Nomenclature
Introduction
There is no official classification of prokaryotes, but the names given to prokaryotes are regulated. The International Code of Nomenclature of Bacteria (Bacteriological Code) and its successors contain General Considerations, Principles, Rules and Recommendations which govern the way in which the names of prokaryotes are to be used. The last revision of the Code is the cornerstone of prokaryotic nomenclature.
In 1975, the Bacteriological Code (1975 Revision) introduced a new concept, that of the ☞ valid publication of names of prokaryotes. Since then nomenclature is regulated in prokaryote systematics by an official system of registering (or indexing) via a centralized system those names which may be used in prokaryote taxonomy. The "valid publication (of a name)" is the formal term for registering a name. The ☞ International Code of Nomenclature of Bacteria (1990 Revision) states that the name of a taxon is validly published, and therefore has standing in nomenclature, if its proposal is accompanied by a number of ☞ criteria.
The designation of a ☞ nomenclatural type is among these criteria. Much like physics, which has reference points for the meter or the kilogram, biology has the nomenclatural types as the reference points for a taxon. In the cases of the species and subspecies, these reference points are represented by ☞ type strains. Given their central importance, it is crucial that type strains be made available as widely as possible.
The publication of the ☞ Approved Lists of Bacterial Names in 1980 was part of the concept of valid publication, and set a new starting point in prokaryotic nomenclature. This system was unique to the International Code of Nomenclature of Bacteria (even though virology has followed this principle) and was introduced in 1980 to combat uncertainties in the usage of the c. 40,000 names that had accumulated over the previous c. 200 years. With the introduction of the Approved Lists of Bacterial Names, only 2,000+ names were accepted for transfer into the modern system.
The Bacteriological Code (1990 Revision) and its successors also state that only ☞ correct names are to be used, i.e. based on (1) valid publication, (2) legitimacy, and (3) priority of publication (Principle 6). This does not mean that there is an official classification of bacteria [1], even though there is an official nomenclature. It is indeed important to be aware that taxonomy is not regulated by the code although nomenclature is formally regulated, i.e. there are names validly published as a result of conformity with the Rules of Nomenclature. For instance, the code recognizes a "valid published species name", but the term "validly published species" has no meaning. It is nevertheless being frequently met with in some of the literature. Similarly, the frequently used term "validly described" is meaningless.
"Many microbiologists are not particularly interested in nomenclature and are unaware of or indifferent to the problem they sometimes create" [2]. However, nomenclature is a vital component of systematic bacteriology and it is neither esoteric nor absurd. The ☞ Bacteriological Code (1990 Revision) and its most recent successor, which is the cornerstone of prokaryotic nomenclature, are not always easy to use. In fact, the formal system of naming bacteria appears sometimes tiresome, confusing and even exasperating to the working bacteriologist [3]. Accordingly, some bacteriologists are not aware of the Rules.
References:
- SNEATH (P.H.A.) and BRENNER (D.J.): "Official" nomenclature lists. ASM News, 1992, 58, 175.
- GIBBONS (N.E.): Reference collections of bacteria. - The need and requirements for type and neotype strains. In: R.E. BUCHANAN and N.E. GIBBONS (editors), Bergey’s Manual of Determinative Bacteriology, eighth edition, The Williams & Wilkins Company, Baltimore, 1974, p. 14-17.
- BOUSFIELD (I.J.): Bacterial nomenclature and its role in systematics. In: M. GOODFELLOW and A.G. O’DONNELL (editors), Handbook of new bacterial systematics, Academic Press, London, 1993, p. 317-338.
Resources
A variety of resources are provided which assist in reading and comprehending this "List of Prokaryotic Names with Standing in Nomenclature". Information on nomenclature available at LPSN:
The notes on the pages for the individual taxon names also included many hints on nomenclatural topics. The taxon pages refer to LPSN glossary for clarifying a variety of issues; aspects of nomenclature are among them.
A selection of publications on nomenclature (cited in chronological order, without Judicial Opinions and Requests for an Opinion and without publications focussing on the formation of names):
1976-1980
- Holt JG. INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY, JUDICIAL COMMISSION: Minutes of the meeting, 3 September 1978, Munich, West Germany. Int. J. Syst. Bacteriol. 1979; 29:267-269.
