The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

David Arahal; Magne Bisgaard; Henrik Christensen; Dominique Clermont; Lenie Dijkshoorn; Birgitta Duim; Stefan Emler; Marian Figge; Markus Göker; Edward R.B. Moore; Alexandr Nemec; Niels Nørskov-Lauritsen; Ulrich Nübel; Stephen L.W. On; Peter Vandamme; Antonio Ventosa

doi:10.1099/ijsem.0.006188

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

David Arahal, Magne Bisgaard, Henrik Christensen, Dominique Clermont, Lenie Dijkshoorn, Birgitta Duim, Stefan Emler, Marian Figge, Markus Göker^*, Edward R.B. Moore, Alexandr Nemec, Niels Nørskov-Lauritsen, Ulrich Nübel, Stephen L.W. On, Peter Vandamme, Antonio Ventosa

^*Corresponding author for this work

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

15 Citations (Scopus)

Abstract

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the ‘Code of Nomenclature of Prokaryotes Described from DNA Sequence Data’ (‘SeqCode’), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

Original language	English
Article number	006188
Journal	International Journal of Systematic and Evolutionary Microbiology
Volume	74
Issue number	1
DOIs	https://doi.org/10.1099/ijsem.0.006188
Publication status	Published - 05 Jan 2024

Keywords

cultivation
deposition
homonyms
priority
reproducibility
valid publication

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10.1099/ijsem.0.006188

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Arahal, D., Bisgaard, M., Christensen, H., Clermont, D., Dijkshoorn, L., Duim, B., Emler, S., Figge, M., Göker, M., Moore, E. R. B., Nemec, A., Nørskov-Lauritsen, N., Nübel, U., On, S. L. W., Vandamme, P., & Ventosa, A. (2024). The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 74(1), Article 006188. https://doi.org/10.1099/ijsem.0.006188

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title = "The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes",

abstract = "The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the {\textquoteleft}Code of Nomenclature of Prokaryotes Described from DNA Sequence Data{\textquoteright} ({\textquoteleft}SeqCode{\textquoteright}), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.",

keywords = "cultivation, deposition, homonyms, priority, reproducibility, valid publication",

author = "David Arahal and Magne Bisgaard and Henrik Christensen and Dominique Clermont and Lenie Dijkshoorn and Birgitta Duim and Stefan Emler and Marian Figge and Markus G{\"o}ker and Moore, {Edward R.B.} and Alexandr Nemec and Niels N{\o}rskov-Lauritsen and Ulrich N{\"u}bel and On, {Stephen L.W.} and Peter Vandamme and Antonio Ventosa",

note = "Funding Information: Another likely post hoc, ergo propter hoc fallacy [62] is the idea that the {\textquoteleft}{\textquoteleft}heavy influence of employees of large culture collections on this ICSP decision may be a financial conflict of interest, as the decision could affect the number of strains deposited{\textquoteright} [61]. This assertion is based on the assumptions that a significant proportion of the revenue of large culture collections is derived from the handling of strain deposits, and that the salaries of culture collection staff involved in the 2020 debate [20] would be affected by changes in the sales volume of the culture collection concerned. No evidence was provided to support these suggestions and other claims made in the same publication [61] were found to be inaccurate [63]. Many public culture collections are non-profit organizations supported by national authorities. For example, the DSMZ (German Collection of Microorganisms and Cell Cultures) is supported by the state of Lower Saxony. The staff of culture collections consists of dedicated experts who not only collect and provide strains, but are often called upon by industry or governmental agencies for their knowledge and expertise. Culture collections are recognized as Biological Research Centres [64], as they are also involved in research on taxonomy, new methodologies, conservation methods and other scientific issues. Publisher Copyright: {\textcopyright} 2024, Microbiology Society. All rights reserved.",

year = "2024",

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doi = "10.1099/ijsem.0.006188",

language = "English",

volume = "74",

journal = "International Journal of Systematic and Evolutionary Microbiology",

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Arahal, D, Bisgaard, M, Christensen, H, Clermont, D, Dijkshoorn, L, Duim, B, Emler, S, Figge, M, Göker, M, Moore, ERB, Nemec, A, Nørskov-Lauritsen, N, Nübel, U, On, SLW, Vandamme, P & Ventosa, A 2024, 'The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes', International Journal of Systematic and Evolutionary Microbiology, vol. 74, no. 1, 006188. https://doi.org/10.1099/ijsem.0.006188

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. / Arahal, David; Bisgaard, Magne; Christensen, Henrik et al.
In: International Journal of Systematic and Evolutionary Microbiology, Vol. 74, No. 1, 006188, 05.01.2024.

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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AU - Duim, Birgitta

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AU - Figge, Marian

AU - Göker, Markus

AU - Moore, Edward R.B.

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N2 - The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the ‘Code of Nomenclature of Prokaryotes Described from DNA Sequence Data’ (‘SeqCode’), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

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KW - priority

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ER -

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

Abstract

Keywords

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