PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
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PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. / Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis.
in: NAT COMMUN, Jahrgang 4, 2013, S. 2304.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
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TY - JOUR
T1 - PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
AU - Segata, Nicola
AU - Börnigen, Daniela
AU - Morgan, Xochitl C
AU - Huttenhower, Curtis
PY - 2013
Y1 - 2013
N2 - 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.
AB - 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.
KW - Bacteria
KW - Biological Evolution
KW - Computer Simulation
KW - Databases, Genetic
KW - Evolution, Molecular
KW - Genome
KW - Internet
KW - Microbiology
KW - Phylogeny
KW - RNA, Ribosomal, 16S
KW - Sulfolobus
KW - Journal Article
KW - Research Support, N.I.H., Extramural
KW - Research Support, Non-U.S. Gov't
KW - Research Support, U.S. Gov't, Non-P.H.S.
U2 - 10.1038/ncomms3304
DO - 10.1038/ncomms3304
M3 - SCORING: Journal article
C2 - 23942190
VL - 4
SP - 2304
JO - NAT COMMUN
JF - NAT COMMUN
SN - 2041-1723
ER -
