Editor: Julian Marchesi
Status of the phylogenetic diversity census of ruminal microbiomes
Version of Record online: 12 JAN 2011
© 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
FEMS Microbiology Ecology
Volume 76, Issue 1, pages 49–63, April 2011
How to Cite
Kim, M., Morrison, M. and Yu, Z. (2011), Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiology Ecology, 76: 49–63. doi: 10.1111/j.1574-6941.2010.01029.x
- Issue online: 7 MAR 2011
- Version of Record online: 12 JAN 2011
- Accepted manuscript online: 11 JAN 2011 09:01AM EST
- Received 16 September 2010; revised 25 November 2010; accepted 2 December 2010., Final version published online 12 January 2011.
- 16S rRNA gene;
- rarefaction analysis;
- ruminal microbiomes
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.