- Stanier RY, Sistrom WR, Hansen TA, Whitton BA, Castenholz RW, Pfennig N, Gorlenko VN, Kondratieva EN, Eimhjellen KE, et al. Proposal to place the nomenclature of the cyanobacteria (blue-green algae) under the rules of the International Code of Nomenclature of Bacteria. Int J Syst Bacteriol 1978; 28:335-336.
- Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420.
1991-1995
- Wayne LG. JUDICIAL COMMISSION: Minutes of the Meeting, 14 September 1990, Osaka, Japan. Int. J. Syst. Bacteriol. 1991; 41:185-187.
- Lapage SP, Sneath PHA, Lessel EF, Skerman VBD, Seeliger HPR, Clark WA. International code of nomenclature of bacteria (1990 revision). American Society for Microbiology, Washington, 1992.
- Moore WEC, Moore LVH. Index of the bacterial and yeast nomenclatural changes published in the International Journal of Systematic Bacteriology since the 1980 Approved Lists of Bacterial Names (1 January 1980 to 1 January 1992). American Society for Microbiology, Washington, 1992.
- Murray RG, Schleifer KH. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol 1994; 44:174-176.
- Wayne LG. Actions of the Judicial Commission of the International Committee on Systematic Bacteriology on requests for opinions published between January 1985 and July 1993. Int. J. Syst. Bacteriol. 1994; 44:177-178.
- Murray RG, Stackebrandt E. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int J Syst Bacteriol 1995; 45:186-187.
2006-2010
- Tindall BJ, Kämpfer P, Euzéby JP, Oren A. Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 2006; 56:2715-2720.
- Watson DRW, Young JM. Proposals that the International Committee on Systematics of Prokaryotes establish a public database of validly published names and that the Bacteriological Code be amended to change the prescription for citation of validly published names. Int J Syst Evol Microbiol 2008; 57:1167-1168.
- Labeda DP, Oren A. International Committee on Systematics of Prokaryotes XIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 23, 24, 26 and 28 July 2005, San Francisco, CA, USA. Int. J. Syst. Evol. Microbiol. 2008; 58:1746-1752.
- Tindall BJ, De Vos P, Trüper HG. Judicial Commission of the International Committee on Systematics of Prokaryotes XIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 23, 24 and 27 July 2005, San Francisco, CA, USA. Int. J. Syst. Evol. Microbiol. 2008; 58:1737-1745.
- Tindall BJ. Clarifying rule 24a of the International Code of Nomenclature of Bacteria. Int J Syst Evol Microbiol 2008; 58:1779-1781.
- Tindall BJ. Rule 15 of the International Code of Nomenclature of Bacteria: a current source of confusion. Int J Syst Evol Microbiol 2008; 58:1775-1778.
- Tindall BJ. Confirmation of deposit, but confirmation of what? Int J Syst Evol Microbiol 2008; 58:1785-1787.
- Tindall BJ, Garrity GM. Should we alter the way that authorship of a subspecies name that is automatically created under Rule 40d of the Bacteriological Code is cited? Int J Syst Evol Microbiol 2008; 58:1991-1992.
- Tindall BJ, Garrity GM. Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 2008; 58:1987-1990.
- Tindall BJ. Are the concepts of legitimate and illegitimate names necessary under the current International Code of Nomenclature of Bacteria? A proposal to make changes to the Code. Int J Syst Evol Microbiol 2008; 58:1979-1986.
- Young JM. An overview of bacterial nomenclature with special reference to plant pathogens. Syst Appl Microbiol 2008; 31:405-424.
- Young JM, Euzéby JP. Proposed revision of Rule 33c to perpetuate the citation of revived names. Int J Syst Evol Microbiol 2008; 58:2468-2469.
- Oren A, Komárek J, Hoffmann L. Nomenclature of the Cyanophyta/Cyanobacteria/Cyanoprokaryotes - what has happened since IAC Luxembourg? Algol Stud 2009; 130:17-26.
- Young JM. Legitimacy is an essential concept of the International Code of Nomenclature of Prokaryotes – a major revision of the Code is called for. Int J Syst Evol Microbiol 2009; 59:1252-1257.
- Kämpfer P. Certificates of deposit-a key element of the Bacteriological Code and an indispensable prerequisite for comparative taxonomic research. Report of a case of falsification and a reply to the Letter to the Editor by Tindall (2008). Int J Syst Evol Microbiol 2010; 60:475-477.
