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Title: A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Here, using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.
Authors:
ORCiD logo [1]
  1. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics; NamesforLife, LLC, East Lansing, MI (United States)
Publication Date:
Grant/Contract Number:
SC0006191
Type:
Accepted Manuscript
Journal Name:
Journal of Clinical Microbiology
Additional Journal Information:
Journal Volume: 54; Journal Issue: 8; Related Information: https://www.researchgate.net/publication/302545989_JCM00200---16-supplement; Journal ID: ISSN 0095-1137
Publisher:
American Society for Microbiology
Research Org:
NamesforLife, LLC, East Lansing, MI (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 99 GENERAL AND MISCELLANEOUS; Taxonomy; classification; genome; bactera; archaea
OSTI Identifier:
1467430

Garrity, George M. A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?. United States: N. p., Web. doi:10.1128/JCM.00200-16.
Garrity, George M. A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?. United States. doi:10.1128/JCM.00200-16.
Garrity, George M. 2016. "A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?". United States. doi:10.1128/JCM.00200-16. https://www.osti.gov/servlets/purl/1467430.
@article{osti_1467430,
title = {A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?},
author = {Garrity, George M.},
abstractNote = {Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Here, using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.},
doi = {10.1128/JCM.00200-16},
journal = {Journal of Clinical Microbiology},
number = 8,
volume = 54,
place = {United States},
year = {2016},
month = {5}
}