Metagenomic species profiling using universal phylogenetic marker genes

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Item Type:	Article
Title:	Metagenomic species profiling using universal phylogenetic marker genes
Creators Name:	Sunagawa, S., Mende, D.R., Zeller, G., Izquierdo-Carrasco, F., Berger, S.A., Kultima, J.R., Coelho, L.P., Arumugam, M., Tap, J., Nielsen, H.B., Rasmussen, S., Brunak, S., Pedersen, O., Guarner, F., de Vos, W.M., Wang, J., Li, J., Dore, J., Ehrlich, S.D., Stamatakis, A. and Bork, P.
Abstract:	To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.
Keywords:	Algorithms, Calibration, Cluster Analysis, Computational Biology, Ribosomal DNA, Genetic Linkage, Genetic Markers, Genome, Intestines, Metagenomics, Microbiota, Phylogeny, 16S Ribosomal RNA, Sequence Alignment, DNA Sequence Analysis
Source:	Nature Methods
ISSN:	1548-7091
Publisher:	Nature Publishing Group
Volume:	10
Number:	12
Page Range:	1196-1199
Date:	December 2013
Official Publication:	https://doi.org/10.1038/nmeth.2693
PubMed:	View item in PubMed

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