Microbial Taxonomy Run Amok
Abstract
DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. Furthermore, we exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.
- Authors:
-
[4]
- University of Illinois at Urbana-Champaign, IL (United States)
- University of Tennessee, Knoxville, TN (United States)
- Georgia Institute of Technology, Atlanta, GA (United States)
- University of Tennessee, Knoxville, TN (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1991923
- Alternate Identifier(s):
- OSTI ID: 1820756
- Grant/Contract Number:
- SC0020369; AC05-00OR22725; 1831582; 1831599; 1831842
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Trends in Microbiology
- Additional Journal Information:
- Journal Volume: 29; Journal Issue: 5; Journal ID: ISSN 0966-842X
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; prokaryotic taxonomy; codes of nomenclature; not-yet-cultured microorganisms; metagenome-assembled genomes; Geobacter; Pelobacter; codes of nomenclature. not-yet-cultured microorganisms
Citation Formats
Sanford, Robert A., Lloyd, Karen G., Konstantinidis, Konstantinos T., and Löffler, Frank E. Microbial Taxonomy Run Amok. United States: N. p., 2021.
Web. doi:10.1016/j.tim.2020.12.010.
Sanford, Robert A., Lloyd, Karen G., Konstantinidis, Konstantinos T., & Löffler, Frank E. Microbial Taxonomy Run Amok. United States. https://doi.org/10.1016/j.tim.2020.12.010
Sanford, Robert A., Lloyd, Karen G., Konstantinidis, Konstantinos T., and Löffler, Frank E. Tue .
"Microbial Taxonomy Run Amok". United States. https://doi.org/10.1016/j.tim.2020.12.010. https://www.osti.gov/servlets/purl/1991923.
@article{osti_1991923,
title = {Microbial Taxonomy Run Amok},
author = {Sanford, Robert A. and Lloyd, Karen G. and Konstantinidis, Konstantinos T. and Löffler, Frank E.},
abstractNote = {DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. Furthermore, we exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.},
doi = {10.1016/j.tim.2020.12.010},
journal = {Trends in Microbiology},
number = 5,
volume = 29,
place = {United States},
year = {Tue Feb 02 00:00:00 EST 2021},
month = {Tue Feb 02 00:00:00 EST 2021}
}
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