Glossary

Introduction

The List of Prokaryotic names with Standing in Nomenclature (LPSN) is extensively annotated to clarify the rules which govern the scientific nomenclature and to clarify how information found on LPSN is to be interpreted. Most definitions and explanations are found right here in this glossary.
An overview of all LPSN pages dedicated to special topics is provided on the navigation page. While an overview on prokaryotic nomenclature is given elsewhere, we attempt to clarify all details in this glossary. Please also see the introduction into LPSN.
Readers are asked to report inaccurate, outdated and missing information as well as malfunctioning links to the LPSN authors.

Abbreviations in etymologies

The following abbreviations are used in the "List of Prokaryotic names with Standing in Nomenclature" within etymology sections. Another important aspect of the formation of names is orthography. How names are formed depends on their category.
abl.
ablative
adj.
adjective
adv.
adverb
Chem.
Chemical term
comp.
comparative
dim.
diminutive
fem.
feminine gender
gen.
genitive case
Gr.
latinized Greek (the original Greek spelling is not given and the word is transliterated into the Latin alphabet)
L.
Latin (indicates that the word is classic Latin and found in an unabridged Latin dictionary)
masc.
masculine gender
M.E.
Middle English
M.L.
Medieval (sometimes pharmaceutical) Latin
n.
noun
neut.
neuter gender
N.Gr.
Neo-Greek (modern Greek)
N.L.
Neo-Latin (a word treated and used as a Latin word)
nom.
nominative case
num.
numerus
part. adj.
participle adjective
part.
participle
pass.
passive
perf.
perfect
pl.
plural
pref.
prefix
prep.
preposition
pres. part.
present participle
pron.
pronoun
sing.
singular
suff.
suffix
sup.
superlative
sync.
syncope
v.
verb
The abbreviation M.L. stands for "Medieval Latin" not "Modern Latin". For the latter, N.L. (Neo-Latin) is to be used. According to Trüper [1] and to Recommendation 6 (8) [2] the abbreviation N.L. (Neo-Latin) is to be used in place of M.L. (Modern Latin).
References:
  1. TRÜPER (H.G.): How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol. Rev., 1999, 23, 231-249.
  2. DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Etymology information provided on LPSN is collected from the original publication of each taxon name. Where necessary and possible these etymology sections are rewritten to more closely correspond to the custom format. As far as possible the LPSN maintainers also check and where necessary correct parts of the original etymology sections. The checked parts are marked by dotted underlining irrespective of whether the original content was confirmed or was corrected.

Abbreviations in proposals

An author should indicate that a name is being proposed for a new taxon by the addition of the appropriate abbreviation for the category to which the taxon belongs [Rule 33a]. Such abbreviations are frequently printed in Roman (or boldface) type when they follow a Latin scientific name in order to differentiate them from the name and draw attention to the abbreviation [Rule 33a Note 2].
class. nov.
appropriate abbreviation for classis nova (new class)
comb. nov.
appropriate abbreviation for combinatio nova ( new combination)
corrig.
appropriate abbreviation for corrigendum (should be corrected)
emend.
appropriate abbreviation for emendavit (he or she has emended)
et al.
appropriate abbreviation for et alii (and others; multiple authorship)
fam. nov.
appropriate abbreviation for familia nova (new family)
gen. nov.
appropriate abbreviation for genus novum (new genus)
nom. approb.
appropriate abbreviation for nomen approbatum (approved name; a name which is included in the Approved Lists of Bacterial Names)
nom. cons.
appropriate abbreviation for nomen conservandum ( conserved name)
nom. nov.
appropriate abbreviation for nomen novum ( new name; this abbreviation is used for a new combination for which an author is obliged to substitute a new epithet as a result of homonymy)
nom. nud.
appropriate abbreviation for nomen nudum ( bare name)
nom. rej. or nom. rejic.
usual abbreviations for nomen rejiciendum ( rejected name)
nom. rev.
appropriate abbreviation for nomen revictum ( revived name)
ord. nov.
appropriate abbreviation for ordo novus (new order)
phyl. nov.
usual abbreviation for phylum novum (new phylum)
pro synon.
appropriate abbreviation for pro synonymon (as synonym)
sp. nov.
appropriate abbreviation for species nova (new species)
subclass. nov.
appropriate abbreviation for subclassis nova (new subclass)
subfam. nov.
appropriate abbreviation for subfamilia nova (new subfamily)
subgen. nov.
appropriate abbreviation for subgenus novum (new subgenus)
subord. nov.
appropriate abbreviation for subordo novus (new suborder)
subsp. nov.
appropriate abbreviation for subspecies nova (new subspecies)
Alternatively, Candidatus names can be proposed. Rule 40d stipulates the automated creation of the name of a subspecies.
To ease the browsing of the hierarchical classification, in particular for connecting child and parent taxa which would otherwise be unlinked, LPSN creates potentially permanent placeholders as well as temporary stubs. The specific reasons for establishing a placeholder or a stub are given on the respective taxon page.

Abbreviations of miscellaneous uses

ICSB
International Committee on Systematic Bacteriology (now, International Committee on Systematics of Prokaryotes)
ICSP
International Committee on Systematics of Prokaryotes
IJSB
International Journal of Systematic Bacteriology
IJSEM
International Journal of Systematic and Evolutionary Microbiology
Opin.
Judicial Opinion
Validation List no.
"Validation of the publication of new names and new combinations previously effectively published outside the IJSB or outside the IJSEM. List no."
bv.
usual abbreviation for biovar
cv.
usual abbreviation for cultivar
f. sp.
usual abbreviation for forma specialis
pv.
usual abbreviation for pathovar
spp.
species plurales (relating to many species)
syn.
synonym
var.
variety; variety is a synonym of subspecies but, this term has no standing in nomenclature since the publication of the Bacteriological Code (1990 Revision)

Ambiguous name

An ambiguous name (nomen ambiguum) is a name which has been used with different meanings and thus has become a source of error. Such a name should be rejected [Rule 56a]. Example: "Mycobacterium aquae" Jenkins et al. 1972, nom. rejic. (Opinion 55).

Approved Lists of Bacterial Names

The Approved Lists of Bacterial Names contain all the bacterial names having standing in nomenclature on 1 January 1980 and they set a new starting point in bacterial nomenclature [Rule 24a]. Names that were not included in the Approved Lists at that time lost standing in bacterial nomenclature. The names validly published prior to 1 January 1980 but not included in these lists have no further standing in nomenclature but are available for revival individually if the provisions for doing so are met [Rules 24a and 33c].
"When bacteriologists agreed to make a new start in bacteriological nomenclature, they were faced with tens of thousands of names in the literature of the past. Except for about 2,500 names, it was impossible to tell exactly what bacteria they referred to. These 2,500 were therefore retained in the Approved Lists. The names are only approved in the sense that they were approved for retention in the new bacteriological nomenclature" [Sneath and Brenner, 1992]. "Hence, we have the "Approved Lists of Bacterial Names" and not "Lists of Approved Bacterial Names" as the title" [2].
The Judicial Commission may correct the Approved Lists [Rule 23a Note 4]. The Judicial Commission may place on the list of rejected names a name previously published in an Approved List of Bacterial Names [Rule 24c].
The Approved Lists of Bacterial Names were edited by V.B.D. Skerman, V. McGowan, and P.H.A. Sneath on behalf of the Ad Hoc Committee of the Judicial Commission of the International Committee on Systematic Bacteriology (now, the International Committee on Systematics of Prokaryotes).
The Approved Lists of Bacterial Names consist of two lists which were published on 1 January 1980 in the International Journal of Systematic Bacteriology [1]:
  • Approved List 1: names of taxa above the rank of genus (124 names).
  • Approved List 2: names of genera, species and subspecies (2212 names).
In a work as complex as the Approved Lists, errors were unavoidable. Corrections to the Approved Lists have been published by L.R. Hill et al. [2] and have been inserted into the amended edition of the Approved Lists of Bacterial Names [3]. However, some errors remained undetected, and some corrections made by L.R. Hill et al. were omitted from the amended edition of the Approved Lists. These errors and omissions have been corrected by J.P. Euzéby [4, 5]. Another errors are cited on the "List of Prokaryotic names with Standing in Nomenclature".
References:
  1. SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.): Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol.,1980, 30, 225-420.
  2. HILL (L.R.), SKERMAN (V.B.D.) and SNEATH (P.H.A.): Corrigenda to the Approved Lists of Bacterial Names edited for the International Committee on Systematic Bacteriology. Int. J. Syst. Bacteriol., 1984, 34, 508-511.
  3. SKERMAN (V.B.D.), McGOWAN (V.) and SNEATH (P.H.A.): Approved Lists of Bacterial Names. Amended edition. American Society for Microbiology, Washington, 1989.
  4. EUZÉBY (J.P.): Corrigenda to the Approved Lists of Bacterial Names and to the amended edition of the Approved Lists of Bacterial Names. Int. J. Syst. Bacteriol., 1997, 47, 1271-1272.
  5. EUZÉBY (J.P.): Necessary corrections according to Judicial Opinions 16, 48 and 52. Int. J. Syst. Bacteriol., 1998, 48, 613.
The amended edition of the Approved Lists of Bacterial Names is a reference document and it is strongly recommended. This inexpensive book is published by the American Society for Microbiology, 1752 N. Street, N.W. Washington, DC 20036-2804, USA.

Assignment of child taxa to parent taxa

In a hierarchical classification such as the Linnaean system [1], each taxon name has a category. Because these categories are ordered, each taxon name also has a rank. Except for taxa of the lowest rank in use, each taxon comprises one to several other taxa of lower rank. Within such a relation, we call the taxon of higher rank "parent taxon" and the taxa of lower rank its "child taxa". Two child taxa of the same rank and with the same parent taxon are "siblings".
By definition, each prokaryotic species must be included in a genus (binary nomenclature established by Carl von Linné [1]). Because the genus name is included in the species name, the authority who created the species name is automatically the one which assigned the species to its genus. This holds for new species as well as for new combinations. The genus name also forms part of the names of subspecies.
A genus is theoretically a member of successively higher ranks: subtribe, tribe, subfamily, family, suborder, order, subclass, class, division (or phylum) and domain (or empire). In practice, not all of them need to be used. However, by assigning a rank to each category the Linnaean hierarchy strictly determines taxa of which category can serve as child taxa or as parent taxon of a taxon of a given other category. The categories division (or phylum) and domain (or empire) are not covered by the Rules of Bacteriological Code (1990 Revision [2]).
In the Linnaean system [1], the assignment of a genus to a family, of a family to an order, of an order to a class etc. is neither reflected in the name of the child taxon nor in the name of the parent taxon. The only exception is the relationship between a parent taxon and the child taxon that serves as its nomenclatural type and from which its name was formed. For instance, the hierarchical relationship is only from the taxon names themselves in the case of orders or families whose name has been derived from the name of a genus which is still classified in that order or family. But this holds for a minority of taxon names.
For this reason, the publication which assigned a certain child taxon of a genus or higher rank to a certain parent taxon needs not correspond to the authority which proposed the name of the child taxon and needs not correspond to the authority which proposed the name of the parent taxon. The child taxon may originally have not been assigned to a parent taxon of that rank at all or may originally have been assigned to another parent taxon of that rank.
LPSN reflects this situation by separately citing the publication in which the assignment of a child taxon to a parent taxon is found. Where possible the earliest among a couple of suitable publications is chosen.
There are some edge cases in which the cited publication may not actually contain the name of the child taxon or the name of the parent taxon. In the case of illegitimate names of parent taxa that have been replaced by a parent taxon with a legitimate name, the cited publication may be the one that highlighted the illegitimacy. The name of the child taxon needs not explicitly be mentioned in that publication. In other cases the child-parent assignment may also only be implicit in the cited publication but not explicitly be made. For instance, the assignment may be implied by a phylogenetic tree, or may be the logical conclusion from statements given in the publication cited for the assignment on the one hand and in the publication that proposed the name of the child taxon on the other hand. Occasionally a publication about LPSN itself is cited for the child-parent assignment. This is necessary if the assignment was made by the LPSN maintainers themselves based on a recent development for which a published record was not available. Further information is then provided in a note.
References:
  1. Von LINNÉ (C.): Systema naturae per regna tria naturae. PDF version in Gallica, la bibliothèque numérique de la Bibliothèque Nationale de France.
  2. LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.): International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C., 1992.

BacDive

The bacterial metadatabase BacDive is the world’s largest database for standardized bacterial phenotypic information. Phenotypic data are mobilized from collections (e.g. CABI, CCUG, CIP, DSMZ) and enriched with data from species descriptions from the literature. Within hundreds of data fields the database offers systematic access to countless data points. BacDive also offers the world’s largest API® test collection, which can be queried using the API test finder tool. BacDive makes uses of nomenclatural and type-strain information from the PNU database, which also powers LPSN. LPSN in turn links to BacDive. All of these services are provided by the Leibniz Institute DSMZ.