2011-2015
- International Committee On Systematics Of Prokaryotes. The van Niel International Prize for Studies in Bacterial Systematics, awarded by The University of Queensland Awarded in 2011 to George M. Garrity. Int J Syst Evol Microbiol 2011; 61:2328-2329.
- Garrity GM, Labeda DP, Oren A. Judicial Commission of the International Committee on Systematics of Prokaryotes. XIIth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 3, 4 and 6 August 2008, Istanbul, Turkey. Int. J. Syst. Evol. Microbiol. 2011; 61:2775-2780.
- Oren A. 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. Int J Syst Evol Microbiol 2011; 61:10-15.
- The Publications Committee Of The Icsp. Statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2013; 63:4361-4369.
- Oren A, Garrity GM. Proposal to change General Consideration 5 and Principle 2 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2014; 64:309-310.
- Oren A, Garrity GM, Schink B. Proposal to modify Rule 6, Rule 10a, and Rule 12c of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2014; 64:1452-1453.
- Palinska KA, Surosz W. Taxonomy of cyanobacteria: a contribution to consensus approach. Hydrobiologia 2014; 740:1-11.
- Parte AC. LPSN — List of Prokaryotic names with Standing in Nomenclature. Nucleic Acids Res 2014; 42:D613-D616.
- Stackebrandt E, Smith D, Casaregola S, Varese GC, Verkleij G, Lima N, Bridge P. Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. Springerplus 2014; 3:208.
- Oren A. Comments on: "A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNP, Planktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP, as genus and species names with nomenclature standing under the ICNP," by V. Gaget, M. Welker, R. Rippka, and N. Tandeau de Marsac, Syst. Appl. Microbiol. (2015), http://dx.doi.org/10.1016/j.syapm.2015.02.004. Syst Appl Microbiol 2015; 38:159-160.
- Oren A, da Costa MS, Garrity GM, Rainey FA, Rossello-Mora R, Schink B, Sutcliffe I, Trujillo ME, Whitman WB. Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2015; 65:4284-4287.
- Oren A, Garrity AGM. Proposal to modify Rule 27 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2015; 65:2342.
- Pinevich AV. 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 2015; 65:1070-1074.
- Tindall BJ. Updating Rule 15 of the International Code of Nomenclature of Bacteria. Int J Syst Evol Microbiol 2015; 65:2766-2768.
2016-2020
- Oren A, Garrity GM. The status of the Notes in the International Code of Nomenclature of Prokaryotes: proposal to emend General Consideration 6. Int J Syst Evol Microbiol 2016; 66:3305-3306.
- Tindall BJ. The undesirable retroactive changes to Rule 8 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2016; 66:4895-4896.
- Tindall BJ. Rule 27 of the International Code of Nomenclature of prokaryotes: the basonym is not enough. Int J Syst Evol Microbiol 2016; 66:4897-4899.
- Tindall BJ. The relationship of validly published names to legitimate and illegitimate names in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2016; 66:4905-4906.
- Tindall BJ. Are Rules 20d and 20e of the International Code of Nomenclature of Prokaryotes superfluous? Int J Syst Evol Microbiol 2016; 66:4907-4909.
- Tindall BJ. The wording and examples given in Rule 47a of the International Code of Nomenclature of Prokaryotes are misleading. Int J Syst Evol Microbiol 2016; 66:4913-4914.
- Tindall BJ. Redefining homonyms under Rule 51b (4) of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2016; 66:5618-5619.
- Whitman WB. Modest proposals to expand the type material for naming of prokaryotes. Int J Syst Evol Microbiol 2016; 66:2108-2112.
- Oren A. Proposal to modify Rule 10a and to delete Recommendation 10a(3) from the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2017; 67:3683-3684.
- Tindall BJ. Clarifying the limitations on Rule 18a and Rule 30 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2017; 67:505-506.
- Dijkshoorn L. International Committee on Systematics of Prokaryotes. Minutes of the meetings, 7, 8 and 9 July 2017, Valencia, Spain. Int J Syst Evol Microbiol 2018; 68:2104-2110.
- Oren A, Garrity GM, Parte AC. Why are so many effectively published names of prokaryotic taxa never validated? Int J Syst Evol Microbiol 2018; 68:2125-2129.
