Status of the phylogenetic diversity census of ruminal microbiomes
Status of the phylogenetic diversity census of ruminal microbiomes
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DOI：
10.1111/j.1574-6941.2010.01029.x
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发表时间：
2011-04-01
影响因子：
4.2
通讯作者：
Yu, Zhongtang
中科院分区：
文献类型：
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作者：
Kim, Minseok;Morrison, Mark;Yu, Zhongtang
在这项研究中，通过对RDP数据库中保存的所有整理的16S rRNA基因（rrn）序列进行荟萃分析，研究了瘤胃中的集体微生物多样性。截至2010年11月，共发现13478个细菌rrn序列和3516个古细菌rrn序列。细菌序列在物种水平（0.03系统发育距离）上被划分为5271个操作分类单位（OTUs），代表19个现有门，其中厚壁菌门（2958个OTUs）、拟杆菌门（1610个OTUs）和变形菌门（226个OTUs）最为优势。这些细菌序列在属水平上被划分为3500多个otu（0.05距离），但仅代表180个现有属。几乎所有的古菌序列都归属于Euryarchaeota门的943个种级otu。虽然聚集在670个属级otu中，但只代表了12个现有的古细菌属。根据稀疏度分析，目前物种水平上的细菌覆盖率为71%，古细菌覆盖率为65%。至少需要78218个细菌序列和24480个古细菌序列才能达到99.9%的覆盖率。本研究结果可作为评估个体群体对瘤胃功能重要性的框架，并指导未来研究确定瘤胃微生物组的α和全球多样性。
In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13 478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At least 78 218 bacterial and 24 480 archaeal sequences would be needed to reach 99.9% coverage. The results of this study may serve as a framework to assess the significance of individual populations to rumen functions and to guide future studies to identify the alpha and global diversity of ruminal microbiomes.