Bacteriological Code, 1990 Revision

The International Code of Nomenclature of Prokaryotes (formerly the International Code of Nomenclature of Bacteria) is an official publication of the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) [Article 12 of the Statutes of the International Committee on Systematic Bacteriology].
The change of the name International Code of Nomenclature of Bacteria to International Code of Nomenclature of Prokaryotes was decided and approved by the Judicial Commission and the ICSP.*
The 1990 revision supersedes all previous editions. It shall be cited as Bacteriological Code (1990 Revision) and will apply from the date of publication (1992) [Rule 1a].
The Bacteriological Code (1990 Revision) applies to all Prokaryotes. The Prokaryotes include groups known by such names as Bacteria, Eubacteria, Archaea, Archaebacteria, Archaeobacteria, Cyanobacteria, Cyanophyceae, Schizomycetes, Schizophycetes [1, 2, 3]. According to Principle 2**, the nomenclature of Prokaryotes is not independent of botanical and zoological nomenclature [3]. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the Zoological Code and the International Code of Botanical Nomenclature. For an example, see: "Illegitimate names and epithets". Other examples are given in "List of Prokaryotic names with Standing in Nomenclature": Microcyclus, Pirella, Rhizomonas, Serpula.
References:
  1. Judicial Commission, Minutes of the Meetings, 2 and 6 July 1994, Prague, Czech Republic. (Minute 8). Int. J. Syst. Bacteriol., 1995, 45, 195-196.
  2. ICSB, XVIth International Congress of Microbiology, Minutes of the Meetings, 2, 3 and 5 July 1994, Prague, Czech Republic. [Minute 12 (iv)]. Int. J. Syst. Bacteriol. 1995, 45, 613-615.
  3. DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
The taxonomic categories which are covered by the Rules are: Class, Subclass, Order, Suborder, Family, Subfamily, Tribe, Subtribe, Genus, Subgenus, Species, and Subspecies [Rules 5b and 5c]. Taxa below the rank of subspecies are not covered by the Rules (see: Infrasubspecific subdivisions) [Rules 5d and 14a].
Alterations to the Bacteriological Code (1990 Revision) can only be made by the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) at one of its plenary sessions [Rule 1b]. Proposals for modification should be published in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology [Rule 1b].
The Rules of the Bacteriological Code (1990 Revision) are retroactive, except where exceptions are specified [Rule 2].
The Code is divided into Principles, Rules, and Recommendations [General Consideration 6]:
  • The Principles form the basis of the Code, and the Rules and Recommendations are derived from them.
  • The Rules are designed to make effective the Principles, to put the nomenclature of the past in order, and to provide for the nomenclature of the future.
  • The Recommendations deal with subsidiary points. Recommendations do not have the force of Rules. Names contrary to a Recommendation cannot be rejected for this reason.
Advisory notes and appendices are added to assist in the application of the Code:
Advisory notes:
  • A. Suggestions for authors and publishers.
  • B. Quotations of authors and names.
  • C. Maintenance of type strains.
Appendices:
  • Appendix 1: Codes of nomenclature.
  • Appendix 2: Approved Lists of Bacterial Names.
  • Appendix 3: Published sources for names of bacterial, algal, protozoal, fungal, and viral taxa.
  • Appendix 4: Conserved and rejected names of bacterial taxa.
  • Appendix 5: Opinions relating to the nomenclature of bacteria.
  • Appendix 6: Published sources for recommended minimal descriptions.
  • Appendix 7: Publication of a new name.
  • Appendix 8: Preparation of a Request for an opinion.
  • Appendix 9: Orthography.
  • Appendix 10: Infrasubspecific subdivisions.
The Bacteriological Code (1990 Revision) includes the "Statutes of the International Committee on Systematic Bacteriology" (now the International Committee on Systematics of Prokaryotes) and the "Statutes of the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies".
* In order to update the Code and to adjust it to modern requirements, the Judicial Commission proposed (August 1999, Sydney, Australia) a number of changes and amendments [1]. The International Committee on Systematics of Prokaryotes voted unanimously in favour of these proposals [2]. Among these changes, the Judicial Commission decided to replace the term Bacteria by the term Prokaryotes. As a logical consequence, the complete text of the Code has to be revised accordingly [1]. So, the name of the International Code of Nomenclature of Bacteria is changed to International Code of Nomenclature of Prokaryotes, and the name of the International Committee on Systematic Bacteriology (ICSB) is changed to International Committee on Systematics of Prokaryotes (ICSP). The last revision of the International Code of Nomenclature of Bacteria must be cited as Bacteriological Code (1990 Revision) [Rule 1a]. According to the proposals of the Judicial Commission (August 1999, Sydney, Australia), the words "Bacteriological Code (1990 Revision)" should be changed to "Prokaryotic Code (1990 Revision)". However, such a change is not formally proposed in the minutes [1] and in this file "Bacteriological Code (1990 Revision)" will be used in place of "Prokaryotic Code (1990 Revision)".
References:
  1. DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
  2. LABEDA (D.P.): International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14 and 17 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2245-2247.
** The Judicial Commission (August 1999, Sydney, Australia) proposed the replacement of Principle 2. The new Principle 2 takes effect with publication of acceptance of this change by the ICSP (August 14, 1999) and is not retroactive.
Old Principle 2: The nomenclature of bacteria is independent of botanical nomenclature, except for algae and fungi, and of zoological nomenclature, except protozoa.
New Principle 2: The nomenclature of Prokaryotes is not independent of botanical and zoological nomenclature. When naming new taxa in the rank of genus or higher, due consideration is to be given to avoiding names which are regulated by the Zoological Code and the International Code of Botanical Nomenclature.
References:
  1. DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
  2. LABEDA (D.P.): International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14 and 17 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2245-2247.

Bare name

A bare name (nomen nudum: nom.nud.) is a name published without a description or a reference to a previously published description [Chapter 4. Advisory notes, B. Quotations of authors and names (4)]. Example: "Halobacterium" Schoop 1935.

Basonym

Original name of a new combination or original name of a nomen novum. Basonyms are earlier homotypic synonyms.
Examples:
  • New combination: Haemophilus pleuropneumoniae Shope 1964 (Approved Lists 1980) is the basonym of Actinobacillus pleuropneumoniae (Shope 1964) Pohl et al. 1983.
  • Nomen novum: Microbispora viridis Miyadoh et al. 1985 is the basonym of Actinomadura rugatobispora Miyadoh et al. 1991.

Candidatus

In 1994, Murray and Schleifer [1] published a taxonomic note in which they proposed the concept of a waiting position for putative taxa in a category called Candidatus, which would have indefinite rank.
Minute 9 of the minutes of the 1994 meetings of the Judicial Commission in Prague [2] introduced a recommendation that the new category of indefinite rank (Candidatus) be established for certain putative taxa that could not be described in sufficient detail to warrant establishment of a novel taxon. The commission also recommended to the ICSB (now ICSP) that a Candidatus list should be established in the International Journal of Systematic Bacteriology (now International Journal of Systematic and Evolutionary Microbiology). The Judicial Commission appointed Murray and Stackebrandt to prepare a taxonomic note to introduce the Candidatus concept.
The taxonomic note proposing the establishment of the provisional status Candidatus for incompletely described prokaryotes was published in the January 1995 issue of the IJSB [3]. According to this note, the category Candidatus should be used for describing prokaryotic entities for which more than a mere sequence is available but for which characteristics required for description according to the Bacteriological Code (1990 Revision) are lacking. In addition to genomic information such as sequences apt to determine the phylogenetic position of the organism, all information, including structural, metabolic, and reproductive features should be included in the description, together with the natural environment in which the organism can be identified by in situ hybridization or other similar techniques for cell identification.
During the 1996 meetings in Jerusalem [4], the Judicial Commission considered the proposal by Murray and Stackebrandt and recommended that the sentence "Cultivated or not cultivated" (see Table I of the paper by Murray and Stackebrandt) should be changed to "Not cultivated or can not be sustained in culture for more than a few serial passages". With that amendment, the Commission unanimously voted to recommend to the ICSB (now ICSP) that the taxonomic note by Murray and Stackebrandt be adopted as an Appendix to the Bacteriological Code (1990 Revision). Thereafter, the proposal of the Judicial Commission was unanimously accepted by the ICSB (now ICSP) [5].
Microbiologists are encouraged to use the "Candidatus" concept for well characterized but as yet uncultured organisms [6].
The names included in the category Candidatus are usually written as follows: Candidatus (in italics), the subsequent name(s) in Roman type (with an initial cap for the first subsequent name or the single subsequent name) and the entire name in quotation marks. For example, "Candidatus Phytoplasma", "Candidatus Phytoplasma allocasuarinae".
According to the "IRPCM Phytoplasma/Spiroplasma Working Team - Phytoplasma taxonomy group" the abbreviation for Candidatus should be Ca. [7].
"List of Prokaryotic names with Standing in Nomenclature" provides names included in the category Candidatus; see the general search page.
References:
  1. MURRAY (R.G.E.) and SCHLEIFER (K.H.): Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol., 1994, 44, 174-176.
  2. JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY: Minutes of the meetings, 2 and 6 July 1994, Prague, Czech Republic. Int. J. Syst. Bacteriol., 1995, 45, 195-196.
  3. MURRAY (R.G.E.) and STACKEBRANDT (E.): Taxonomic Note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol., 1995, 45, 186-187.
  4. JUDICIAL COMMISSION OF THE INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY: VIIth International Congress of Microbiology and Applied Bacteriology. Minutes of the meetings, 17 and 22 August 1996, Jerusalem, Israel. Int. J. Syst. Bacteriol., 1997, 47, 240-241.
  5. INTERNATIONAL COMMITTEE ON SYSTEMATIC BACTERIOLOGY: VIIth International Congress of Microbiology and Applied Bacteriology. Minutes of the meetings, 17, 18, and 22 August 1996, Jerusalem, Israel. Int. J. Syst. Bacteriol., 1997, 47, 597-600.
  6. STACKEBRANDT (E.), FREDERIKSEN (W.), GARRITY (G.M.), GRIMONT (P.A.D.), KÄMPFER (P.), MAIDEN (M.C.J.), NESME (X.), ROSSELLO-MORA (R.), SWINGS (J.), TRÜPER (H.G.), VAUTERIN (L.), WARD (A.C.) and WHITMAN (W.B.): Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol., 2002, 52, 1043-1047.
  7. The IRPCM Phytoplasma/Spiroplasma Working Team - Phytoplasma taxonomy group: ’Candidatus Phytoplasma’, a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int. J. Syst. Evol. Microbiol., 2004, 54, 1243-1255.

Changes in names of taxa as a result of change in rank

When a genus is lowered in rank to subgenus, the original name must be retained unless it is rejected under the Rules [Rule 49]. This also applies when a subgenus is elevated to a genus [Rule 49]. Example: The genus Branhamella has been lowered in rank to subgenus and the name of this subgenus is Branhamella.
When a subspecies is elevated in rank to a species, the subspecific epithet in the name of the subspecies must be used as the specific epithet unless the resulting combination is illegitimate [Rule 50a]. Example: Micromonospora halophytica subsp. nigra Weinstein et al. 1968 (Approved Lists 1980) becomes Micromonospora nigra (Weinstein et al. 1968) Kasai et al. 2000.
When a species is lowered in rank to a subspecies, the specific epithet in the name of the species must be used as the subspecific epithet of the name of the subspecies unless the resulting combination is illegitimate [Rule 50b]. Example: Bifidobacterium globosum (ex Scardovi et al. 1969) Biavati et al. 1982 becomes Bifidobacterium pseudolongum subsp. globosum (Biavati et al. 1982) Yaeshima et al. 1992.

Changes in names of taxa as a result of division

If a genus is divided into genera or subgenera, the generic name must be retained for the genus or for the the subgenus which includes the type species [Rules 39a and 39b]. Example: The genus Moraxella has been divided into the two subgenera Moraxella and Branhamella. The subgenus which includes the type species is named Moraxella.
If a species is divided into species or subspecies the specific epithet of the original species must be retained for the species or for the subspecies which includes the type strain [Rules 40a and 40b]. Example: The species Bacillus subtilis has been divided into subspecies. The subspecies containing the type strain is named Bacillus subtilis subsp. subtilis.

Changes in names of taxa as a result of transfer

The name of a taxon must be changed if the nomenclatural type of the taxon is excluded [Rule 37a (1)]. Example: The type species of the genus Arachnia has been transferred in the genus Propionibacterium. So, the name Arachnia must be changed to Propionibacterium.
Retention of a name in a sense which excludes the type can only be effected by conservation and only by the Judicial Commission [Rule 37a (2)]. Example: Methanococcus mazei was designated as the type species of the genus Methanococcus in the Approved Lists of Bacterial Names, but without a type strain. Mah and Kuhn requested that the Judicial Commission conserve the genus Methanococcus with a new type, Methanococcus vannielii, for which a type strain was included in the Approved Lists. The Judicial Commission has voted to award an opinion conserving Methanococcus with the type species Methanococcus vannielii (see: Opinion 62).
In the case of a species, the specific epithet remains the same on transfer of a species from one genus to another unless an author is obliged to substitute a new specific epithet as a result of homonymy (see: Nomen novum) [Rule 23a Note 1 and Rule 41a]. Examples:
  • The species Haemophilus pleuropneumoniae bears this name in the genus Haemophilus. When placed in the genus Actinobacillus, it bears the name Actinobacillus pleuropneumoniae.
  • Bernardet et al. 1996 proposed Flavobacterium hydatis for Cytophaga aquatilis Strohl and Tait 1978 (Approved Lists 1980) on transfer to Flavobacterium because in that genus the name Flavobacterium aquatile already existed.
In the case of a subspecies, the subspecific epithet remains the same on transfer of a subspecies from one species to another unless an author is obliged to substitute a new subspecific epithet as a result of homonymy (see: Nomen novum) [Rule 23a Note 2]. Example: The subspecies Pseudomonas avenae subsp. avenae bears this name in the genus Pseudomonas. When placed in the genus Acidovorax, it bears the name Acidovorax avenae subsp. avenae.

Changes in names of taxa as a result of union

When two or more taxa of the same rank are united, then the name of the taxon under which they are united (and therefore the type of the taxon) is chosen by the rule of priority of publication [Rules 38 and 42]. Example: Stackebrandt and Kroppenstedt (1988) united Ampullariella Couch 1964 (Approved Lists 1980), and Amorphosporangium Couch 1963 (Approved Lists 1980) with Actinoplanes Couch 1955 (Approved Lists 1980) and retained the early name, Actinoplanes.
If species of different genera are brought together to form a genus, the name of the genus is that associated with the type species having the earliest legitimate name [Rule 44].
If no type species is placed in the genus, a new generic name must be proposed and a type species selected [Rule 44]. Example: The genus Brevibacterium was first proposed by Breed (1953) for a number of rods formerly classified in several genera (Bacillus, "Bacterium", "Bactridium", Flavobacterium). None of the included species was a type species of the genera from which the species were transferred, so a new name, Brevibacterium, was proposed, with Brevibacterium linens as the type species.
When taxa of the same rank from subtribe to family inclusive are united under a taxon of higher rank, the higher-ranking taxon should derive its name (except if there is a risk of confusion) from the name of the earliest legitimate genus that is a type genus of one the lower-ranking taxa [Rule 47a]. If the use of this generic name would lead to confusion, then the author may choose as type a genus which leads to the least confusion and, if in doubt, should refer the matter to the Judicial Commission. Example: The law of priority has been followed in combining the families Beggiatoaceae Migula 1894 (Approved Lists 1980) and Vitreoscillaceae Pringsheim 1949 (Approved Lists 1980) into the new order Beggiatoales Buchanan 1957 (Approved Lists 1980) [type genus, Beggiatoa Trevisan 1842 (Approved Lists 1980)]. In contrast, Pseudomonas Migula 1894 (Approved Lists 1980) has been chosen over Spirillum Ehrenberg 1832 (Approved Lists 1980) and Nitrobacter Winogradsky 1892 (Approved Lists 1980) to form the name of the suborder Pseudomonadineae Breed et al. 1957 (Approved Lists 1980).

