Status of the phylogenetic diversity census of ruminal microbiomes

被引:314
作者
Kim, Minseok [1 ]
Morrison, Mark [1 ,2 ]
Yu, Zhongtang [1 ]
机构
[1] Ohio State Univ, Dept Anim Sci, Columbus, OH 43210 USA
[2] CSIRO Livestock Ind, St Lucia, Qld, Australia
关键词
16S rRNA gene; rrn; OTUs; rarefaction analysis; ruminal microbiomes; RUMEN BACTERIAL DIVERSITY; HERBIVORE GASTROINTESTINAL-TRACT; RIBOSOMAL-RNA GENES; REAL-TIME PCR; SP-NOV; BOVINE RUMEN; METHANOGENIC ARCHAEA; MOLECULAR DIVERSITY; SEQUENCE-ANALYSIS; COMMUNITY;
D O I
10.1111/j.1574-6941.2010.01029.x
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
引用
收藏
页码:49 / 63
页数:15
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