Metagenomic species profiling using universal phylogenetic marker genes

Research output: Contribution to journalJournal articleResearchpeer-review

Shinichi Sunagawa, 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 Borbye Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis & 1 others Peer Bork

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
Original languageEnglish
JournalNature Methods
Issue number12
Pages (from-to)1196-1199
Number of pages4
Publication statusPublished - 2013

ID: 61098289