1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 12

Status of the SeqCode in the Open Access

Abstract

The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names ‘validly published’ under that code in the (IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only ‘validly published’ under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since ‘validly published under the SeqCode’ is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.

  • Received:
  • Published Online:
Keyword(s): archaea , bacteria , classification , cultivation , DNA sequences and nomenclature
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005754
2022-12-16
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/72/12/ijsem005754.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005754&mimeType=html&fmt=ahah

References

  1. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217–222 [View Article] [PubMed]
     [Google Scholar]
  2. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes – Prokaryotic Code (2008 revision). Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article]
     [Google Scholar]
  3. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. in press; International Code of Nomenclature of Prokaryotes – Prokaryotic Code (2022 revision). Int J Syst Evol Microbiol [View Article]
     [Google Scholar]
  4. Whitman WB. Modest proposals to expand the type material for naming of prokaryotes. Int J Syst Evol Microbiol 2016; 66:2108–2112 [View Article] [PubMed]
     [Google Scholar]
  5. Whitman WB, Sutcliffe IC, Rossello-Mora R. Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names. Int J Syst Evol Microbiol 2019; 69:2174–2175 [View Article]
     [Google Scholar]
  6. Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Janda JM et al. The use of genomic DNA sequences as type material for valid publication of bacterial species names will have severe implications for clinical microbiology and related disciplines. Diagn Microbiol Infect Dis 2019; 95:102–103 [View Article] [PubMed]
     [Google Scholar]
  7. Overmann J, Huang S, Nübel U, Hahnke RL, Tindall BJ. Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms. Syst Appl Microbiol 2019; 42:22–29 [View Article] [PubMed]
     [Google Scholar]
  8. Rosselló-Móra R, Whitman WB. Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5–14 [View Article] [PubMed]
     [Google Scholar]
  9. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  10. Rossello-Mora R, Konstantinidis KT, Sutcliffe I, Whitman W. Opinion: response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes. Syst Appl Microbiol 2020; 43:126070 [View Article]
     [Google Scholar]
  11. Whitman WB, Bull CT, Busse H-J, Fournier P-E, Oren A et al. Request for revision of the statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:584–593 [View Article]
     [Google Scholar]
  12. Sutcliffe IC, Dijkshoorn L, Whitman WB, Executive Board O. Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote. Int J Syst Evol Microbiol 2020; 70:4416–4417 [View Article]
     [Google Scholar]
  13. Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P et al. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987–994 [View Article] [PubMed]
     [Google Scholar]
  14. Palmer M, Sutcliffe I, Venter SN, Hedlund BP. It is time for a new type of type to facilitate naming the microbial world. New Microbes New Infect 2022; 47:100991 [View Article] [PubMed]
     [Google Scholar]
  15. Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT et al. Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305 [View Article] [PubMed]
     [Google Scholar]
  16. Oren A, Garrity GM. Uncultivated microbes-in need of their own nomenclature?. ISME J 2018; 12:309–311 [View Article] [PubMed]
     [Google Scholar]
  17. Oren A. Nomenclature of prokaryotic “Candidatus” taxa: establishing order in the current chaos. New Microbes New Infect 2021; 44:100932 [View Article] [PubMed]
     [Google Scholar]
  18. Pallen MJ. The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis. Int J Syst Evol Microbiol 2021; 71:5000 [View Article]
     [Google Scholar]
  19. Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE et al. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat Microbiol 2022; 7:1702–1708 [View Article] [PubMed]
     [Google Scholar]
  20. Turland N, Wiersema J, Barrie F, Greuter W, Hawksworth D et al. International Code of Nomenclature for algae, fungi, and plants. In Königstein Im Taunus: Koeltz Botanical Books 2018 [View Article]
     [Google Scholar]
  21. Oren A, Arahal DR, Rosselló-Móra R, Sutcliffe IC, Moore ERB. Emendation of general consideration 5 and Rules 18a, 24a and 30 of the International Code of Nomenclature of Prokaryotes to resolve the status of the Cyanobacteria in the prokaryotic nomenclature. Int J Syst Evol Microbiol 2021; 71:4939 [View Article]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005754
Loading

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error