New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online.

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes / Segata, Nicola; D., Börnigen; X. C., Morgan; C., Huttenhower. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 4:(2013), p. 2304. [10.1038/ncomms3304]

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.

Segata, Nicola;
2013-01-01

Abstract

New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online.
2013
Segata, Nicola; D., Börnigen; X. C., Morgan; C., Huttenhower
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes / Segata, Nicola; D., Börnigen; X. C., Morgan; C., Huttenhower. - In: NATURE COMMUNICATIONS. - ISSN 2041-1723. - 4:(2013), p. 2304. [10.1038/ncomms3304]
File in questo prodotto:
File Dimensione Formato  
PhyloPhlAn.pdf

accesso aperto

Tipologia: Versione editoriale (Publisher’s layout)
Licenza: Creative commons
Dimensione 3.65 MB
Formato Adobe PDF
3.65 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/34852
Citazioni
  • ???jsp.display-item.citation.pmc??? 364
  • Scopus 565
  • ???jsp.display-item.citation.isi??? 565
social impact