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Metagenomic species profiling using universal phylogenetic marker genes

Official URL:https://doi.org/10.1038/nmeth.2693
PubMed:View item in PubMed
Creators Name:Sunagawa, S. and Mende, D.R. and Zeller, G. and Izquierdo-Carrasco, F. and Berger, S.A. and Kultima, J.R. and Coelho, L.P. and Arumugam, M. and Tap, J. and Nielsen, H.B. and Rasmussen, S. and Brunak, S. and Pedersen, O. and Guarner, F. and de Vos, W.M. and Wang, J. and Li, J. and Dore, J. and Ehrlich, S.D. and Stamatakis, A. and Bork, P.
Journal Title:Nature Methods
Journal Abbreviation:Nat Methods
Page Range:1196-1199
Date:December 2013
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
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/.
Publisher:Nature Publishing Group (U.S.A.)
Item Type:Article

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