J.P. Euzéby: List of Prokaryotic names with Standing in Nomenclature

Cartoon of bacterium used with permission of the Society for General Microbiology (see http://www.microbiologyonline.org.uk/home)

Introduction

"Names, especially those ascribed to organisms, serve as a primary entry point into the scientific, medical, and technical literature and figure prominently in countless laws and regulations governing various aspects of commerce, public safety and public health. These names also serve as a primary entry point into many of the central databases that the scientific community and the general public now rely upon."
G.M. Garrity and C. Lyons: Future-proofing biological nomenclature.

Since January 2000, names of prokaryotes change at a rate approaching 750 validly published names every year. Keeping up with changes in prokaryotic nomenclature has always been problematic. "List of Prokaryotic names with Standing in Nomenclature" was conceived as a solution to this problem. It provides accurate information about the current status of a name, synonyms, and other useful information.

There is no official classification of prokaryotes, but the names given to prokaryotes are regulated. The International Code of Nomenclature of Bacteria (Bacteriological Code) contains General Considerations, Principles, Rules and Recommendations which govern the way in which the names of prokaryotes are to be used.

In 1975, the Bacteriological Code (1975 Revision) introduced a new concept, that of the valid publication of names of prokaryotes. The publication of the Approved Lists of Bacterial Names (Int. J. Syst. Bacteriol., 1980, 30, 225-420) was part of this concept, and set a new starting point in prokaryotic nomenclature. The Approved Lists of Bacterial Names contain 2,212 names of genera, species or subspecies, and 124 names of higher taxa.

The International Code of Nomenclature of Bacteria (1990 Revision) is the cornerstone of prokaryotic nomenclature. It states that the name of a taxon is validly published, and therefore has standing in nomenclature, if one of the following criteria is met:

1) The name is cited in the Approved Lists of Bacterial Names.

2) The name is published in papers in the International Journal of Systematic Bacteriology (IJSB) or in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) and conforms to requirements laid down in the Bacteriological Code.
Note: Starting in August 2002, it is also a requirement of the IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in at least two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). New names and/or combinations will not be published until such documentation has been received by the IJSEM Editorial Office.

3) The name is validly published by announcement in a Validation List.
Validation Lists are lists published in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology validating prokaryotic names effectively, but not validly published.
Announcement in a Validation List is the responsibility of the author of the name or new combination. Authors wishing to have new names and/or combinations included in a list should send the pertinent reprint or a photocopy thereof to the IJSEM Editorial Office or to the Lists Editor.
Note: Starting in August 2002, it is also a requirement of the IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in at least two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). New names and/or combinations will not be cited in Validation Lists until such documentation has been received by the Lists Editor.

In addition to valid publication of a name, the Bacteriological Code (1990 Revision) also states that only correct names are to be used, i.e. based on valid publication, legitimacy, and priority of publication (Principle 6).

Purposes of the List of Prokaryotic names with Standing in Nomenclature

List of Prokaryotic names with Standing in Nomenclature includes, alphabetically and chronologically, the nomenclature of prokaryotes and the nomenclatural changes as cited in the Approved Lists of Bacterial Names or validly published in the International Journal of Systematic Bacteriology (IJSB) or in the International Journal of Systematic and Evolutionary Microbiology (IJSEM).
A classification is proposed for all taxa (except tribes), and a hierarchical classification of prokaryotes is available in the file Classification of domains and phyla - Hierarchical classification of prokaryotes.
As far as possible, the GenBank/EMBL/DDBJ accession numbers for the 16S rRNA genes sequences of type strains are available.

The citations of names are in the correct format according to the Bacteriological Code (1990 Revision), and the nomenclatural types are provided. Abbreviations and addresses of collections from which designated type strains are available are listed alphabetically in the file Culture collections of prokaryotes. Basonyms and synonyms are included to clarify the previous names or histories of individual taxa.

List of Prokaryotic names with Standing in Nomenclature is extensively annotated to clarify the Rules which govern the scientific nomenclature.

The names in this list are "valid" only in the sense of being validly published as a result of conformity with the Rules of Nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
The names which are to be used are those which are correct in the opinion of the bacteriologist (especially a combinatio nova or a nomen novum) and a particular name does not have to be adopted in all circumstances; it is possible for two or more validly published names to remain in use. For example, a bacteriologist can use the names Corynebacterium pyogenes or Actinomyces pyogenes or Arcanobacterium pyogenes according to his (her) scientific judgment, providing that their use is in accordance with the Rules.
Warning: In the List of Prokaryotic names with Standing in Nomenclature, an arrow (--->) only indicates the sequence of valid publication of names and does not mean that the last name in the sequence must be used.

Some names not validly published are also cited in the file Some prokaryotic names without standing in nomenclature.
Infrasubspecific subdivisions, taxa above the rank of class, and the category Candidatus are not covered by the Rules of the Bacteriological Code (1990 Revision). However, a list of Taxa above the rank of class, and a list of Candidatus are available.

The List of Prokaryotic names with Standing in Nomenclature will be updated with the publication of each new issue of the International Journal of Systematic and Evolutionary Microbiology.

As says Le Gros, cited by Buchanan et al.(Index Bergeyana, Williams & Wilkins Company, Baltimore, Md, 1966, pp. VII-XII), "Dans ce genre de travail il est presque impossible de ne pas faire d'erreurs..." (In this kind of work it is very difficult to avoid errors). So, the author (J.P. Euzéby) would greatly appreciate factual information concerning any errors or corrections for this list.

For more information, see:
. EUZEBY (J.P.): List of bacterial names with standing in nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol., 1997, 47, 590-592.
. TINDALL (B.J.): Misunderstanding the Bacteriological Code. Int. J. Syst. Bacteriol., 1999, 49, 1313-1316.
. Definitions and abbreviations
. Names included in the Approved Lists of Bacterial Names
. Names validly published by announcement in Validation Lists
. Taxa above the rank of class
. List of Candidatus
. Some prokaryotic names without standing in nomenclature
. Culture collections of prokaryotes

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