- Oren A, Garrity GM. Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2018; 68:3371-3376.
- Oren A, Garrity GM. Proposal to modify Rules 27 and 30(3)(b) of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2018; 68:3951-3953.
- Parte AC. LPSN — List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825-1829.
- Whitman WB, Oren A, Chuvochina M, da Costa MS, Garrity GM, Rainey FA, Rossello-Mora R, Schink B, Sutcliffe I, Trujillo ME, et al. Proposal of the suffix -ota to denote phyla. Addendum to "Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes". Int J Syst Evol Microbiol 2018; 68:967-969.
- Oren A. Proposal to modify the Rules of the International Code of Nomenclature of Prokaryotes to abolish the taxonomic categories Subfamily, Subtribe and Kingdom. Int J Syst Evol Microbiol 2019; 69:1524-1525.
- Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1-S111.
- Tindall BJ. Names above the rank of genus; the radical approach. Int J Syst Evol Microbiol 2019; 69:1833-1834.
- Tindall BJ. An analysis of the term "standing in nomenclature", as used in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:2166-2168.
- Tindall BJ. Comments on minutes of the Subcommittee on the Taxonomy of Chlamydiae and the Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Int J Syst Evol Microbiol 2019; 69:2599-2601.
- Tindall BJ. Introducing the concept of the isonym into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:1515-1518.
- Tindall BJ. The name Bradyrhizobiaceae Garrity et al. 2006 contains Nitrobacter Winogradsky 1892 (Approved Lists 1980), the nomenclatural type of the family Nitrobacteraceae Buchanan 1917 (Approved Lists 1980), is illegitimate and proposals to alter the wording of Rule 54 of the International Code of Nomenclature of Prokaryotes to clarify the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 is replaced by the family name Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) the only correct name. Int J Syst Evol Microbiol 2019; 69:2609-2611.
- Tindall BJ. Proposed modifications to Rule 40d of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:1519-1520.
- Tindall BJ. Rule 29 and combined generic and specific descriptions. Int J Syst Evol Microbiol 2019; 69:2597-2598.
- Tindall BJ. Clarifying the definition and role of effective publication in the International Code of Nomenclature of Prokaryotes with proposals to make changes. Int J Syst Evol Microbiol 2019; 69:2602-2605.
- Tindall BJ. The status of names whose nomenclatural types are based on strains deposited solely for patent purposes. Int J Syst Evol Microbiol 2019; 69:2616-2620.
- Tindall BJ. The role of incorrect citation of the International Code of Nomenclature of Prokaryotes and subsequent misinterpretation in causing unnecessary nomenclatural confusion. Int J Syst Evol Microbiol 2019; 69:2621-2625.
- Tindall BJ. Rule 24b of the International Code of Nomenclature of Prokaryotes and regulating the priority of names and epithets considered to be associated with heterotypic synonyms. Int J Syst Evol Microbiol 2019; 69:3980-3983.
- Whitman WB, Bull CT, Busse HJ, Fournier PE, Oren A, Ventura S. Request for revision of the Statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:584-593.
- 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.
- Oren A, Garrity GM. Emendation of circumscriptions of taxa in the Lists of Changes in Taxonomic Opinion. Int J Syst Evol Microbiol 2020; 70:2163-2164.
- Oren A. 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 2020; 70:4406-4408.
- Oren A, Garrity GM. New combinations, synonymy and emendations can only be proposed based on names that were previously validly published. Int J Syst Evol Microbiol 2020; 70:4419-4420.
- Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607-5612.
- Sutcliffe IC, Dijkshoorn L, Whitman WB, Executive Board OBOTI. 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.
- Sutcliffe IC, Whitman WB. The van Niel International Prize for Studies in Bacterial Systematics, awarded in 2020 to Tanja Woyke. Int J Syst Evol Microbiol 2020; 70:5594-5595.
- Tindall BJ. Clarification of access regulations to genetic resources that are subject to the sovereign rights of sovereign states and the deposit of nomenclatural types under the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2020; 70:317-320.
Discontinued pages
The collections of internet links found in the previous versions of LPSN may not be continued as such but the content distributed over pages dedicated to specific topics. Please see the archived version.
Some of the ancient LPSN pages on nomenclature are not going to be moved to the new system. The contained information is either outdated or available via the general search page. The archived versions of these pages are found here: