Guo Wei, Li Ying, Wang Lizhi, Wang Jiwen, Xu Qin, Yan Tianhai, Xue Bai
Institute of Animal Nutrition, Sichuan Agricultural University, Yaan, Sichuan, 625014, China.
Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
Anaerobe. 2015 Aug;34:74-9. doi: 10.1016/j.anaerobe.2015.04.010. Epub 2015 Apr 21.
The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4-V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks.
牦牛（Bos grunniens）是一种独特的反刍动物物种，对青藏高原的农业至关重要，并且拥有复杂的肠道微生物群落。本研究的目的是使用16S rRNA基因高通量测序技术来表征牦牛瘤胃中微生物群的组成和个体变异性。本研究中使用的瘤胃样本取自中国四川省甘孜藏族自治州一个商业农场中放牧的成年雄性牦牛（n = 6）。通用原核生物引物用于靶向16S rRNA基因的V4 - V5高变区。经过序列过滤和嵌合体去除后，共获得7200个可操作分类单元（OTU）。在这些OTU中，0.56%属于古菌（40个OTU），7.19%属于未分类物种（518个OTU），所有样本中其余的OTU（6642个）为细菌来源。在检查细菌群落结构时，分类汇总后我们在159个科中鉴定出23个门。拟杆菌门和厚壁菌门是主要的门，分别占39.68%（标准差 = 0.05）和45.90%（标准差 = 0.06）。此外，3764个OTU被鉴定为共享OTU（即在所有牦牛中都有），属于35个属，在各个样本中丰度变化很大。检查了这些属在各个样本中的系统发育位置。此外，我们使用UniFrac通过添加分类单元系统发育来评估6个瘤胃样本之间的距离，占平均距离的24.1%。总之，当前研究揭示了共享的瘤胃微生物组和系统发育谱系，并提供了关于牦牛瘤胃中细菌群落组成和个体变异性的新信息。
