Metagenomic species profiling using universal phylogenetic marker genes

@article{Sunagawa2013MetagenomicSP,
  title={Metagenomic species profiling using universal phylogenetic marker genes},
  author={Shinichi Sunagawa and Daniel R. Mende and Georg Zeller and Fernando Izquierdo-Carrasco and Simon A. Berger and Jens Roat Kultima and Lu{\'i}s Pedro Coelho and Manimozhiyan Arumugam and J. Tap and Henrik Bj{\o}rn Nielsen and Simon Rasmussen and S{\o}ren Brunak and Oluf Pedersen and Francisco Guarner and Willem Meindert de Vos and Jun Wang and Junhua Li and Jo{\"e}l Dor{\'e} and Stanislav Dusko Ehrlich and Alexandros Stamatakis and Peer Bork},
  journal={Nature Methods},
  year={2013},
  volume={10},
  pages={1196-1199}
}
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… 

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