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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
by
Chuvochina, Maria
, Waite, David W
, Chaumeil, Pierre-Alain
, Rinke, Christian
, Parks, Donovan H
, Skarshewski, Adam
, Hugenholtz, Philip
in
45/23
/ 631/181/2480
/ 631/181/757
/ 631/326/41
/ Agriculture
/ Bacteria
/ Bacterial genetics
/ Bioinformatics
/ Biological evolution
/ Biomedical Engineering/Biotechnology
/ Biomedicine
/ Biotechnology
/ Classification
/ Culture
/ Datasets
/ Developmental biology
/ Divergence
/ Divergent evolution
/ Ecological monitoring
/ Evolution
/ Evolution (Biology)
/ Gene sequencing
/ Genetic aspects
/ Genomes
/ Genomics
/ Life Sciences
/ Microorganisms
/ Names
/ Phenotypes
/ Phylogenetics
/ Phylogeny
/ Physiological aspects
/ Proteins
/ Proteobacteria
/ Pure culture
/ Radiation (Physics)
/ resource
/ Taxonomic revision
/ Taxonomy
/ Taxonomy (Biology)
2018
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
by
Chuvochina, Maria
, Waite, David W
, Chaumeil, Pierre-Alain
, Rinke, Christian
, Parks, Donovan H
, Skarshewski, Adam
, Hugenholtz, Philip
in
45/23
/ 631/181/2480
/ 631/181/757
/ 631/326/41
/ Agriculture
/ Bacteria
/ Bacterial genetics
/ Bioinformatics
/ Biological evolution
/ Biomedical Engineering/Biotechnology
/ Biomedicine
/ Biotechnology
/ Classification
/ Culture
/ Datasets
/ Developmental biology
/ Divergence
/ Divergent evolution
/ Ecological monitoring
/ Evolution
/ Evolution (Biology)
/ Gene sequencing
/ Genetic aspects
/ Genomes
/ Genomics
/ Life Sciences
/ Microorganisms
/ Names
/ Phenotypes
/ Phylogenetics
/ Phylogeny
/ Physiological aspects
/ Proteins
/ Proteobacteria
/ Pure culture
/ Radiation (Physics)
/ resource
/ Taxonomic revision
/ Taxonomy
/ Taxonomy (Biology)
2018
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
by
Chuvochina, Maria
, Waite, David W
, Chaumeil, Pierre-Alain
, Rinke, Christian
, Parks, Donovan H
, Skarshewski, Adam
, Hugenholtz, Philip
in
45/23
/ 631/181/2480
/ 631/181/757
/ 631/326/41
/ Agriculture
/ Bacteria
/ Bacterial genetics
/ Bioinformatics
/ Biological evolution
/ Biomedical Engineering/Biotechnology
/ Biomedicine
/ Biotechnology
/ Classification
/ Culture
/ Datasets
/ Developmental biology
/ Divergence
/ Divergent evolution
/ Ecological monitoring
/ Evolution
/ Evolution (Biology)
/ Gene sequencing
/ Genetic aspects
/ Genomes
/ Genomics
/ Life Sciences
/ Microorganisms
/ Names
/ Phenotypes
/ Phylogenetics
/ Phylogeny
/ Physiological aspects
/ Proteins
/ Proteobacteria
/ Pure culture
/ Radiation (Physics)
/ resource
/ Taxonomic revision
/ Taxonomy
/ Taxonomy (Biology)
2018
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Journal Article
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
2018
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Overview
Interpretation of microbial genome data will be improved by a fully revised bacterial taxonomy.
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.
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