Sunagawa, Shinichi15; Mende, Daniel R15; Zeller, Georg15; Izquierdo-Carrasco, Fernando5; Berger, Simon A5; Kultima, Jens Roat15; Coelho, Luis Pedro15; Arumugam, Manimozhiyan15; Tap, Julien15; Nielsen, Henrik Bjørn6; Rasmussen, Simon7; Brunak, Søren7; Pedersen, Oluf8; Guarner, Francisco9; de Vos, Willem M10; Wang, Jun16; Li, Junhua12; Doré, Joël13; Ehrlich, S Dusko13; Stamatakis, Alexandros13; Bork, Peer14
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 Biology 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 Department of Bio and Health Informatics, Technical University of Denmark8 Hagedorn Research Institute9 University Hospital Vall d’Hebron10 Wageningen IMARES11 King Abdulaziz University12 Beijing Genomics Institute Hong Kong13 L'Institut National de la Recherche Agronomique14 Max Delbrück Center for Molecular Medicine15 European Molecular Biology Laboratory16 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/.