和成年驯鹿瘤胃微生物群（RM）的分类学及预测的代谢途径。
使用MiSeq（Illumina，美国加利福尼亚州圣地亚哥）平台的下一代测序方法研究驯鹿的RM。使用软件包PICRUSt2（v.2.3.0）进行宏基因组、基因家族和酶的功能谱重建及预测。
WS和SA日粮的营养价值显著不同。与SA相比，WS日粮中的粗纤维含量高22.4%（P < 0.05），这表明消化率可能较低，且RM需要适应这种季节变化。在瘤胃中总共发现了22个细菌超群和门，拟杆菌门和厚壁菌门是主要分类群（分别高达48.1% ± 4.30%和46.1% ± 4.80%）；而仅发现两个古菌门作为次要群落（总计不超过0.54% ± 0.14%）。主要分类群的百分比不受年龄或季节的影响。然而，在某些次要群落中发现了显著变化，其中季节变化比与年龄相关的变化更显著。与WS相比，成年驯鹿中放线菌门的百分比在SA中显著增加（19.3倍）（P = 0.02），蓝细菌门在成年驯鹿和犊鹿中的百分比增加了7倍（P = 0.002）。RM的季节变化可以提高驯鹿在营养物质供应不足季节的耐受能力。PICRUSt2结果揭示了RM中257条预测的代谢途径：41条途径受到季节和/或年龄的显著影响（P < 0.05），包括维生素、挥发性脂肪酸和色素的合成过程；蛋白质、脂质和能量的代谢；发病机制、甲烷生成、丁二醇到丙酮酸的生物合成、细胞壁生物合成、神经递质降解、乳酸发酵和核酸生物合成。这些可变途径中的很大一部分（41条中的13条）与维生素K同系物的合成有关。
获得的结果增进了我们对驯鹿RM结构及其与季节变化相关的可能代谢途径的了解。
