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Metagenomic species profiling using universal phylogenetic marker genes

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
Publisher:Nature Publishing Group
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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