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International Code of Nomenclature of Prokaryotes

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This is an old revision of this page, as edited by Artoria2e5 (talk | contribs) at 04:56, 18 December 2023 (→Type strain: SeqCode should be own section. It's not in the Prokaryotic Code system, though makes heavy references to it). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

The International Code of Nomenclature of Prokaryotes (ICNP) or Prokaryotic Code, formerly the International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC), governs the scientific names for Bacteria and Archaea.[1][2] It denotes the rules for naming taxa of bacteria, according to their relative rank. As such it is one of the nomenclature codes of biology.

Originally the International Code of Botanical Nomenclature dealt with bacteria, and this kept references to bacteria until these were eliminated at the 1975 International Botanical Congress. An early Code for the nomenclature of bacteria was approved at the 4th International Congress for Microbiology in 1947, but was later discarded.

The latest version to be printed in book form is the 1990 Revision,[3] but the book does not represent the current rules. The 2008 Revision has been published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM).[2] Rules are maintained by the International Committee on Systematics of Prokaryotes (ICSP; formerly the International Committee on Systematic Bacteriology, ICSB).

The baseline for bacterial names is the Approved Lists[4] with a starting point of 1980. New bacterial names are reviewed by the ICSP as being in conformity with the Rules of Nomenclature and published in the IJSEM.

Cyanobacteria

Since 1975, most bacteria were covered under the bacteriological code. However, cyanobacteria were still covered by the botanical code. Starting in 1999, cyanobacteria were covered by both the botanical and bacteriological codes. This situation has caused nomenclatural problems for the cyanobacteria.[5][6] By 2020, there were three proposals for how to resolve the situation:

  1. Exclude cyanobacteria from the bacteriological code.[7]
  2. Apply the bacteriological code to all cyanobacteria.[8]
  3. Treat valid publication under the botanical code as valid publication under the bacteriological code.[9]

In 2021, the ICSP held a formal vote on the three proposals and the third option was chosen.[10]

Type strain

Main article: Type (biology)

Since 2001, when a new bacterial or archaeal species is described, a type strain must be designated.[11] The type strain is a living culture to which the scientific name of that organism is formally attached. For a new species name to be validly published, the type strain must be deposited in a public culture collection in at least two different countries.[12] Before 2001, a species could also be typified using a description, a preserved specimen, or an illustration.[11] There is a single type strain for each prokaryotic species, but different culture collections may designate a unique name for the same strain. For example, the type strain of E. coli (originally strain U5/41) is called ATCC 11775 by the American Type Culture Collection, DSM 30083 by the German Collection of Microorganisms and Cell Cultures, JCM 1649 by the Japan Collection of Microorganisms, and LMG 2092 by the Belgian Coordinated Collections of Microorganisms.[13][14] When a prokaryotic species cannot be cultivated in the laboratory (and therefore cannot be deposited in a culture collection), it may be given a provisional candidatus name, but is not considered validly published.[15]

SeqCode

The Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode) is a separate nomenclatural code produced by the unrelated International Society for Microbial Ecology. It establishes a standard for "validly publishing" Candidatus names using high-quality genome sequences as type, using rules of priority very similar to that of the ICNP. The SeqCode team initially wished to simply amend the ICNP to add such a system, but ICSP rejected the petitition, necessitating the creation of a separate code.[16]

Versions

  • Buchanan, R. E., and Ralph St. John-Brooks. (1947, June) (Editors). Proposed Bacteriological Code of Nomenclature. Developed from proposals approved by International Committee on Bacteriological Nomenclature at the Meeting of the Third International Congress for Microbiology. Publication authorized in Plenary Session, pp. 61. Iowa State College Press, Ames, Iowa. U.S.A. Hathi Trust.
  • Buchanan R. E., St , John-Brooks R., Breed R. S. (1948). "International bacteriological code of nomenclature". Journal of Bacteriology. 55 (3): 287–306. doi:10.1128/jb.55.3.287-306.1948. PMC 518444. PMID 16561459.{{cite journal}}: CS1 maint: multiple names: authors list (link) Reprinted 1949, Journal of General Microbiology 3, 444–462.
  • International Committee on Bacteriological Nomenclature. (1958, June). International code of nomenclature of bacteria and viruses. Ames, Iowa State College Press. BHL.
  • Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. & Clark, W.A. (1975). International Code of Nomenclature of Bacteria. 1975 Revision. American Society of Microbiology, Washington, D.C
  • Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. & Clark, W.A. (1992). International Code of Nomenclature of Bacteria. Bacteriological Code. 1990 Revision. American Society for Microbiology, Washington, D.C. link.
  • Parker, C.T., Tindall, B.J. & Garrity, G.M., eds. (2019). International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2008 Revision). International Journal of Systematic and Evolutionary Microbiology 69(1A): S1–S111. doi: 10.1099/ijsem.0.000778
  • Oren, Aharon; Arahal, David R.; Göker, Markus; Moore, Edward R. B.; Rossello-Mora, Ramon; Sutcliffe, Iain C. (1 May 2023). "International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision)". International Journal of Systematic and Evolutionary Microbiology. 73 (5a). doi:10.1099/ijsem.0.005585.