Characterization

The characterization of organisms is no longer restricted by methodological barriers, as it is now not only possible to study single genes, or to use amplified fragment length polymorphism, random amplification of polymorphic DNA (RAPD), and G+C content analysis to examine the genetic information by using, but also to fully sequence the entire genome of a strain. However, it is becoming increasingly evident that the study of biochemical pathways, the roles of structural elements (proteins and lipopolysaccharides, etc.) in morphology, or the chemical composition of the cell should be related to the underlying genetic information of an organism. Genes just do not exist on their own. The more reliable the classification and characterization, the higher the likelihood of being able to pick identification methods which are both sustainable and accurate.
References:
  1. TINDALL (B.J.), SIKORSKI (J.), SMIBERT (R.A.) and KRIEG (K.R.): Phenotypic Characterization and the Principles of Comparative Systematics. In: C.A. REDDY, T.J. BEVERIDGE, J.A. BREZNAK, G. MARZLUF, T.M. SCHMIDT, L.R. SNYDER (editors), Methods for General and Molecular Microbiology, 3rd Edition, ASM Science, Washington (D.C.), p. 330-393.

Citation of names and authors

The citation of a name of a taxon should include both the name of the author (s) who first published the name and the year of publication. If there are more than two authors of the name, the citation includes only the first author followed by "et al." and the year [Rule 33b]. Example: Streptococcus hyovaginalis Devriese, Pot, Vandamme, Kersters, Collins, Alvarez, Haesebrouck and Hommez 1997 or Streptococcus hyovaginalis Devriese et al. 1997.
The citation of a name which is included in the Approved Lists of Bacterial Names can be made as follows [Rule 33b Note 3]:
  • The name of the original author and date of publication followed by the words "Approved Lists 1980" in parentheses. Example: Streptococcus Rosenbach 1884 (Approved Lists 1980).
  • Alternatively the name may be cited simply by the addition of the words "Approved Lists 1980" in parentheses. Example: Streptococcus (Approved Lists 1980).
  • If indication is given that a name is included in an Approved List of Bacterial Names without specification of that list, the name may be cited by the addition of the abbreviation "nom. approb." ( nomen approbatum). Example: Streptococcus nom. approb.
If an author wishes to indicate the names of the original authors of a revived name ( nomen revictum), he may do so by citation of the name of the taxon, followed by the word "ex" and the name of the original author and the year of publication, in parentheses, followed by the abbreviation nom. rev. (nomen revictum) [Rule 33c, Note 2]. Example: Streptococcus dysgalactiae (ex Diernhofer 1932) Garvie et al. 1983.
If an author wishes to indicate that a reused name has been used for a different taxon, indication is made by citation of the name and the author and year of publication followed by the word "non" (or "not") and the name and year of the publication of the author who first used the name [Rule 33c, Note 3]. Example: Achromobacter Yabuuchi and Yano 1981 non Achromobacter Bergey et al. 1923.
If a name is a new combination, the citation should include the name of the taxon followed by the names of the original authors and the year of publication, in parentheses, followed by the names of the authors who proposed the new combination and the year of publication of the new combination [Rules 34a and 34b]. Example: Actinobacillus pleuropneumoniae (Shope 1964) Pohl et al. 1983.
When the author who formed the new combination was obliged to substitute a new specific epithet to avoid homonymy ( nomen novum), the name of the author of the original specific epithet is omitted [Rule 34b]. Example: Bernardet et al. 1996 proposed Flavobacterium hydatis for Cytophaga aquatilis Strohl and Tait 1978 (Approved Lists 1980) on transfer to Flavobacterium because in that genus the name Flavobacterium aquatile already existed. Flavobacterium hydatis Bernardet et al. 1996 is correct, not Flavobacterium hydatis (Strohl and Tait 1978) Bernardet et al. 1996.
If an alteration of the diagnostic characters or of the circumscription of a taxon modifies the nature of the taxon, the author responsible may be indicated by the addition to the author citation of the abbreviation "emend." ( emendavit) followed by the name of the author responsible of the change [Rule 35]. Example: Corynebacteriaceae Lehmann and Neumann 1907 (Approved Lists 1980) emend. Stackebrandt et al. 1997.
When a subspecies is automatically created under Rule 40d (see: Names of subspecies), the authorship of such an automatically created subspecific name is cited to the original author of the epithet followed by the author of the subspecies. Example: Vibrio subtilis Ehrenberg ---> Bacillus subtilis comb. nov. Cohn ---> Bacillus subtilis subspecies subtilis subsp. nov. Nakamura. The correct authorship of the subspecies is Bacillus subtilis subspecies subtilis (Ehrenberg) Nakamura [Ehrenberg for the epithet and Nakamura for the new subspecies].
The name of a subgenus (see: Names of subgenera) when included with the name of a species, is placed in parentheses and it is preceded by the abbreviation "subgen." (subgenus novum). When included, the citation should be inserted before closure of the parentheses [Rule 10c]. Example: Moraxella (subgen. Moraxella Lwoff 1939, 173) lacunata; Moraxella (subgen. Branhamella Catlin 1970, 157) catarrhalis. In the "List of Prokaryotic names with Standing in Nomenclature" the name of a subgenus is always placed in parentheses with the abbreviation "subgen." (even if the name of a species is not included) and the citation is inserted before closure of the parentheses. For example: Acetobacter (subgen. Acetobacter Beijerinck 1898) subgen. nov.
A conserved name shall be indicated by the addition of the abbreviation "nom. cons." (nomen conservandum) to the citation [Advisory Notes]. Example: Erysipelothrix rhusiopathiae (Migula 1900) Buchanan 1918 (Approved Lists 1980) nom. cons. (Opinion 32).

Classification

Classification is the arrangement of objects into groups. Distinct forms of classification may have different goals. The classification of things in general, or of organisms such as prokaryotes, may use numbers or names for the resulting groups. Organisms may be arranged according to their pathogenic potentials (biological safety levels) or grouped in a way that is based on more complex theories (i.e., the course of evolution). Nomenclature is the naming of those groups. If the groups are species, genera, and families, etc., then how to name them, and how to link between names currently in use and names which have been used in the past, is governed by an International Code of Nomenclature. The more reliable the classification and characterization, the higher the likelihood of being able to pick identification methods which are both sustainable and accurate.
References:
  1. TINDALL (B.J.), SIKORSKI (J.), SMIBERT (R.A.) and KRIEG (K.R.): Phenotypic Characterization and the Principles of Comparative Systematics. In: C.A. REDDY, T.J. BEVERIDGE, J.A. BREZNAK, G. MARZLUF, T.M. SCHMIDT, L.R. SNYDER (editors), Methods for General and Molecular Microbiology, 3rd Edition, ASM Science, Washington (D.C.), p. 330-393.

Conserved name

A conserved name (nomen conservandum: nom. Cons.) is a name which must be used instead of all earlier synonyms and homonyms [Rules 23a Note 4, and 56b].
Only the Judicial Commission can place names on the list of conserved names (nomina conservanda) [Rules 23a Note 4 (i) and 56b Note 2].
A conserved name (nomen conservandum) is conserved against all other names for the taxon, whether these are cited in the corresponding list of rejected names or not, so long as the taxon concerned is not united with another taxon bearing a legitimate name [Rule 56b Note 1].
A conserved name shall be indicated by the addition of the abbreviation "nom. cons." (nomen conservandum) to the citation [Advisory Notes]. Example: Mycobacterium avium Chester 1901 (Approved Lists 1980) nom. cons. (Opinion 47).
Conserved names can be obtained via the general search.

Correct name

The naming of prokaryotes is controlled by the ICNP. The correct name of a taxon is based upon valid publication, legitimacy, and priority of publication [Principle 6]. Only correct names are to be used [Rule 23a Note 5]. The situations in which the taxonomist has a choice between several names that could be regarded as the correct name are explained in an article freely available on LPSN.
The List of Prokaryotic Names with Standing in Nomenclature selects certain taxon names as correct names. Whenever several options are available that are in accordance with the rules of the International Code of Nomenclature of Prokaryotes, the choice of a correct name in LPSN reflects one of the taxonomic opinions expressed in the literature. LPSN indicates alternative taxonomic arrangements, if any, in addition to the preferred one. Other researchers may well express distinct taxonomic opinions and the Code permits them to do so. Readers who would recommend preferring alternative taxonomic arrangements that are also in accordance with the rules of the Code are encouraged to provide appropriate evidence to the LPSN maintainers.

Corrigendum

The abbreviation "corrig." (corrigendum) may be appended to the name if an unintentional typographical or orthographic error has been corrected by a subsequent author. Such a correction does not affect the validity and original date of publication [Rule 61]. Example: Flavobacterium branchiophilum corrig. Wakabayashi et al. 1989 (in place of Flavobacterium branchiophila (sic) Wakabayashi et al. 1989).
The liberty of correcting a name or epithet must be used with reserve especially if the change affects the first syllable and above all the first letter of the name or epithet [Rule 61 Note].
As from December 14, 2000 (date of the publication of the minutes of the meetings of the Judicial Commission, August 1999, Sydney, Australia), except for changes of gender in specific epithets when species are transferred to other genera, no grammatical or orthographic corrections are accepted for names on the Approved Lists of Bacterial Names, the Validation Lists and the Notification Lists.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
See also: Orthography.

Definition of a subspecies

According to Staley and Krieg, a subspecies is "based on minor but consistent phenotypic variations within the species or on genetically determined clusters of strains within the species".
According to Wayne et al., "Subspecies designations can be used for genetically close organisms that diverge in phenotype. There is some evidence, based on frequency distribution of Tm values in DNA hybridization, that the subspecies concept is phylogenetically valid. (...) There is a need for further guidelines for designation of subspecies."
References:
  1. STALEY (J.) and KRIEG (N.R.): Bacterial classification I. Classification of procaryotic organisms: an overview. In: N.R. KRIEG and J.G. HOLT (editors), Bergey’s Manual of Systematic Bacteriology, vol. 1, The Williams & Wilkins Co, Baltimore, 1984, p. 1-4.
  2. WAYNE (L. G.), BRENNER (D.J.), COLWELL (R.R.), GRIMONT (P.A.D.), KANDLER (O.), KRICHEVSKY (M.I.), MOORE (L.H.), MOORE (W.E.C.), MURRAY (R.G.E.), STACKEBRANDT (E.), STARR (M.P.) and TRUPER (H.G.): Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol., 1987, 37, 463-464.

Diacritic signs

Diacritic signs are not used in names or epithets in bacteriology [Rule 64]. In names or epithets derived from words with diacritic signs, the signs are transcribed as follows [Rule 64]:
  • ä, ö, and ü become ae, oe, and ue, respectively.
  • é, è, and ê become e.
  • æ, ø and å become ae, oe, and aa, respectively.
Example: Moraxella boevrei (named in honor of K. Bøvre), not "Moraxella bøvrei".
On the "List of Prokaryotic names with Standing in Nomenclature", the omission of some diacritical signs in the names of authors was dictated by the limitations of the software. These limitations are not in effect any more. Diacritic signs may well be missing from the textual descriptions of literature references, however.

Domain

Woese et al. propose the new rank of domain for the highest taxon above kingdom, and assigned all living organisms to three domains: the Eucarya (comprising all Eukaryotes), the Bacteria (comprising eubacteria, mitochondria and chloroplasts) and the Archaea (comprising all the groups of archaebacteria).
Thereafter, Trüper proposes to change the term domain (dominium) to empire (imperium) and to change the term Bacteria to Eubacteria.
The taxonomic category domain or empire is not covered by the Rules.
References:
  1. TRÜPER (H.G.): Taxonomic notes: Names for the higher taxa and their impact on the Code of Nomenclature of Bacteria. Int. J. Syst. Bacteriol., 1994, 44, 368-369.
  2. WOESE (C.R.), KANDLER (O.) and WHEELIS (M.L.): Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc. Natl. Acad. Sci. USA, 1990, 87, 4576-4579.

Doubtful name

A doubtful name (nomen dubium) is a name whose application is uncertain. Such a name should be rejected [Rule 56a]. Example: Methanosarcina methanica nom. rejic. (Opinion 63).

Effective publication

Publication of the name and description of a taxon in a recognized scientific printed and/or electronic publication [Rule 23a Note 5 and Rule 25a]. When proposed in full articles in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology the publications are automatically effective and valid publications [Rule 27]. However, the publications must conform to requirements laid down in the Bacteriological Code (1990 Revision) and its successors.
Reference: TINDALL (B.J.), DE VOS (P.) and TRÜPER (H.G.): 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.
No other kind of publication (communications at meetings, minutes of meetings, abstracts of papers presented at meetings, catalogues of collections, microfilms, nonscientific periodicals, newsletters, patents...) is accepted as effective [Rule 25b]. When a name of a new taxon is published in a work written in a language unfamiliar to the majority of workers in bacteriology, it is recommended that the author(s) include in the effective publication a description in English [Recommendation 25a].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Date of effective publication does not determine priority [Rules 23b and 27]. Example: Haemophilus felis was effectively published in 1992 (J. Clin. Microbiol., 1992, 30, 2108-2112.) but validly published in 1999 (Validation List no. 69: Int. J. Syst. Bacteriol., 1999, 49, 341-342). The date of this name is 1999.

Emendation

If an alteration of the diagnostic characters or of the circumscription of a taxon modifies the nature of the taxon, the author responsible may be indicated by the addition to the author citation of the abbreviation "emend." (emendavit) followed by the name of the author responsible for change [Rule 35]. Example: Aquaspirillum serpens (Müller 1786) Hylemon et al. 1973 (Approved Lists 1980) emend. Boivin et al. 1985.
There is no validation procedure for emendations but emendations can be included in a List of Changes in Taxonomic Opinion in IJSEM. The purpose of these lists is similar to the one of Notification Lists.

Empire

See domain.

