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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guid... Full description

Journal Title: Nature biotechnology 2018-11, Vol.36 (10), p.996-1004
Main Author: Parks, Donovan H
Other Authors: Chuvochina, Maria , Waite, David W , Rinke, Christian , Skarshewski, Adam , Chaumeil, Pierre-Alain , Hugenholtz, Philip
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Link: https://www.ncbi.nlm.nih.gov/pubmed/30148503
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title: A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
format: Article
creator:
  • Parks, Donovan H
  • Chuvochina, Maria
  • Waite, David W
  • Rinke, Christian
  • Skarshewski, Adam
  • Chaumeil, Pierre-Alain
  • Hugenholtz, Philip
subjects:
  • Bacteria
  • Biological evolution
  • Biology
  • Classification
  • Divergence
  • Divergent evolution
  • Ecological monitoring
  • Evolution
  • Gene sequencing
  • Genetic aspects
  • Genomes
  • Identification and classification
  • Phenetics
  • Phenotypes
  • Phylogeny
  • Physiological aspects
  • Proteins
  • Proteobacteria
  • Pure culture
  • Radiation
  • Taxonomy
ispartof: Nature biotechnology, 2018-11, Vol.36 (10), p.996-1004
description: Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


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descriptionTaxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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subjectBacteria ; Biological evolution ; Biology ; Classification ; Divergence ; Divergent evolution ; Ecological monitoring ; Evolution ; Gene sequencing ; Genetic aspects ; Genomes ; Identification and classification ; Phenetics ; Phenotypes ; Phylogeny ; Physiological aspects ; Proteins ; Proteobacteria ; Pure culture ; Radiation ; Taxonomy
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abstractTaxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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