TY - JOUR
T1 - The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis
AU - Pallen, Mark J.
N1 - Funding Information: Mark Pallen is supported by the Quadram Institute Bioscience BBSRC-funded Strategic Program: Microbes in the Food Chain (project no. BB/R012504/1) and its constituent project BBS/E/F/000PR10351 (Theme 3, Microbial Communities in the Food Chain) and by the Medical Research Council CLIMB-BIG-DATA grant MR/T030062/1.
PY - 2021/9/13
Y1 - 2021/9/13
N2 - The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Can-didatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in imple-mentation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and data-bases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thou-sands of newly discovered but uncultured species.
AB - The status Candidatus was introduced to bacterial taxonomy in the 1990s to accommodate uncultured taxa defined by analyses of DNA sequences. Here I review the strengths, weaknesses, opportunities and threats (SWOT) associated with the status Can-didatus in the light of a quarter century of use, twinned with recent developments in bacterial taxonomy and sequence-based taxonomic discovery. Despite ambiguities as to its scope, philosophical objections to its use and practical problems in imple-mentation, the status Candidatus has now been applied to over 1000 taxa and has been widely adopted by journals and data-bases. Although lacking priority under the International Code for Nomenclature of Prokaryotes, many Candidatus names have already achieved de facto standing in the academic literature and in databases via description of a taxon in a peer-reviewed publication, alongside deposition of a genome sequence and there is a clear path to valid publication of such names on culture. Continued and increased use of Candidatus names provides an alternative to the potential upheaval that might accompany creation of a new additional code of nomenclature and provides a ready solution to the urgent challenge of naming many thou-sands of newly discovered but uncultured species.
KW - Bacterial nomenclature
KW - Candidatus
KW - Genome-based taxonomy
KW - Uncultured bacteria
UR - http://www.scopus.com/inward/record.url?scp=85114765492&partnerID=8YFLogxK
U2 - 10.1099/ijsem.0.005000
DO - 10.1099/ijsem.0.005000
M3 - Review article
C2 - 34516368
AN - SCOPUS:85114765492
VL - 71
JO - International Journal of Systematic and Evolutionary Microbiology
JF - International Journal of Systematic and Evolutionary Microbiology
SN - 1466-5026
IS - 9
M1 - 005000
ER -