Etymology and accentuation

The derivation (etymology) of a new name (and if necessary of a new combination) must be given [Rule 27(2) b]. For all practical purposes, the Rule 27(2) b applies from 01 January 2001 and it is not retroactive.
References:
In the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology, the etymology is provided with accentuation of names. "Frequently accentuation of Latin names appears to pose problems, especially when Greek word elements are involved. In such cases, however, Greek accentuation has to be replaced by Latin accentuation, because the Bacteriological Code stipulates Latin as the language of prokaryote names."[1]. In 1957, the late Professor R.E. Buchanan wrote an excellent chapter "How bacteria are named and identified" [2] with the intention of helping bacteriologists and students. Pr. Buchanan has described and exemplified the accentuation of Latin words and the main recommendations are given below:
(1) No Latin word consisting of two or more syllables is accented on the last syllable.
(2) A Latin word consisting of two syllables is accented on the first syllable. Examples: lentum, parvus, rubra etc.
(3) A Latin word consisting of three or more syllables is accented either on the next to the last syllable (the penult) or on the second to the last syllable (the antepenult). If the penult is long it should be accented; if short the antepenult is to be accented. If a syllable has a single long vowel, the syllable is long (a Latin dictionary indicates whether the vowel is long). If a syllable contains a diphthong, it is long. If there is a double consonant or two consonants following a vowel, the syllable is long.
Examples:
odoratus. The accent is on the penult because the vowel of the penult is long.
Bacteroides. The accent is on the penult because the syllable contains a diphthong.
Bacil’lus. The accent is on the penult because of the double "l".
fermen’tum. The accent is on the penult because there are two consonants following the vowel "e".
Acetobacte’rium. The accent is on the antepenult because the vowel in the penult is short.
Bacilla’ceae. The accent is on the antepenult because the vowel in the penult is short.
References:
  1. TRÜPER (H.G.): How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol. Rev., 1999, 23, 231-249.
  2. BUCHANAN (R.E.): How bacteria are named and identified. In: R.S. BREED, E.G.D. MURRAY and N.R. SMITH (ed.): Bergey’s Manual of Determinative Bacteriology, The Williams & Wilkins Company, Baltimore, seventh edition, 1957, pp. 15-28.

Gender of names or epithets

A Latin or Greek word adopted as a generic name retains the classical gender of its language of origin [Rule 65 (1), Rule 65 (2)]. Examples: Bacillus (L. masc. n. bacillus, a little staff) is in the masculine gender; Sarcina (L. fem. n. sarcina, a bundle, pack) is in the feminine gender, Serpens (L. masc. n. serpens, a snake, serpent) is in the masculine gender; Stella (L. fem. n. stella, a star) is in the feminine gender etc.
Generic or subgeneric names which are modern compounds from two or more Latin or Greek words take the gender of the last component of the compound word [Rule 65 (2)]. Examples:
  • Generic or subgeneric names ending in -bacillus (L. masc. n. bacillus, a little staff), in -coccus (Gr. masc. n. coccos, grain; N.L. masc. n. coccus, grain)... are in the masculine gender.
  • Generic or subgeneric names ending in -rhabdus (Gr. fem. n. rhabdos, a staff; N.L. fem. n. rhabdus, a staff), in -monas (Gr. fem. n. monas, unit, monad), in -catella (L. fem. n. catella, a small chain)... are in the feminine gender.
  • Generic or subgeneric names ending in -baculum (L. neut. n. baculum, a staff), in -filamentum (L. neut. n. filamentum, a thread, yarn), in -nema (Gr. neut. n. nema, thread)... are in the neuter gender.
Arbitrarily formed generic names or vernacular names used as generic names take the gender assigned to them by their authors [Rule 65 (3)]. When the original author failed to indicate the gender, a subsequent author has the right of choice [Rule 65 (3)]. Examples: Afipia (derived from AFIP: Armed Force Institute of Pathology), Cedecea (derived from CDC: Centers for Disease Control), Desemzia (derived from DSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen) and Waddlia (derived from WADDL: Washington Animal Disease Diagnostic Laboratory) are in the feminine gender.
Generic or subgeneric names which commemorate a man or a woman are in the feminine gender [Recommendation 10a (2)]. Examples: Burkholderia (named in honor of Mr W.H. Burkholder) and Rothia (named in honor of Mrs G.D. Roth) are in the feminine gender.
The names of bacterial genera which end in -bacter should be regarded as having the masculine gender [Judicial Opinion 3].
Names of orders, suborders, tribes, subtribes, families, and subfamilies are in the feminine gender [Rule 7].
Specific epithets or subspecific epithets treated as adjectives must agree in gender with the generic name [Rules 12c (1) and 13b]. Examples: L. adj. albus -a -um, white: Marinococcus albus (masculine gender), Brevundimonas alba (feminine gender), Methylomicrobium album (neuter gender), Streptomyces albus subsp. albus (masculine gender), Nocardiopsis alba subsp. alba (feminine gender)...
See also the page on etymology and the links therein.

Homonym

Homonymy is the term applied when the same name is given to two or more different taxa of the same rank based on different types. The first published name is known as the senior homonym and any later published name as a junior homonym [Rule 11 Note]. Example: Holospora obtusa (ex Hafkine 1890) Preer and Preer 1982, is a junior homonym of Holospora obtusa (ex Hafkine 1890) Gromov and Ossipov 1981 because these two taxa are based on different types.

Identification

In contrast to taxonomy, identification is concerned with comparing unknown organisms to organisms that have already been classified. In this respect, identification can be carried through only once a taxonomy has been established. Usually, identification protocols aim at quickly assigning an organism to a known group by applying the minimum possible number of methods. To the contrary, a novel organism should be characterized as comprehensibly as possible to ensure that subsequent identification systems have a reliable basis on which to work. The more reliable the classification and characterization, the higher the likelihood of being able to pick identification methods which are both sustainable and accurate.
References:
  1. TINDALL (B.J.), SIKORSKI (J.), SMIBERT (R.A.) and KRIEG (K.R.): Phenotypic Characterization and the Principles of Comparative Systematics. In: C.A. REDDY, T.J. BEVERIDGE, J.A. BREZNAK, G. MARZLUF, T.M. SCHMIDT, L.R. SNYDER (editors), Methods for General and Molecular Microbiology, 3rd Edition, ASM Science, Washington (D.C.), p. 330-393.

Illegitimate names and epithets

The correct name of a taxon is based upon legitimacy [Principle 6]. A name contrary to a Rule is illegitimate and may not be used [Rules 3 and 51a]. Among the reasons for which a name may be illegitimate are the following:
  • The name is a junior homonym of a name of a taxon regulated by the Zoological Code and the International Code of Botanical Nomenclature [Principle 2, Rule 51b(4)]. See also Bacteriological Code (1990 Revision). Example: The name Micromonas Murdoch and Shah 2000 is illegitimate because of precedence of the fungal genus Micromonas.
  • The name is merely an ordinal adjective higher than ten used for enumeration [Rule 52 (2)]. Example: undecimus, duodecimus etc. This means that epithet formed from ordinal numbers (primus, secundus etc. up to decimus) have standing in nomenclature. Example: Clostridium tertium is legitimate because the specific epithet is an ordinal adjective below undecimus (Latin adj. tertius -a -um: third).

Incidental mention

Incidental mention of a new name means mention by an author who does not clearly state or indicate that he is proposing a new name or a new combination [Rule 28b (3)]. Example: "Methanothermobacter defluvii" (Kotelnikova et al. 1994) Wasserfallen et al. 2000.
An incidental mention is not validly published [Rule 28]. Example: "Methanothermobacter defluvii" (Kotelnikova et al. 1994) Wasserfallen et al. 2000 is not validly published.

Indexes of the bacterial and yeast nomenclatural changes

The "Indexes of the bacterial and yeast nomenclatural changes" include the valid nomenclature of bacteria and yeasts recognized by the International Committee on Systematic Bacteriology (now the International Committee on Systematics of Prokaryotes) as validly published or validly published in the International Journal of Systematic Bacteriology since the 1980 Approved Lists of Bacterial Names. These indexes are among the major sources for names of bacterial taxa [Appendix 2, Appendix 3]. The nomenclatural type and a simplified reference (year, volume, and page number) are given for every taxon. Basonyms are included to clarify the previous names or histories of individual taxa. Annotations are made to clarify the rules or rationale for some nomenclatural changes. Three indexes have been published.
References:
  • MOORE (W.E.C.), CATO (E.P.) and MOORE (L.V.H.): 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 1985). Int. J. Syst. Bacteriol., 1985, 35, 382-407.
  • MOORE (W.E.C.) and MOORE (L.V.H.): 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 1989). American Society for Microbiology, Washington, D.C., 1989.
  • MOORE (W.E.C.) and MOORE (L.V.H.): 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, D.C., 1992.

Infrasubspecific subdivisions

Taxa below the rank of subspecies (infrasubspecific subdivisions) are not covered by the Rules of the Bacteriological Code (1990 Revision) [Rules 5d and 14a].
The preferred names of infrasubspecific subdivisions are [Appendix 10]: biovar (usual abbreviation: bv.), chemoform, chemovar, cultivar (usual abbreviation: cv.), forma specialis (abbreviation: f. sp.), morphovar, pathovar (usual abbreviation: pv.), phagovar, phase, serovar, and state. The introduction of the suffix "-var" or "-form" to replace "-type" is recommended to avoid confusion with the strict use of term "type" to mean nomenclatural type. Examples: biovar, serovar, or chemoform in place of biotype, serotype, or chemotype.
A Latin or latinized infrasubspecific designation may be elevated by a subsequent author to the status of a subspecies or species [Rule 14b]. If so elevated, it is attributed to the author by whom it was elevated [Rule 14b]. Example: Pseudomonas cannabina (ex Šutic and Dowson 1959) Gardan et al. 1999, elevation of Pseudomonas syringae pathovar Cannabina of (Šutic and Dowson 1959) Young et al. 1978 by Gardan et al. in 1999.
When a name of an infrasubspecific subdivision is cited in the "List of Prokaryotic names with Standing in Nomenclature", to avoid confusion, it is printed in Roman type (not italics), starting with a capital letter (see: LE MINOR (L.) and POPOFF (M.Y.): Designation of Salmonella enterica sp. nov., nom. rev., as the type and only species of the genus Salmonella. Request for an opinion. Int. J. Syst. Bacteriol., 1987, 37, 465-468.).

INSDC accession numbers

Gene sequences are represented in LPSN by INSDC accession numbers, specifically nucleotide accession numbers which yield direct links to the European Nucleotide Archive (ENA) and to GenBank. The most relevant single gene is the 16S rRNA gene, which is available for almost all validly published names of species and subspecies.
A link is provided to the DSMZ phylogeny server for phylogenetically analysing the selected 16S rRNA gene sequences and calculating similarities between then in a standardized manner. Sequences can also be downloaded in FASTA format. Phylogeny and FASTA links for species include sequences of their subspecies, if any; phylogeny and FASTA links for genera include sequences of all species and subspecies currently assigned to the respective genus.

International Bulletin of Bacterial Nomenclature and Taxonomy

The International Bulletin of Bacterial Nomenclature and Taxonomy was founded in 1951 and published by Iowa State College Press. Since 1 January 1951 to 31 December 1965, the International Bulletin of Bacterial Nomenclature and Taxonomy was the official organ of the Judicial Commission and of the International Association of Microbiologists. Its aim was "to contribute to the stabilization of bacteriological nomenclature by opening up a channel of free communication between those concerned in the naming and classification of bacteria". In 1966, the official journal became the International Journal of Systematic Bacteriology (IJSB). Since January 2000, beginning with volume 50, the title of the International Journal of Systematic Bacteriology (IJSB) is changed to International Journal of Systematic and Evolutionary Microbiology (IJSEM).
Reference: PARTE (A.): A short history of the official journal of bacterial names. Int. J. Syst. Evol. Microbiol., 2000, 50, 1.

International Committee on Systematics of Prokaryotes

The International Committee on Systematics of Prokaryotes (ICSP) [formerly the International Committee on Systematic Bacteriology (ICSB)] is a committee of the International Union of Microbiological Societies established to deal with taxonomic matters on an international basis. Publishing the Bacteriological Code, and the International Journal of Systematic and Evolutionary Microbiology (formerly the International Journal of Systematic Bacteriology) and approving the recommendations and opinions of the Judicial Commission are some of the responsibilities of the International Committee on Systematics of Prokaryotes [Statutes of the International Committee on Systematic Bacteriology].
The change of the name International Committee on Systematic Bacteriology (ICSB) to International Committee on Systematics of Prokaryotes (ICSP) was decided and approved by the Judicial Commission and the ICSP (IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. August 1999, Sydney, Australia.).
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.

International Journal of Systematic Bacteriology

Since 1 January 1966 to 31 December 1999, the International Journal of Systematic Bacteriology (IJSB; formerly the International Bulletin of Bacteriological Nomenclature and Taxonomy) was the official organ of the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) of the International Union of Microbiological Societies [General Consideration 6 (4). Article 12 of the Statutes of the International Committee on Systematic Bacteriology].
Since 1 January 1966 to 31 December 1999, the International Journal of Systematic Bacteriology was the only journal in which names can be validly published (see: Valid publication) [Rule 27].
Since 1 January 1966 to 31 December 1999, the date of valid publication was that of publication in the International Journal of Systematic Bacteriology [Rules 23 and 27 Note].
Since May 1999, International Journal of Systematic Bacteriology is available online.
Since January 2000, beginning with volume 50, the title of the journal is changed to International Journal of Systematic and Evolutionary Microbiology.

