Status of the phylogenetic diversity census of ruminal microbiomes

Kim, Minseok, Morrison, Mark and Yu, Zhongtang (2011) Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiology Ecology, 76 1: 49-63. doi:10.1111/j.1574-6941.2010.01029.x


Author Kim, Minseok
Morrison, Mark
Yu, Zhongtang
Title Status of the phylogenetic diversity census of ruminal microbiomes
Journal name FEMS Microbiology Ecology   Check publisher's open access policy
ISSN 0168-6496
1574-6941
Publication date 2011-01-01
Sub-type Article (original research)
DOI 10.1111/j.1574-6941.2010.01029.x
Open Access Status Not yet assessed
Volume 76
Issue 1
Start page 49
End page 63
Total pages 15
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell
Language eng
Abstract 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, 13478 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 78218 bacterial and 24480 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.
Keyword 16S rRNA gene
OTUs
Rarefaction analysis
rrn
Ruminal microbiomes
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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