doi: 10.1038/nmeth.2693. Epub 2013 Oct 20.
Metagenomic species profiling using universal phylogenetic marker genes
Shinichi Sunagawa 1, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis, Peer Bork
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- PMID:24141494
- DOI: 10.1038/nmeth.2693
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Metagenomic species profiling using universal phylogenetic marker genes
Shinichi Sunagawa et al. Nat Methods.2013 Dec.
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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/.
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