International Journal of Systematic and Evolutionary Microbiology

In January 2000, beginning with volume 50, the title of the International Journal of Systematic Bacteriology (IJSB) was changed to International Journal of Systematic and Evolutionary Microbiology (IJSEM). (According to the system followed by BIOSIS Serial Sources, the abbreviation of the International Journal of Systematic and Evolutionary Microbiology is Int. J. Syst. Evol. Microbiol.) This change has been initiated by the International Committee on Systematic Bacteriology (now the International Committee on Systematics of Prokaryotes) during the VIIIth IUMS Congress in Jerusalem, Israel, August 1996, and approved during the IXth IUMS Congress held in Sydney, Australia, August 1999. This change of name of the journal, which will be included in the next revision of the International Code of Nomenclature of Prokaryotes, does not affect the status of names of taxa previously published in the International Journal of Systematic Bacteriology.
References:
  1. STACKEBRANDT (E.) and TINDALL (B.J.): International Journal of Systematic Bacteriology will become International Journal of Systematic and Evolutionary Microbiology from January 2000. Int. J. Syst. Bacteriol., 1999, 49, 1323.
  2. PARTE (A.): A short history of the official journal of bacterial names. Int. J. Syst. Evol. Microbiol., 2000, 50, 1.
  3. LABEDA (D.P.): International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14 and 17 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2245-2247.
The International Journal of Systematic and Evolutionary Microbiology is the official journal of the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) and fulfils all functions laid down in the Principles and Rules of the International Code of Nomenclature of Prokaryotes.
References:
  1. STACKEBRANDT (E.) and TINDALL (B.J.): International Journal of Systematic Bacteriology will become International Journal of Systematic and Evolutionary Microbiology from January 2000. Int. J. Syst. Bacteriol., 1999, 49, 1323.
  2. PARTE (A.): A short history of the official journal of bacterial names. Int. J. Syst. Evol. Microbiol., 2000, 50, 1.
The International Journal of Systematic and Evolutionary Microbiology is published by the Microbiology Society (formerly Society for General Microbiology, SGM) (SGM) on behalf of the International Union of Microbiological Societies.
This journal (URL: http://ijs.microbiologyresearch.org/content/journal/ijsem) is strongly recommended.

International Union of Microbiological Societies

The International Union of Microbiological Societies (IUMS) is the organization responsible for the International Congresses on Microbiology and ultimately for the International Committee on Systematics of Prokaryotes.

Italic type versus roman type

Bacterial nomenclatures are Latin or Latinized words and such names are usually printed in italics (or underlined in manuscripts). The Bacteriological Code (1990 Revision) sets no binding standard in this respect, as typography is a matter of editorial style and tradition not of nomenclature. The name of genera, species, and subspecies are generally printed in italics (or underlined) but for higher categories conventions vary: in Britain they are often in ordinary Roman type, but in America or in France they are often in italics.
It is also interesting to note the following points.
(1) According to Chapter 4 (Advisory Notes) of the Bacteriological Code (1990 Revision), scientific names of taxa should be preferably indicated by a different type face, e.g., italic or by some other device to distinguish them from the rest of the text.
(2) Bacterial names cited in the Bacteriological Code (1990 Revision), irrespective of rank, are consistently printed in italic type.
(3) The preface of the next Code should include the following paragraph: "As in the previous edition, scientific names under the jurisdiction of the Code, irrespective of rank, are consistently printed in italic type. The Code sets no binding standard in this respect, as typography is a matter of editorial style and tradition not of nomenclature. Nevertheless, editors and authors, in the interest of international uniformity, may wish to consider adhering to the practice exemplified by the Code, which has been well received in general and is being followed in an increasing number of microbiological journals."
Consequently, in the "List of Prokaryotic names with Standing in Nomenclature" all bacterial names (except names of infrasubspecific subdivisions) are in italics to remind the reader that they are Latinized scientific names.
References:
  • Advisory Notes. In: LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.) (editors): International Code of Nomenclature of Bacteria (1990 Revision). Washington, DC: American Society for Microbiology, 1992, pp. 51-53.
  • SNEATH (P.H.A.): Bacterial Nomenclature. In: D.R. BOONE, R.W. CASTENHOLZ and G.M. GARRITY (editors): Bergey’s Manual of Systematic Bacteriology, second edition, vol. 1 (The Archaea and the deeply branching and phototrophic Bacteria), Springer-Verlag, New York, 2001, pp. 83-88.

Judicial Commission

The Judicial Commission is a subcommittee elected by the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) to regulate and advise on nomenclatural matters on its behalf [Articles 8, 8a, 8b, and 8c of the Statutes of the International Committee on Systematic Bacteriology].
The Judicial Commission consists of seventeen members, twelve elected by the members of the International Committee on Systematics of Prokaryotes, the Chairman of the ICSP, and the three Secretaries. The Editor of the IJSEM (formerly IJSB) is, ex officio, a member of the Judicial Commission.
Some functions of the Judicial Commission are the following:
  • To consider all Requests for Opinion.
  • To consider each proposal for emendation of the International Code of Nomenclature of Prokaryotes.
  • To make recommendations to the International Committee on Systematics of Prokaryotes relative to the official designation of subdivisions of species and subspecies below the category of subspecies.
  • To review lists prepared by the Editorial Board for the International Code of Nomenclature of Prokaryotes (nomina conservanda, nomina rejicienda...).
  • To request Subcommittees on Taxonomy to suggest minimal standards for the description of new taxa.
  • To consider recommendations from Subcommittees on Taxonomy for the acceptance of a list of names as valid and applicable to recognizable taxa.

Judicial Opinion

A Judicial Opinion is an official decision taken by the Judicial Commission in favour of a proposal (published in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology) for nomenclatural change or for interpretation of the Principles, Rules, and Recommendations of the Bacteriological Code (1990 Revision) [Article 8c (2) of the Statutes of the International Committee on Systematic Bacteriology].
An Opinion shall be issued when ten or more Commissioners vote in favour of it. All Opinions shall be reported to the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology), and unless rescinded by a majority of those voting in this Committee, such Opinions shall be considered final [General Consideration 6 (4). Article 8c (2) of the Statutes of the International Committee on Systematic Bacteriology]. Opinions are denied if the Judicial Commission disagrees with the proposal.
Opinions A, B and C, issued by the International Committee on Bacteriological Nomenclature at the second International Congress for Microbiology, London 1936, are included in the Appendix 5 of the Bacteriological Code (1990 Revision). Opinions 1 to 63, issued by the Judicial Commission, appear in the Appendix 5 of the Bacteriological Code (1990 Revision). Opinions and actions of the Judicial Commission on requests for opinions, not included in the Bacteriological Code (1990 Revision), are provided on the page about Requests for Opinions and Judicial Opinions. See also: Request for an opinion.
Reference: General Consideration 6(4), and Article 8c(2) of the Statutes of the International Committee on Systematic Bacteriology, Rule 4 and Appendix 8 of the Bacteriological Code (1990 Revision). In: LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.): International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C., 1992, pp. 152-155.

Legitimacy

Names and epithets may be: (i) legitimate: in accordance with the Rules; (ii) illegitimate: contrary to the Rules [Rule 23a Note 5].

Linking to LPSN

LPSN provides stable Uniform Resource Locator (URLs) for pages on individual taxon names. These URLs are derived from the taxonomic category and from the taxon name in a straightforward manner. Homonyms are taken into account by appending numbers. URLs of LPSN stubs and placeholders are not regarded as stable and should not be linked to. LPSN does not provide stable numeric IDs for the time being.

Minimal standards for the description of new taxa

One of the functions of the Subcommittees on Taxonomy is to recommend to the ICSB (now ICSP) through the Judicial Commission minimal standards for the description of new taxa for the purpose of establishing validity of publication. Such recommendations shall include a list of characters and methods for their assessment, and shall be reviewed, at the request of the Judicial Commission, at regular intervals. If accepted by the ICSB (now ICSP), they shall be published in the IJSB (now IJSEM) and other microbiological journals. They shall specify the minimal requirements only and shall in no way limit the extent of investigation beyond these limits. The Judicial Commission may, at the request of any specialist in the field of study, whether a member of the Subcommittee or not, call for a revision of the minimal standards if the evidence before the Commission is considered sufficient to warrant such a call.
Reference: Statutes of the International Committee on Systematic Bacteriology of the International Union of Microbiological Societies. Article 9, Organization and Functions of Subcommittees on Taxonomy. In: LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.): International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C., 1992, pp. 152-155.
According to Recommendation 30b, before publication of the name and description of a new species, the examination and description should conform at least to the minimal standards (if available) required for the relevant taxon of bacteria [see also: Rule 27, Chapter 4 (Advisory Notes) and Appendix 7 (Publication of a New Name)].
Reference: LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.): International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C., 1992, XLII + 189 pages.
According to the Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, "Minimal characteristics should be provided and follow the guidelines set forth by various subcommittees of the ICSP. Where such guidelines do not exist, descriptions should follow guidelines for closely related taxa."
Reference: STACKEBRANDT (E.), FREDERIKSEN (W.), GARRITY (G.M.), GRIMONT (P.A.D.), KÄMPFER (P.), MAIDEN (M.C.J.), NESME (X.), ROSSELLO-MORA (R.), SWINGS (J.), TRÜPER (H.G.), VAUTERIN (L.), WARD (A.C.) and WHITMAN (W.B.): Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol., 2002, 52, 1043-1047.
For a listing of published minimal standards see the dedicated page.

Multiple authorship

When the new name of a taxon is validly published under more than two authors, and when there is not definite designation of a single individual as the author of the name, the citation may be made by listing the names of all the authors or by giving the name of the first author, followed by the abbreviation "et al." (et alii) [Chapter 4. Advisory notes. B. Quotations of authors and names (1)]. Example: Afipia felis Brenner, Hollis, Moss, English, Hall, Vincent, Radosevic, Birkness, Bibb, Quinn, Swaminathan, Weaver, Reeves, O’Connor, Hayes, Tenover, Steigerwalt, Perkins, Daneshvar, Hill, Washington, Woods, Hunter, Hadfield, Ajello, Kaufmann, Wear and Wenger 1992 or Afipia felis Brenner et al. 1992.

Name causing confusion

A name causing confusion (nomen confusum) is a name based upon a mixed culture. Such a name should be rejected [Rule 56a]. Example: Methanosarcina methanica nom. rejic. (Opinion 63).

Names of classes

The name of a class is a Latin or latinized word. The name of a class is in the neuter gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -ia to the stem of the name of the type genus of the type order of the class [Rule 8].
Many validly published names of classes deviate from that scheme. A separate LPSN page provides on overview on the real composition of the names of classes.

Names of families

The name of a family is formed by the addition of the suffix -aceae to the stem of the name of the type genus [Rule 9]. There is an important exception to Rule 9: according to Judicial Opinion 15 the type genus of the family Enterobacteriaceae Rahn 1937 (Approved Lists 1980) is the genus Escherichia Castellani and Chalmers 1919 (Approved Lists 1980); not the genus Enterobacter Hormaeche and Edwards 1960 (Approved Lists 1980).
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].

Names of genera

The name of a genus is a substantive, or an adjective used as a substantive, in the singular number and written with an initial capital letter [Rule 10a]. The name is treated as a Latin substantive [Rule 10a].
The name may be taken from any source and may even be composed in an arbitrary manner [Rule 10a]. Examples: Afipia (derived from AFIP: Armed Force Institute of Pathology), Cedecea (derived from CDC: Centers for Disease Control), Desemzia (derived from DSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen), Waddlia (derived from WADDL: Washington Animal Disease Diagnostic Laboratory)...
Authors should not name genera after themselves or after co-authors [Recommendation 6 (10)].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Authors should not name genera after persons quite unconnected with bacteriology or at least with natural science [Recommendation 10a (1)].
When a genus is lowered in rank to subgenus, the original name must be retained unless it is rejected under the Rules [Rule 49]. This also applies when a subgenus is elevated to a genus [Rule 49]. Example: The genus Branhamella has been lowered in rank to subgenus and the name of this subgenus is Branhamella.
Gender of a name of a genus, see: Gender of names or epithets and the page on etymology and the links therein.

Names of orders

The name of an order is formed by the addition of the suffix -ales to the stem of the name of the type genus [Rule 9].
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].

Names of phyla

Names of phyla are not currently regulated by the Code. The ending -aeota has been proposed in the literature to standardize the formation of phylum names.

Names of species

The name of a species is a binary combination consisting of the name of the genus followed by a single specific epithet [Rules 12a and 23a].
A specific epithet, even one derived from the name of a person, is not written with an initial capital letter [Rule 59]. Example: Acinetobacter grimontii (named after the French bacteriologist P.A.D. Grimont).
A specific epithet may be taken from any source except a word which is merely an ordinal adjective, a number or letter [Rules 12c and 52]. Example: Clostridium tertium (L. adj. tertius -a -um, third) is illegitimate.
A specific epithet may be composed arbitrarily [Rule 12c]. Example: thetaiotaomicron in Bacteroides thetaiotaomicron derived from a combination of the Greek letters theta, iota and omicron.
Authors should not name species after themselves or after co-authors [Recommendation 6 (10)].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Authors should ensure that, if taken from the name of a person, the name of a species recalls the name of one who discovered or described it, or was in some way connected with it. [Recommendation 12c (3)].
If an epithet has been hyphenated, its parts should be joined [Rule 12a]. Example: Nocardia otitidis-caviarum has been corrected to Nocardia otitidiscaviarum.
A specific epithet must be treated as an adjective that must agree in gender with the generic name (example: aureus in Staphylococcus aureus), or as a substantive (noun) in apposition in the nominative case (example: gigas in Desulfovibrio gigas), or as a substantive (noun) in the genitive case (example: coli in Escherichia coli) [Rule 12c].
A specific epithet, even derived from the name of a person, should not be written with an initial capital letter [Rule 59]. Example: Corynebacterium falsenii named in honor of E. Falsen.
No specific epithets within the same genus may be the same if based on different types [Rule 12b].
When a species is lowered in rank to a subspecies, the specific epithet in the name of the species must be used as the subspecific epithet of the name of the subspecies unless the resulting combination is illegitimate [Rule 50b]. Example: Bifidobacterium globosum (ex Scardovi et al. 1969) Biavati et al. 1982 becomes Bifidobacterium pseudolongum subsp. globosum (Biavati et al. 1982) Yaeshima et al. 1992.
Chapter 4. Advisory notes. - A. Suggestions for authors and publishers:
  • The name of a genus should be spelled without abbreviation the first time it is used with a specific epithet in a publication and in the summary of that publication.
  • Later use of the name of the species previously cited usually has the name of the genus abbreviated, commonly to the first letter of the generic name. However, the subcommittee on the taxonomy of phototrophic bacteria agreed the use of three-letter abbreviations for genera of the anoxygenic phototrophic bacteria. - Reference: ICSB, SUBCOMMITTEE ON THE TAXONOMY OF THE PHOTOTROPHIC BACTERIA: Minutes of the meetings, 10 September 1997, Vienna, Austria. Int. J. Syst. Bacteriol., 1999, 49, 925-926.
  • In a series of species names all belonging to the same genus, it is customary to abbreviate the name of the genus in all but the first species, even if it is the first mention of the succeeding species.
  • If, however, species are listed belonging to two or more genera which have the same initial letter, the generic name should be used in a full.
  • In the "List of Prokaryotic names with Standing in Nomenclature", to help the reading, the names of genera are always spelled without abbreviation.

Names of subclasses

The name of a subclass is a Latin or latinized word. The name of a subclass is in the feminine gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -idae to the stem of the name of the type genus of the type order of the subclass [Rule 8].

Names of subfamilies

The name of a subfamily is formed by the addition of the suffix -oideae to the stem of the name of the type genus [Rule 9].
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].
No name has been validly published for this category.

Names of subgenera

The name of a subgenus is a substantive, or an adjective used as a substantive, in the singular number and written with an initial capital letter [Rule 10a].
The name may be taken from any source and may even be composed in an arbitrary manner [Rule 10a].
Authors should not name subgenera after themselves or after co-authors [Recommendation 6 (10)].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Authors should not name subgenera after persons quite unconnected with bacteriology or at least with natural science [Recommendation 10a (1)].
Gender of a name of a subgenus, see: Gender of names or epithets.
The name of a subgenus, when included with the name of a species, is placed in parentheses between the generic name and specific epithet and it is preceded by the abbreviation "subgen." (subgenus novum). When included, the citation should be inserted before closure of the parentheses [Rule 10c]. Example: Moraxella (subgen. Moraxella Lwoff 1939, 173) lacunata; Moraxella (subgen. Branhamella Catlin 1970, 157) catarrhalis.
In the "List of Prokaryotic names with Standing in Nomenclature" the name of a subgenus is always placed in parentheses with the abbreviation "subgen." (even if the name of a species is not included) and the citation is inserted before closure of the parentheses. For example: Acetobacter (subgen. Acetobacter Beijerinck 1898) subgen. nov.

Names of suborders

The name of a suborder is formed by the addition of the suffix -ineae to the stem of the name of the type genus [Rule 9].
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].

Names of subspecies

The name of a subspecies is a ternary combination consisting of the name of the genus followed by a single specific epithet, the abbreviation subsp. (subspecies), and finally the subspecific epithet [Rule 13a]. Example: Staphylococcus aureus subsp. aureus.
A subspecific epithet, even one derived from the name of a person, is not written with an initial capital letter [Rule 59]. Example: Campylobacter hyointestinalis subsp. lawsonii (named after Lawson).
A specific epithet may be taken from any source except a word which is merely an ordinal adjective, a number or letter [Rules 13b and 52].
A specific epithet may be composed arbitrarily [Rule 13b]. Example: arupensis in Bartonella vinsonii subsp. arupensis (derived from ARUP: Associated and Regional University Pathologists).
Authors should not name subspecies after themselves or after co-authors [Recommendation 6 (10)].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
If an epithet has been hyphenated, its parts should be joined [Rule 12a]. Example: Salmonella cholerae-suis subsp. cholerae-suis has been corrected to Salmonella choleraesuis subsp. choleraesuis.
A subspecific epithet must be treated as an adjective that must agree in gender with the generic name (example: Fibrobacter succinogenes subsp. elongatus), or as a substantive (noun) in apposition in the nominative case (example: Photobacterium damselae subsp. piscicida), or as a substantive (noun) in the genitive case (example: Lactococcus lactis subsp. cremoris) [Rule 13b].
A subspecific epithet, even derived from the name of a person, should not be written with an initial capital letter [Rule 59]. Example: Eubacterium yurii subsp. margaretiae (named in honor of B.S. Margaret).
A subspecies that includes the type strain of the species must bear the same epithet as the species [Rules 13d and 45]. Example: Staphylococcus aureus subsp. aureus (this subspecies includes the type strain of the species Staphylococcus aureus).
The valid publication of a subspecies name which excludes the type of the species automatically creates another subspecies which includes the type and whose name bears the same specific and subspecific epithets as the name of the type. The authorship of such an automatically created subspecific name is cited to the original author(s) of the epithet followed by the author (s) of the subspecies. Example: Vibrio subtilis Ehrenberg ---> Bacillus subtilis comb. nov. Cohn ---> Bacillus subtilis subspecies subtilis subsp. nov. Nakamura. The correct authorship of the subspecies is Bacillus subtilis subspecies subtilis (Ehrenberg) Nakamura [Ehrenberg for the epithet and Nakamura for the new subspecies].
When a subspecies is elevated in rank to a species, the subspecific epithet in the name of the subspecies must be used as the specific epithet unless the resulting combination is illegitimate [Rule 50a]. Example: Micromonospora halophytica subsp. nigra Weinstein et al. 1968 (Approved Lists 1980) becomes Micromonospora nigra (Weinstein et al. 1968) Kasai et al. 2000.
No two subspecies within the same species or within the same genus may bear the same subspecific epithet [Rules 12b and 13c]. Example: The subspecific epithet urealyticus in the name Staphylococcus cohnii subsp. urealyticus corrig. Kloos and Wolfshohl 1991 will have to be replaced because it is a junior homonym of urealyticus used in the name Staphylococcus capitis subsp. urealyticus corrig. Bannerman and Kloos 1991.

Names of subtribes

The name of a subtribe is formed by the addition of the suffix -inae to the stem of the name of the type genus [Rule 9].
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].
No name has been validly published for this category.

Names of tribes

The name of a tribe is formed by the addition of the suffix -eae to the stem of the name of the type genus [Rule 9].
The name is a substantive or an adjective used as a substantive of Latin or Greek origin, or a latinized word, it is in the feminine gender, the plural number, and written with a capital letter [Rule 7].
The rank tribe falls into disuse.

Neotype strain

If a strain on which the original description was based cannot be found, a neotype strain may be proposed [Rule 18c].
The term "strain" is not restricted to the strain bearing the culture collection number mentioned in the valid publication, but refers to any culture knowingly derived from the original strain [Rule 18c Note].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
A neotype strain must be proposed (proposed neotype) in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology. The neotype becomes established (established neotype) two years after the date of its publication, provided that there are no objections. Objections must be referred within the first year of the publication of the neotype to the Judicial Commission for consideration. Example: Roop et al. 1986 proposed a neotype strain, strain VPI S-17 = ATCC 35980, for Campylobacter sputorum (Prévot 1940) Véron and Chatelain 1973 (Approved List 1980) because the type strain Forsyth ER33 was no longer extant. No objection has been referred to the Judicial Commission and the neotype strain of Campylobacter sputorum is the strain VPI S-17 = ATCC 35980.

New combination

A new combination (combinatio nova: comb. nov.) is a validly published species transferred to another genus, or a validly published subspecies transferred to another species. The author who makes the transfer should indicate the formation of the new combination by the addition to the citation of the abbreviation "comb. nov." The original name is referred to as the basonym [Rule 34a].
When a species (or a subspecies) proposed after 1 January 1980 but not validly published is transferred to another genus (or to another species) then it is a new species (or a new subspecies) not a new combination. For example, see Roseospira mediosalina in "List of Prokaryotic names with Standing in Nomenclature".
The citation of a new combination should include the name of the original author in parentheses followed by the name of the author who proposed the new combination and the year of valid publication of the new combination [Rule 34b]. Example: Methanosarcina siciliae (Stetter and König 1989) Ni et al. 1994 (basonym: Methanolobus siciliae Stetter and König 1989).
If an author is obliged to substitute a new specific epithet as a result of homonymy, the new combination is a nomen novum [Rule 34a]. See: Nomen novum.
A new combination does not have to be adopted in all circumstances; it is possible for two or more validly published names to remain in use. Example: A bacteriologist can use the names Corynebacterium pyogenes, Actinomyces pyogenes or Arcanobacterium pyogenes according to his (her) scientific judgment.
The Bacteriological Code does not envisage the statute of a species transferred to another species as a subspecies. In the "List of Prokaryotic names with Standing in Nomenclature", such a subspecies is considered as a new combination. Example: Bifidobacterium pseudolongum subsp. globosum (Biavati et al. 1982) Yaeshima et al. 1992, comb. nov. Basonym: Bifidobacterium globosum (ex Scardovi et al. 1969) Biavati et al. 1982.

Nomen approbatum

A nomen approbatum (nom. approb.) is a name which is included in the Approved Lists of Bacterial Names. The abbreviation "nom. approb." (nomen approbatum) may be appended to the name of a taxon included in an Approved List [Rule 33b Note 3 (iii)]. Example: Methanospirillum nom. approb.

Nomen novum

A nomen novum (nom. nov.) is a new combination for which an author is obliged to substitute a new specific epithet or a new subspecific epithet as a result of homonymy [Rules 34a, 41a (1), 23a Note 1, and 23a Note 2]. The author who makes the transfer should indicate the formation of the nomen novum by the addition to the citation of the abbreviation "nom. nov." The original name is referred to as the basonym [Rule 34a]. Example: Flavobacterium hydatis Bernardet et al. 1996, nom. nov. Basonym: Cytophaga aquatilis Strohl and Tait 1978 (Approved Lists 1980). Bernardet et al. 1996 proposed Flavobacterium hydatis for Cytophaga aquatilis Strohl and Tait 1978 (Approved Lists 1980) on transfer to Flavobacterium because in that genus the name Flavobacterium aquatile already existed.
The name of the author of the original specific epithet should be omitted from the citation [Rule 34b Note 2]. Example: Flavobacterium hydatis Bernardet et al. 1996 is correct, not Flavobacterium hydatis (Strohl and Tait 1978) Bernardet et al. 1996.
A nomen novum does not have to be adopted in all circumstances; it is possible for two or more validly published names to remain in use. Example: A bacteriologist can use the name Cytophaga aquatilis or the name Flavobacterium hydatis according to his (her) scientific judgment.

Nomenclatural type

For each named taxon of the various taxonomic categories, there shall be designated a nomenclatural type [Rule 15]. The type of a taxon must be designated by the author at the time the name of the taxon is validly published in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology [Rules 16 and 27 (3)].
If a previous effective publication does not designate a type then the type must be designated at the time of valid publication, in accordance with the Rules [Rule 16 Note].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
The nomenclatural type is not necessarily the most typical or representative element of the taxon [Rule 15].
The name of a taxon must be changed if the nomenclatural type is excluded [Rule 37a (1)]. Retention of a name in a sense which excludes the type can only be effected by conservation and only by the Judicial Commission [Rule 37a (2)]. Example: Methanococcus mazei was designated as the type species of the genus Methanococcus in the Approved Lists of Bacterial Names, but without a type strain. Mah and Kuhn requested that the Judicial Commission conserve the genus Methanococcus with a new type, Methanococcus vannielii, for which a type strain was included in the Approved Lists. The Judicial Commission has voted to award an opinion conserving Methanococcus with the type species Methanococcus vannielii (see: Opinion 62).
Type of a species or a subspecies, see: Type of a species or subspecies.
For subgenus and genus, the nomenclatural type is the type species [Rules 15, 20a and 20g].
  • If the genus when originally published included only one species, then that species is the type species [Rule 20c].
  • Only species whose names are legitimate may serve as types [Rule 20a].
  • The valid publication of a new generic name as a deliberate substitute for an earlier one does not change the type species of the genus [Rule 20f].
  • A genus and its type subgenus share the same type species [Rule 20g].
For subtribe, tribe, subfamily, family, suborder, and order, the nomenclatural type is the the legitimate name of the included genus on whose name the name of the relevant taxon is based [Rules 15 and 21a]. There is an important exception to Rule 21a: the genus Escherichia is the type genus of the family Enterobacteriaceae [Rule 21b, Judicial Opinion 15].
In some cases it has been assumed that the nomenclatural type of an order is one of the families included when the name was validly published. However, such an assumption is contrary to Rule 21a. For examples see: Acholeplasmatales Freundt et al. 1984, Halanaerobiales corrig. Rainey and Zhilina 1995, Halobacteriales Grant and Larsen 1989, Methanobacteriales Balch and Wolfe 1981, Methanococcales Balch and Wolfe 1981, Methanomicrobiales Balch and Wolfe 1981, Planctomycetales Schlesner and Stackebrandt 1987, Prochlorales (ex Lewin 1977) Florenzano et al. 1986, Sulfolobales Stetter 1989, Thermococcales Zillig et al. 1988, Thermoproteales Zillig and Stetter 1982, and Verrucomicrobiales Ward-Rainey et al. 1996.
For a taxon higher than order, the nomenclatural type is one of the contained orders [Rule 22]. If not designated, the type of a taxon higher than order may be later designated by a Judicial Opinion [Rule 22].
Several classes have been proposed without the designation of a nomenclatural type and they are illegitimate according to Rule 15 and 22. For examples, see: Actinobacteria Stackebrandt et al. 1997, Actinomycetes Krasil’nikov 1949 (Approved Lists 1980), Bacteria Haeckel 1894 (Approved Lists 1980), Mollicutes Edward and Freundt 1967 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980)...

Notes in LPSN

Notes on LPSN pages for individual taxon names cover a variety of topics, including but not limited to alternative taxonomic arrangements, alternative placements of the nomenclatural type, corrections of the orthography, homonyms, synonyms, questionable identity of type-strain deposits, and misprints of taxon names occurring in the literature.

Notification Lists

The Notification Lists ("Notification that new names and new combinations have appeared in volume X, N° Y, of the IJSB or IJSEM") are published regularly in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology. The first Notification List was published on July 8, 1991 (Int. J. Syst. Bacteriol., 1991, 41, 457-458).
These lists have no formal status in prokaryote nomenclature except to allow for orthographic corrections to be made. The lists are provided as a service to bacteriology to assist in the recognition of new names and new descriptions. The names and citations to appear in the Notification Lists are those that are validly published in full articles in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology.
The names given in these lists have priority according to the issue of the International Journal of Systematic Bacteriology or according to the issue of the International Journal of Systematic and Evolutionary Microbiology in which they were published. This procedure was proposed by the Judicial Commission.
Reference: JUDICIAL COMMISSION: Minutes of the meeting, 14 September 1990, Osaka, Japan. Int. J. Syst. Bacteriol., 1991, 41, 185-187.

Orthography

The names of all taxa are Latin or latinized words treated as Latin regardless of their origin [Principle 3, Rule 6].
Words from languages other than Latin or Greek should be avoided as long as equivalents exist in Latin or Greek or can be constructed by combining word elements from these two languages [Recommendation 6 (3)]. Example: The name Macrococcus bovicus should be changed to Macrococcus bovilis (L. adj. bovilis e, relating to cows) or Macrococcus bovillus (L. adj. bovillus a um, relating to cows) or Macrococcus bovinus (L. adj. bovinus a um, relating to cows), because the Latin adjective bovicus a um (pertaining to cows) does not exist.
The Greek K and Z and the Medieval Latin J (for consonantic I) should be maintained to avoid confusion [Recommendation 6 (7)].
Authors should not name organisms after themselves or after co-authors [Recommendation 6 (10)].
Any name or epithet should be written in conformity with the spelling of the word from which it is derived and in strict accordance with the rules of Latin and latinization [Rule 57a].
Intentional latinizations involving changes in orthography of personal names, particularly those of earlier authors, must be preserved [Rule 60]. Example: "Bacillus pastorianus" (Winogradsky 1902) Lehmann and Neumann 1907, derived from Pastor (latinisation of Pasteur).
The abbreviation "corrig." ( corrigendum) may be appended to the name if an unintentional typographical or orthographic error has been corrected by a subsequent author. Such a correction does not affect the validity and original date of publication [Rule 61]. Example: Campylobacter lari corrig. Benjamin et al. 1984 (in place of Campylobacter laridis (sic) Benjamin et al. 1984).
The liberty of correcting a name or epithet must be used with reserve especially if the change affects the first syllable and above all the first letter of the name or epithet [Rule 61 Note].
As from December 14, 2000 (date of the publication of the minutes of the meetings of the Judicial Commission, August 1999, Sydney, Australia), except for changes of gender in specific epithets when species are transferred to other genera, no grammatical or orthographic corrections are accepted for names on the Approved Lists of Bacterial Names, the Validation Lists and the Notification Lists.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Some examples of grammatical or orthographical changes prohibited by Rule 61 are given in the file "Grammatical or orthographical errors" (editor comment: this file appears to be lost).
Bacteriologists who are willing to acquire nomenclatural literacy or who are about to describe and/or name prokaryotes, should read the following literature sources.
References:
  1. Appendix 9 of the Bacteriological Code (1990 Revision).
  2. BOONE (D.R.), OCM (Oregon Collection of Methanogens): Naming a new procaryotic taxon (Help for naming new taxa). Available on the Internet: http://caddis.esr.pdx.edu/OCM/naming.html
  3. BUCHANAN (R.E.): Chemical terminology and microbiological nomenclature. Int. Bull. Bacteriol. Nomencl. Taxon., 1960, 10, 16-22. Reprint: Int. J. Syst. Bacteriol., 1994, 44, 588-590. Also available on the Internet.
  4. MacADOO (T.O.): Nomenclatural literacy. In: M. GOODFELLOW and A.G. O’DONNELL (editors), Handbook of new bacterial systematics, Academic Press, London, 1993, p. 339-358.
  5. TRÜPER (H.G.): Help! Latin! How to avoid the most common mistakes while giving Latin names to newly discovered prokaryotes. Microbiología (Sociedad Española de Microbiología), 1996, 12, 473-475. Also available on the Internet.
  6. TRÜPER (H.G.): How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol. Rev., 1999, 23, 231-249.
This glossary contains detailed information on how names of classes, families, genera, orders, phyla, species, subclasses, subfamilies, subgenera, suborders, subspecies, subtribes and tribes are formed.
Of particular relevance is the stem of a Greek or Latin word.

Perilous name

A perilous name (nomen periculosum) is a name whose application is likely to lead to accidents endangering health or life or both or of serious economic consequences. Such a name should be rejected [Rule 56a]. Example: Yersinia pseudotuberculosis subsp. pestis (Lehmann and Neumann 1896) Bercovier et al. 1981 is placed on the list of nomina rejicienda because of practical concerns about human welfare (nomen periculosum). See: Judicial Opinion 60.

Perplexing name

A perplexing name (nomen perplexum) is a name whose application is known but which causes uncertainty in bacteriology. Such a name should be rejected [Rule 56a]. Example: "Peptococcus anaerobius" (Hamm 1912) Douglas 1957, nom. rejic. (Opinion 56).
When two or more generic names or two or more epithets in the same genus are so similar as to cause uncertainty, they may be treated as perplexing names and the matter referred to the Judicial Commission [Rule 57c].

Phylogenetic definition of a species

The species is the only taxonomic unit that can be defined in phylogenetic terms.
The phylogenetic definition of a species (genomospecies) generally would include strains with approximatively 70% or greater DNA-DNA relatedness at optimal conditions and with 5 °C or less ΔTm [divergence (unpaired bases) within related nucleotide sequences is 5% or less]. Both values must be considered. It is possible to use the additional criterion that DNA relatedness of strains within a species remains above 55% (or 60%) in reactions carried out under stringent incubation conditions with 5% or less divergence within related nucleotide sequences (5 °C or less ΔTm).
A strain is assigned to a given species when the relatedness of its DNA to labelled DNA from the type strain of that species fulfils the above species definition.
Investigators are encouraged to propose new species based upon other genomic methods or techniques provided that they can demonstrate that, within the taxa studied, there is a sufficient degree of congruence between the technique used and DNA-DNA reassociation (see: "Report of the Ad Hoc Committee for the Re-Evaluation of the Species Definition in Bacteriology").
The "Report of the ad hoc committee on reconciliation of approaches to bacterial systematics" states: It is recommended that a distinct genomospecies that cannot be differentiated from another genomospecies on the basis of any known phenotypic property not be named until they can be differentiated by some phenotypic property. Fifteen years later, the "Report of the Ad Hoc Committee for the Re-Evaluation of the Species Definition in Bacteriology" emphasizes this point: "Species should be identifiable by readily available methods (phenotypic, genomic). Efforts should be made to establish standardized methods of reporting phenotypic and genomic data. [...] Minimal characteristics should be provided and follow the guidelines set forth by various subcommittees of the ICSP. Where such guidelines do not exist, descriptions should follow guidelines for closely related taxa. Comparisons should always include type material from closely related species."
Microbiologists are encouraged to base a species description on more than a single strain on the basis of the arguments in Christensen et al., 2001 (see: "Report of the Ad Hoc Committee for the Re-Evaluation of the Species Definition in Bacteriology")
References:
  1. BRENNER (D.J.): Personal communication cited in: DROZ (S.), CHI (B.), HORN (E.), STEIGERWALT (A.G.), WHITNEY (A.M.) and BRENNER (D.J.): Bartonella koehlerae sp. nov., isolated from cats. J. Clin. Microbiol., 1999, 37, 1117-1122.
  2. BRENNER (D.J.), O’HARA (C.M.), GRIMONT (P.A.D.), JANDA (J.M.), FALSEN (E.), ALDOVA (E.), AGERON (E.), SCHINDLER (J.), ABBOTT (S.L.) and STEIGERWALT (A.G.): Biochemical identification of Citrobacter species defined by DNA hybridization and description of Citrobacter gillenii sp. nov. (formerly Citrobacter genomospecies 10) and Citrobacter murliniae sp. nov. (formerly Citrobacter genomospecies 11). J. Clin. Microbiol., 1999, 37, 2619-2624.
  3. CHRISTENSEN (H.), BISGAARD (M.), FREDERIKSEN (W.), MUTTERS (R.), KUHNERT (P.) and OLSEN (J.E.): Is characterization of a single isolate sufficient for valid publication of a new genus or species? Proposal to modify Recommendation 30b of the Bacteriological Code (1990 Revision). Int. J. Syst. Evol. Microbiol. 2001, 51, 2221-2225.
  4. STACKEBRANDT (E.), FREDERIKSEN (W.), GARRITY (G.M.), GRIMONT (P.A.D.), KÄMPFER (P.), MAIDEN (M.C.J.), NESME (X.), ROSSELLO-MORA (R.), SWINGS (J.), TRÜPER (H.G.), VAUTERIN (L.), WARD (A.C.) and WHITMAN (W.B.): Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol., 2002, 52, 1043-1047.
  5. WAYNE (L. G.), BRENNER (D.J.), COLWELL (R.R.), GRIMONT (P.A.D.), KANDLER (O.), KRICHEVSKY (M.I.), MOORE (L.H.), MOORE (W.E.C.), MURRAY (R.G.E.), STACKEBRANDT (E.), STARR (M.P.) and TRUPER (H.G.): Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol., 1987, 37, 463-464.

Priority and publication of names

Priority means that the name or epithet first validly published in accordance with the Rules is the correct name, or epithet, for a taxon [Rule 11 Note]. After 1 January 1980, under Rule 24a all priorities date from 1 January 1980 (not from the date of publication of Linnaeus’ Species Plantarum, edition 1 (1 May 1753)) [Rules 23a Note 3 and 24a].
The correct name of a taxon is based upon priority of publication [Principle 6]. The date of publication of a scientific work is the date of publication of the printed or electronic matter (not the date of acceptance of an article for publication) [Rules 26a and 26b].
The date of a name or epithet (even for a revived name) is that of its valid publication in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology [Rule 28a Note 2 and Rule 23b]. Example: Haemophilus felis was effectively published in 1992 (J. Clin. Microbiol., 1992, 30, 2108-2112.) but validly published in 1999 (Validation List no. 69: Int. J. Syst. Bacteriol., 1999, 49, 341-342). The date of this name is 1999.
If an infrasubspecific designation is elevated to the status of subspecies or species, it ranks for purposes of priority from its date of elevation [Rule 14b].
If two names compete for priority and if both names are listed on the Approved Lists of Bacterial Names, the priority shall be determined by the date of the effective publication of the name before 1 January 1980 [Rule 24b (1)]. Example: Kelly and Wood (Int. J. Syst. Evol. Microbiol., 2000, 50, 511-516) regard Thiobacillus concretivorus Parker 1945 (Approved Lists 1980) as a heterotypic synonym of Thiobacillus thiooxidans Waksman and Joffe 1922 (Approved Lists 1980). Thiobacillus thiooxidans Waksman and Joffe 1922 has priority over Thiobacillus concretivorus Parker 1945.
If two names listed on the Approved Lists of Bacterial Names bear the same date, the priority shall be determined by page number. If this fails to determine priority then it shall be determined by the order of publication in the effective publication.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
If two names validly published after 1 January 1980 compete for priority, priority is determined by the date of the valid publication of the name in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology [Rule 24b (2)]. Example: Gordonia amarae (Lechevalier and Lechevalier 1974) Klatte et al. 1994 has priority over Gordonia amarae (Lechevalier and Lechevalier 1974) Ruimy et al. 1995.
If two names appear in the same issue of the International Journal of Systematic Bacteriology or in the same issue of the International Journal of Systematic and Evolutionary Microbiology, priority is determined by page number [Rule 24b (2)]. Example: Mycobacterium chlorophenolicum (Apajalahti et al. 1986) Häggblom et al.1994 (valid publication: Int. J. Syst. Bacteriol., 1994, 44 (issue 3), 491) has priority over Mycobacterium chlorophenolicum (Apajalahti et al. 1986) Briglia et al. 1994 (valid publication: Int. J. Syst. Bacteriol., 1994, 44 (issue 3), 498).
If the page number does not determine priority, this shall be determined by the order of valid publication of the names in original articles in IJSB or in IJSEM.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
If two names, previously published in other journals, are validly published by announcement on the same Validation List in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology, priority is established by the sequence number on the list (the sequence number reflects the date of receipt on the validation request in the form that is accepted for publication) [Rule 24b (2), Note 1]. Example: Sly et al. (Int. J. Syst. Evol. Microbiol., 1997, 47, 893-894) regard Streptococcus caprinus Brooker et al. 1996 as a heterotypic synonym of Streptococcus gallolyticus Osawa et al. 1996. Streptococcus gallolyticus (Validation List no. 56, priority number 2) has priority over Streptococcus caprinus (Validation List no. 56, priority number 7).

Protologue for descriptions of taxa

The introduction of a "protologue" for descriptions of taxa has been supported by the Judicial Commission. The aim is to standardize the format of descriptions of new taxa.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
This "protologue" is constituted by the following paragraphs added to Rule 27(2):
a: The new name or new combination should be clearly stated and indicated as such (i.e. fam. nov., sp. nov. etc.).
b: The derivation of a new name (and if necessary of a new combination) must be given (see: Etymology and accentuation).
c: The properties of the taxon being described must be given directly after (a) and (b). This may include reference to tables or figures in the same publication, or reference to previously effectively published work.
See also: Publication of a new name.

Publication of a new name

Valid publication of the name of a taxon (including a new combination or a nomen novum) requires publication in the IJSB or in the IJSEM of (i) the name of the taxon in the correct form, (ii) the designation of a type, and (iii) a description or a reference to an effectively published description. Where possible, the title of the paper should include any new names or combinations that are proposed in the text.
The derivation of a new name (and if necessary of a new combination) must be given (see: Etymology and accentuation).
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
The name should be clearly proposed as a new name or combination appending the abbreviations divisio nov., class. nov., subclass. nov., ord. nov., subord. nov., fam. nov., subfam. nov., gen. nov., subgen. nov., sp. nov., subsp. nov., comb. nov., or nom. nov.
The name should not be a later homonym of a previously validly published name which is regulated by the Zoological Code and the International Code of Botanical Nomenclature. See also Bacteriological Code (1990 Revision). Example: The name Rhizomonas van Bruggen et al. 1990 is illegitimate because it is a junior homonym of a name of a taxon of protozoa (Rhizomonas Kent 1880). See: Judicial Opinion 14.
Descriptions of taxa should include the following information: (i) those characteristics which are essential for membership in the taxon; (ii) those characteristics which qualify the taxon for membership in the next higher taxon; and (iii) the diagnostic characteristics. In the case of species, the total number of strains studied, the strains designations and the number of strains which are either positive or negative for each characteristic should be given.
If recommendations have been published in the IJSB or in the IJSEM, descriptions should conform at least to such recommended minimal descriptions as have approved by International Subcommittees on Taxonomy.
See also: Protologue for descriptions of taxa; Appendix 7.

Reference strains

A reference strain is a strain that is neither a type or a neotype strain but a strain used in comparative studies, e.g., taxonomic or serological, or for chemical assay [Rule 19].

