Sunagawa, Shinichi4; Mende, Daniel R4; Zeller, Georg4; Izquierdo-Carrasco, Fernando5; Berger, Simon A5; Kultima, Jens Roat4; Coelho, Luis Pedro4; Arumugam, Manimozhiyan4; Tap, Julien4; Nielsen, Henrik Bjørn6; Rasmussen, Simon1; Brunak, Søren1; Pedersen, Oluf7; Guarner, Francisco8; de Vos, Willem M9; Wang, Jun14; Li, Junhua11; Doré, Joël12; Ehrlich, S Dusko12; Stamatakis, Alexandros12; Bork, Peer13
1 Department of Systems Biology, Technical University of Denmark2 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark3 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark4 European Molecular Biological Laboratory5 The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg6 Behavioral Phenomics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark7 Hagedorn Research Institute8 University Hospital Vall d’Hebron9 Wageningen IMARES10 King Abdulaziz University11 Beijing Genomics Institute Hong Kong12 L'Institut National de la Recherche Agronomique13 Max Delbrück Center for Molecular Medicine14 King Abdulaziz University
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/.
Nature Methods, 2013, Vol 10, Issue 12, p. 1196-1199