Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.
Candidatus
Metagenome
Nomenclatural code
Nomenclatural type
SeqCode
Journal
Systematic and applied microbiology
ISSN: 1618-0984
Titre abrégé: Syst Appl Microbiol
Pays: Germany
ID NLM: 8306133
Informations de publication
Date de publication:
Sep 2022
Sep 2022
Historique:
received:
09
11
2021
revised:
30
01
2022
accepted:
31
01
2022
pubmed:
2
9
2022
medline:
24
9
2022
entrez:
1
9
2022
Statut:
ppublish
Résumé
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
Identifiants
pubmed: 36049255
pii: S0723-2020(22)00012-1
doi: 10.1016/j.syapm.2022.126305
pmc: PMC9489671
mid: NIHMS1825923
pii:
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
126305Subventions
Organisme : NIGMS NIH HHS
ID : P20 GM103440
Pays : United States
Informations de copyright
Copyright © 2022 The Author(s). Published by Elsevier GmbH.. All rights reserved.
Références
Syst Appl Microbiol. 2015 Jun;38(4):209-16
pubmed: 25747618
Integr Comp Biol. 2018 Dec 1;58(6):1122-1131
pubmed: 30113637
Syst Appl Microbiol. 2015 Jun;38(4):231-6
pubmed: 25921438
Front Microbiol. 2016 Dec 20;7:2003
pubmed: 28066339
Sci Rep. 2016 Dec 07;6:38392
pubmed: 27924912
Nature. 2015 May 14;521(7551):173-179
pubmed: 25945739
Nat Biotechnol. 2020 Sep;38(9):1079-1086
pubmed: 32341564
Nucleic Acids Res. 2022 Jan 7;50(D1):D785-D794
pubmed: 34520557
Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91
pubmed: 17220447
Nature. 2009 Dec 24;462(7276):1056-60
pubmed: 20033048
New Microbes New Infect. 2022 Jun 01;47:100991
pubmed: 35800027
Nat Microbiol. 2021 Jul;6(7):946-959
pubmed: 34155373
Int J Syst Evol Microbiol. 2020 Apr;70(4):2937-2948
pubmed: 32242793
Syst Appl Microbiol. 2019 Jan;42(1):15-21
pubmed: 30098831
Genome Res. 2020 Mar;30(3):315-333
pubmed: 32188701
Int J Syst Evol Microbiol. 2016 May;66(5):2108-2112
pubmed: 26902077
Genes (Basel). 2018 Aug 01;9(8):
pubmed: 30071618
Syst Appl Microbiol. 2015 Jun;38(4):217-22
pubmed: 25769508
Int J Syst Evol Microbiol. 2019 Jul;69(7):2174-2175
pubmed: 31066658
Int J Syst Evol Microbiol. 2020 Jul;70(7):3956-4042
pubmed: 32603289
Front Microbiol. 2020 Apr 07;11:468
pubmed: 32373076
Nature. 2004 Mar 4;428(6978):37-43
pubmed: 14961025
Nat Biotechnol. 2021 Apr;39(4):499-509
pubmed: 33169036
Psychol Rev. 1956 Mar;63(2):81-97
pubmed: 13310704
Int J Syst Evol Microbiol. 2020 Apr;70(4):2782-2858
pubmed: 32293557
Syst Appl Microbiol. 2019 Jan;42(1):5-14
pubmed: 30017185
Appl Environ Microbiol. 2021 Feb 26;87(6):
pubmed: 33452027
Nat Biotechnol. 2020 Jun;38(6):701-707
pubmed: 32042169
Int J Syst Evol Microbiol. 2021 Apr;71(4):
pubmed: 33881984
Nat Biotechnol. 2008 May;26(5):541-7
pubmed: 18464787
Int J Syst Evol Microbiol. 2020 Jul;70(7):4416-4417
pubmed: 32628106
BMC Bioinformatics. 2013 Feb 21;14:60
pubmed: 23432962
Nat Microbiol. 2022 Sep 19;:
pubmed: 36123442
Science. 1980 Jul 25;209(4455):457-63
pubmed: 6771870
New Microbes New Infect. 2021 Sep 25;44:100942
pubmed: 34621526
Int J Syst Bacteriol. 1994 Jan;44(1):174-6
pubmed: 8123559
BMC Microbiol. 2012 Dec 23;12:302
pubmed: 23259572
Front Microbiol. 2015 Mar 18;6:214
pubmed: 26074881
Int J Syst Evol Microbiol. 2019 Jan;69(1A):S1-S111
pubmed: 26596770
Nature. 2020 Jan;577(7791):519-525
pubmed: 31942073
Nat Biotechnol. 2017 Sep 12;35(9):833-844
pubmed: 28898207
Int J Syst Bacteriol. 1995 Jan;45(1):186-7
pubmed: 7857801
Gigascience. 2018 May 1;7(5):
pubmed: 29718202
Int J Syst Evol Microbiol. 2019 May;69(5):1524-1525
pubmed: 30806612
Environ Microbiol. 2020 Mar;22(3):819-822
pubmed: 31997493
Int J Syst Evol Microbiol. 2018 Jan;68(1):461-466
pubmed: 29292687
Int J Syst Evol Microbiol. 2015 Mar;65(Pt 3):1086-1087
pubmed: 25589736
ISME J. 2017 Nov;11(11):2399-2406
pubmed: 28731467
Syst Appl Microbiol. 2015 Jun;38(4):223-30
pubmed: 25681255
Int J Syst Evol Microbiol. 2014 Jan;64(Pt 1):293-297
pubmed: 24408949
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31
pubmed: 19855009
Int J Syst Evol Microbiol. 2020 Nov;70(11):5607-5612
pubmed: 32701423
Trends Microbiol. 2021 Apr;29(4):289-298
pubmed: 33288384
Stand Genomic Sci. 2013 Dec 17;9(3):1278-84
pubmed: 25197443
Nature. 2017 Jan 19;541(7637):353-358
pubmed: 28077874
Nat Microbiol. 2020 Aug;5(8):987-994
pubmed: 32514073
Nat Biotechnol. 2017 Aug 8;35(8):725-731
pubmed: 28787424
Science. 2013 Nov 29;342(6162):1057-8
pubmed: 24288324
Int J Syst Evol Microbiol. 2021 Sep;71(9):
pubmed: 34516368
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72
pubmed: 15701695