See also

References

  1. ^ "Home". the-icsp.org.
  2. ^ a b P. H. A. Sneath, 2003. A short history of the Bacteriological Code URL Archived 2012-05-24 at the Wayback Machine
  3. ^ Lapage, S. P.; Sneath, P. H. A.; Lessel, E. F.; Skerman, V. B. D.; Seeliger, H. P. R.; Clark, W. A. (March 5, 1992). "Rules of Nomenclature with Recommendations". ASM Press – via ncbi.nlm.nih.gov.
  4. ^ VBD Skerman, Vicki McGowan, and PHA Sneath, 1989. Approved Lists of Bacterial Names, Amended edition Washington (DC): ASM Press
  5. ^ Oren, A. (2011). "Cyanobacterial systematics and nomenclature as featured in the International Bulletin of Bacteriological Nomenclature and Taxonomy / International Journal of Systematic Bacteriology / International Journal of Systematic and Evolutionary Microbiology". International Journal of Systematic and Evolutionary Microbiology. 61 (1): 10–15. doi:10.1099/ijs.0.018838-0. PMID 21097637.
  6. ^ Oren A, Ventura S. (2017). "The current status of cyanobacterial nomenclature under the "prokaryotic" and the "botanical" code". Antonie van Leeuwenhoek. 110 (10): 1257–1269. doi:10.1007/s10482-017-0848-0. PMID 28243951. S2CID 23489558.
  7. ^ Oren A, Garrity GM. (2014). "Proposal to change General Consideration 5 and Principle 2 of the International Code of Nomenclature of Prokaryotes". Int J Syst Evol Microbiol. 64 (1): 309–10. doi:10.1099/ijs.0.059568-0. PMID 24408952.
  8. ^ Pinevich AV. (2015). "Proposal to consistently apply the International Code of Nomenclature of Prokaryotes (ICNP) to names of the oxygenic photosynthetic bacteria (cyanobacteria), including those validly published under the International Code of Botanical Nomenclature (ICBN)/International Code of Nomenclature for algae, fungi and plants (ICN), and proposal to change Principle 2 of the ICNP". Int J Syst Evol Microbiol. 65 (3): 1070–4. doi:10.1099/ijs.0.000034. PMID 25505344.
  9. ^ Oren A. (2020). "Three alternative proposals to emend the Rules of the International Code of Nomenclature of Prokaryotes to resolve the status of the Cyanobacteria in the prokaryotic nomenclature". Int J Syst Evol Microbiol. 70 (7): 4406–4408. doi:10.1099/ijsem.0.004268. PMID 32602831. S2CID 220270571.
  10. ^ Oren A, Arahal DR, Rosselló-Móra R, Sutcliffe IC, Moore ERB. (2021). "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". International Journal of Systematic and Evolutionary Microbiology. 71 (8): 004939. doi:10.1099/ijsem.0.004939. PMID 34342563. S2CID 236884663.
  11. ^ a b Prokaryotic Code (2008 Revision), Rule 18a.
  12. ^ Prokaryotic Code (2008 Revision), Rule 30.
  13. ^ Euzéby JP, Parte AC. "Escherichia coli". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved June 21, 2022.
  14. ^ Reimer LC, Sardà Carbasse J, Koblitz J, Ebeling C, Podstawka A, Overmann J. "Escherichia coli U5/41". BacDive. Retrieved June 21, 2022.
  15. ^ Prokaryotic Code (2008 Revision), Appendix 11.
  16. ^ Hedlund BP, Chuvochina M, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe IC, Venter SN, Whitman WB (October 2022). "SeqCode: a nomenclatural code for prokaryotes described from sequence data". Nat Microbiol. 7 (10): 1702–1708. doi:10.1038/s41564-022-01214-9. PMC 9519449. PMID 36123442.
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