Metagenomic species profiling using universal phylogenetic marker genes

Nat Methods. 2013 Dec;10(12):1196-9. doi: 10.1038/nmeth.2693. Epub 2013 Oct 20.


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Calibration
  • Cluster Analysis
  • Computational Biology / methods
  • DNA, Ribosomal / genetics
  • Genetic Linkage
  • Genetic Markers
  • Genome
  • Humans
  • Intestines / microbiology
  • Metagenomics*
  • Microbiota*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods


  • DNA, Ribosomal
  • Genetic Markers
  • RNA, Ribosomal, 16S