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
  • Julien Tap
  • Henrik Bjørn Nielsen
  • Søren Brunak
  • Francisco Guarner
  • Willem M de Vos
  • Jun Wang
  • Junhua Li
  • Joël Doré
  • S Dusko Ehrlich
  • Alexandros Stamatakis
  • 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