Accurate and universal delineation of prokaryotic species

Nat Methods. 2013 Sep;10(9):881-4. doi: 10.1038/nmeth.2575. Epub 2013 Jul 28.


The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool;, a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Barcoding, Taxonomic / methods*
  • Databases, Factual
  • Genetic Markers*
  • Genome*
  • Phylogeny*
  • Prochlorococcus / classification
  • Prochlorococcus / genetics
  • Prokaryotic Cells / physiology*
  • Proteins / genetics
  • RNA, Ribosomal, 16S
  • Sequence Alignment / methods


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