Accurate and universal delineation of prokaryotic species.
2013 Sep 28; 10(9): 881-4. Epub 2013 Jul 28; PubMed: 23892899.
Abstract + PDF
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; http://www.bork.embl.de/software/specI/), 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.
Metagenomic species profiling using universal phylogenetic marker genes.
, Mende DR
, Zeller G
, Izquierdo-Carrasco F, Berger SA, Kultima JR
, Coelho LP
, Arumugam M
, Tap J
, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P
2013 Dec 20; 10(12): 1196-9. Epub 2013 Oct 20; PubMed: 24141494.
Abstract + PDF
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/.