TY - JOUR
T1 - Microbial Taxonomy Run Amok
AU - Sanford, Robert A.
AU - Lloyd, Karen G.
AU - Konstantinidis, Konstantinos T.
AU - Löffler, Frank E.
N1 - Funding Information:
The authors acknowledge funding through the Dimensions of Biodiversity program of the US National Science Foundation (awards 1831582 to K.T.K. 1831599 to F.E.L. and 1831842 to R.A.S.), and the US Department of Energy, Biological and Environmental Research, Genomic Science Program (award DE-SC0020369 to K.G.L.). The authors are grateful to two anonymous reviewers for constructive criticisms, and appreciate comments from William Whitman, University of Georgia, GA, USA and Aharon Oren, The Hebrew University of Jerusalem, Israel, on Figure 1. Many thanks to Alison Murray, Desert Research Institute, NV, USA, for helpful discussions during the early stage of manuscript preparation.
Funding Information:
The authors acknowledge funding through the Dimensions of Biodiversity program of the US National Science Foundation (awards 1831582 to K.T.K., 1831599 to F.E.L., and 1831842 to R.A.S.), and the US Department of Energy, Biological and Environmental Research, Genomic Science Program (award DE-SC0020369 to K.G.L.). The authors are grateful to two anonymous reviewers for constructive criticisms, and appreciate comments from William Whitman, University of Georgia, GA, USA and Aharon Oren, The Hebrew University of Jerusalem, Israel, on Figure 1 . Many thanks to Alison Murray, Desert Research Institute, NV, USA, for helpful discussions during the early stage of manuscript preparation.
Publisher Copyright:
© 2020 Elsevier Ltd
PY - 2021/5
Y1 - 2021/5
N2 - 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. 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.
AB - 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. 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.
KW - Geobacter
KW - Pelobacter
KW - codes of nomenclature
KW - metagenome-assembled genomes
KW - not-yet-cultured microorganisms
KW - prokaryotic taxonomy
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UR - http://www.scopus.com/inward/citedby.url?scp=85100415636&partnerID=8YFLogxK
U2 - 10.1016/j.tim.2020.12.010
DO - 10.1016/j.tim.2020.12.010
M3 - Review article
C2 - 33546975
AN - SCOPUS:85100415636
SN - 0966-842X
VL - 29
SP - 394
EP - 404
JO - Trends in Microbiology
JF - Trends in Microbiology
IS - 5
ER -