Rejected name

As for a rejected name (nomen rejiciendum: nom.rej., or nom. rejic.), only the Judicial Commission can reject names (nomina rejicienda) [Rules 23a Note 4 (i) and 56a, b]. The Judicial Commission may place on the list of rejected names (nomina rejicienda) a name previously published in an Approved List [Rule 24c]. A name may be placed on this list for various reasons, including the following [Rule 56a].
  • An ambiguous name (nomen ambiguum), i.e., a name which has been used with different meanings and thus has become a source of error.
  • A doubtful name (nomen dubium), i.e., a name whose application is uncertain.
  • A name causing confusion (nomen confusum), i.e., a name based upon a mixed culture.
  • A perplexing name (nomen perplexum), i.e. a name whose application is known but which causes uncertainty in bacteriology (see Rule 57c).
  • A perilous name (nomen periculosum), i.e., a name whose application is likely to lead to accidents endangering health or life or both or of serious economic consequences.
Names contrary to a Recommendation cannot be rejected for this reason [General Consideration 6 (3)].
Rejected names are available via the general search.

Request for an opinion

In those cases where strict adherence to the Rules of nomenclature would produce confusion or would not result in nomenclatural stability, exceptions to the Rules may be requested of the Judicial Commission of the International Committee on Systematics of Prokaryotes (formerly International Committee on Systematic Bacteriology) [Rule 4, Appendix 8].
Request for an opinion should be published in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology [Appendix 8]. Request for an opinion must be accompanied by a fully documented statement of the relevant facts [Appendix 8].
The Judicial Commission will consider all Requests for Opinions and either issue an Opinion in the International Journal of Systematic and Evolutionary Microbiology (formerly International Journal of Systematic Bacteriology) or signify its attitude in some other way. A request is considered first by the Judicial Commission and if approved by 10 or more members is then submitted to the International Committee on Systematics of Prokaryotes (formerly the International Committee on Systematic Bacteriology) for final approval [Article 8c (3) of the Statutes of the International Committee on Systematic Bacteriology]. All Opinions shall be reported to the International Committee on Systematics of Prokaryotes (ICSP), and unless rescinded by a majority of those voting in this Committee, such Opinions shall be considered final.
Opinions and actions of the Judicial Commission on requests for opinions, not included in the Bacteriological Code (1990 Revision), are provided on the page Requests for Opinions and Judicial Opinions.
Reference: General Consideration 6(4), and Article 8c(2) of the Statutes of the International Committee on Systematic Bacteriology, Rule 4 and Appendix 8 of the Bacteriological Code (1990 Revision). In: LAPAGE (S.P.), SNEATH (P.H.A.), LESSEL (E.F.), SKERMAN (V.B.D.), SEELIGER (H.P.R.) and CLARK (W.A.): International Code of Nomenclature of Bacteria (1990 Revision). American Society for Microbiology, Washington, D.C., 1992, pp. 152-155.

Revived name

A revived name (nomen revictum: nom. rev.) is a name which was published prior to 1 January 1980 but not included in the Approved Lists of Bacterial Names and which is proposed by an author for a different or for the same taxon (in the author’s opinion) [Rules 28a and 33c].
If an author wishes to indicate the names of the original authors of a revived name, he may do so by citation of the name of the taxon, followed by the word "ex" and the name of the original author and the year of publication, in parentheses, followed by the abbreviation "nom. rev" (nomen revictum) [Rule 33c Note 2]. Example: Streptococcus dysgalactiae (ex Diernhofer 1932) Garvie et al. 1983 (synonym: "Streptococcus dysgalactiae" Diernhofer 1932).
The date of valid publication of a revived name is that of the publication in the International Journal of Systematic Bacteriology or, from January 2000, in the the International Journal of Systematic and Evolutionary Microbiology [Rule 28a Note 2]. Example: The date of valid publication of Streptococcus dysgalactiae (ex Diernhofer 1932) Garvie et al. 1983 is 1983 not 1932.
A rejected name cannot be revived [Rule 28a].

Risk group

The LPSN risk-group classification is taken from the German TRBA 466 [“Einstufung von Prokaryonten (Bacteria und Archaea) in Risikogruppen”], downloaded on March 2nd 2020. Risk groups 1-3 are those given by TRBA 466; a risk group of 0 indicates taxon names which are mentioned in TRBA 466 but for which a risk group is not given therein. Risk group 3** is treated as 3 to ease searching. Notes from TRBA 466, if any, are provided in the LPSN notes. Note that many risk-group assessments are made at the level of subspecies while many samples are only identified at the species level.
It is difficult to provide generally applicable and up-to-date hints on the classification of biological hazards because this is a matter of national legislation. The competent bodies usually provide documents on their own websites. For instance, the German classification of prokaryotes into risk groups, TRBA 466, is available from the Bundesanstalt für Arbeitsschutz und Arbeitsmedizin. It is also debatable whether or not this topic fits to the scope of LPSN. However, users asked for it, and LPSN attempts to provide comprehensive information.
A risk-group assessment is of relevance when dealing with strains. LPSN provides links to type-strain deposits in culture collections, which usually indicate the risk group of some strain, particularly if it constitutes a biological hazard.

Sequence number

Since January 1988 (Validation List no. 24), the Validations Lists include sequence numbers that reflect the dates of receipt of names submitted for inclusion in Validation Lists [Rule 24b (2) Note 1].
If two names are validly published by announcement on the same Validation List in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology, priority is established by the sequence number on the list [Rule 24b (2), Note 1] Example: Sly et al. (Int. J. Syst. Evol. Microbiol., 1997, 47, 893-894) regard Streptococcus caprinus Brooker et al. 1996 as a heterotypic synonym of Streptococcus gallolyticus Osawa et al. 1996. Streptococcus gallolyticus (Validation List no. 56, priority number 2) has priority over Streptococcus caprinus (Validation List no. 56, priority number 7). If the sequence number does not determine priority, the order of priority will be determined by page number followed by order of publication in the effective publication [Rule 24b (2), Note 2].
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.

Stem of a Greek or Latin word

The stem of a Greek or Latin word is found in the genitive case of the noun or adjective. A Latin or Greek dictionary indicates the genitive cases and scientists should be able to identify the stem of a Latin or Greek word.
Examples:
Latin nouns and Greek nouns latinized by ancient Romans
  • First declension: the stem of capsa capsae (box) is caps-; of catena catenae (chain) is caten-; of sphaera sphaerae (sphere) is sphaer-; of spira spirae (coil) is spir-...
  • Second declension: the stem of ager agri (field) is agr-; of bacillus (or bacillum) bacilli (little staff) is bacill-; of equus equi (horse) is equ-; of oscillum oscilli (swing) is oscill-; of puer pueri (child) is puer-; of vir viri (man) is vir-...
  • Third declension: the stem of animal animalis (animal) is animal-; of bos bovis (cow) is bov-; of canis canis (dog) is can-; of caro carnis (flesh) is carn-; of caput capitis (head) is capit-; of corpus corporis (body) is corpor-; of feles (or felis) felis (cat) is fel-; of leo leonis (lion) is leon-; of mare maris (sea) is mar-...
  • Fourth declension: the stem of cornu cornus (horn) is corn-; of flexus flexus (a bending, turning) is flex-; of gelus (or gelu) gelus (frost) is gel-; of genu genus (knee) is gen-; of lacus lacus (lake, basin, tank) is lac-; of manus manus (hand) is man-...
  • Fifth declension: the stem of dies diei (day) is di-; of facies faciei (face) is faci-; of glacies glaciei (ice) is glaci-; of scabies scabiei (the scab, mange, itch) is scabi-...
Greek nouns
The scientific names of all taxa are Latin or latinized words treated as Latin regardless of their origin [Principle 3], and Greek words should be latinized. The stems of some latinized nouns of Greek origin are as follows: The stem of chlamys chlamidis (coat) is chlamyd-; of coma comae (hair) is com-; of coccus cocci (grain) is cocc-; of hals halis (salt) is hal-; of monas monadis (unit, monad) is monad-; of myces mycetis (fungus) is mycet-; of nema nematis (thread) is nemat-; of ornis ornithis (bird) is ornith-; of plasma plasmatis (form) is plasmat-; of soma somatis (body) is somat-; of thrix trichis (hair) is trich-...
Stems of compound bacterial generic names ending in -bacterium, -bacter or -bactrum
According to the Judicial Opinion 2, the stem of the last component of names ending in -bacterium is -bacteri, of those ending in -bactrum or -bactron is -bactr, and those ending in -bacter is -bacter.
Some correctly and incorrectly formed names (according to the stem of the name of the type genus) of taxa above the rank of genus up to and including order
Correctly formed names: Actinomycetales (Actinomycet+ales), Bacillales (Bacill+ales), Chlamydiales (Chlamydi+ales), Crenotrichaceae (Crenotrich+aceae), Leucotrichaceae (Leucotrich+aceae), Micrococceae (Micrococc+eae), Microsphaeraceae (Microsphaer+aceae), Mycoplasmatales (Mycoplasmat+ales), Oscillospiraceae (Oscillospir+aceae), Pseudomonadeae (Pseudomonad+eae), Thiocapsaceae (Thiocaps+aceae), Treponemataceae (Treponemat+aceae), Vitreoscillaceae (Vitreoscill+aceae).
Incorrectly formed names (wrong stems): Actinomycineae (Actinomyc+ineae), Ferroplasmaceae (Ferroplasm+aceae), Glycomycineae (Glycomyc+ineae), Spirosomaceae (Spirosom+aceae), Streptomycineae (Streptomyc+ineae).

Symbols

The following signs are or at least were used in the "List of Prokaryotic names with Standing in Nomenclature"; some of them are not in use any more.
an arrow used to indicate (i) that a taxon is emended (emend.); (ii) that one author (or several authors) proposes the transfer of a species to another genus or the transfer of a subspecies to another species ( comb. nov.; eventually nom. nov.); (iii) that the name of a taxon must be changed as a result of transference [Rule 37(a)]; (iv) that the rank of a taxon is changed; (v) that a taxon is a later synonym of an another taxon; (vi) that an exception to the rules has been awarded by the Judicial Commission.
this symbol indicates a link to an entry in this glossary
" "
names in quotation marks are not on the Approved Lists of Bacterial Names, have not been validly published since 1 January 1980, and therefore have no nomenclatural standing; in general, names not considered to be validly published should no longer be used or should be used in quotation marks to denote that the name is not validly published
=
an equal sign used to mean that two taxa are homotypic synonyms [Rules 24a and 24b (1)]
[ ]
the references given in brackets used to be references for effective publications when the names are cited in the Approved Lists of Bacterial Names or in Validation Lists

Synonyms

Synonyms [Rule 24a Notes 2 and 3] may be homotypic (formerly objective) synonyms (i.e., more than one name has been associated with the same type) or heterotypic (formerly subjective) synonyms (i.e., different names have been associated with different types that in opinion of the bacteriologist concerned belong to the same taxa). The synonym first validly published is known as the earlier synonym (formerly senior synonym), and later synonyms are known as later synonyms (formerly junior synonyms). Basonyms are earlier homotypic synonyms.
Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
Examples:
  • Homotypic synonyms: Brevibacterium albidum, type strain ATCC 15831 and Curtobacterium albidum, type strain ATCC 15831.
  • Heterotypic synonyms: Kelly and Wood (Int. J. Syst. Evol. Microbiol., 2000, 50, 511-516) regard Thiobacillus concretivorus Parker 1945 as a heterotypic synonym of Thiobacillus thiooxidans Waksman and Joffe 1922. These two species have different types.
When citing a name published as a synonym, the words "as synonym" or "pro synon." (pro synonymon, as synonym) should be added to the citation [Chapter 4. Advisory notes, B. Quotations of authors and names (3) (b)]. Example: Rhodothermus obamensis Sako et al. 1996 pro synon. Rhodothermus marinus Alfredsson et al. 1995.

Taxonomic categories

According to Rule 5b, the taxonomic categories which are covered by the Rules are as follows (in descending taxonomic rank): class (classis), subclass (subclassis), order (ordo), suborder (subordo), family (familia), subfamily (subfamilia), tribe (tribus), subtribe (subtribus), genus (genus), subgenus (subgenus), species (species), subspecies (subspecies). No validly published names have been proposed for the categories subfamily and subtribe. The taxonomic categories (in descending taxonomic rank) domain (dominium) [or empire (imperium)], kingdom (regnum), phylum (phylum) = division (diviso), and infrasubspecific subdivisions are not covered by the Rules.
This glossary contains detailed information on how names of classes, families, genera, orders, phyla, species, subclasses, subfamilies, subgenera, suborders, subspecies, subtribes and tribes are formed. Of particular relevance is the stem of a Greek or Latin word.
The rank of each category, i.e. its position in the Linnaean hierarchy, determines how child taxa can be assigned to parent taxa.

TYGS

The Type (Strain) Genome Server (TYGS) allows for genome-based phylogeny and classification as a replacement of traditional techniques such as DNA:DNA hybridization (DDH), G+C-content measurement, 16S rRNA gene sequencing and multi-locus sequence analysis. The TYGS includes a comprehensive, continuously growing database of genome sequences from nomenclatural types. The database genome sequences relevant for comparative purposes are determined automatically but can also be specified by the user. TYGS results include species and subspecies boundaries, genome-scale and 16S rRNA gene phylogenetic trees with branch support, links to the taxonomic literature and links to deposits of type strains in culture collections.

Type of a species or subspecies

Whenever possible, the type of a species or a subspecies is a designated strain. The type strain is made up of living cultures of an organism, which are descended from a strain designated as the nomenclatural type. The strain should have been maintained in pure culture and should agree closely to its characters with those in the original description.
Until December 14, 2000 (date of the publication of the minutes of the meetings of the Judicial Commission, August 1999, Sydney, Australia [1]), for a species which as not so far been maintained in laboratory cultures or for which a type does not exist, a description, preserved specimen, or illustration may serve as the type [Rule 18a (1)].
If a description or illustration constitutes, or a dead preserved specimen has been designated as a type of a species and a later strain of this species is cultivated, then the type strain may be designated by the person who isolated the strain or by a subsequent author [Rule 18f]. This type strain shall then replace the description, illustration or preserved specimen as the nomenclatural type [Rule 18f]. The designation of a type strain in this manner must be published in the IJSEM, the authorship and date of priority of publication being determined by the effective and valid publication of the name by original authors [Rule 18f].
As from December 14, 2000 (date of the publication of the minutes of the meetings of the Judicial Commission, August 1999, Sydney, Australia [1]), a description, preserved (non-viable) specimen, or illustration may not serve as the type [Rule 18a].
Given the central importance of type strains for the concept of valid publication, it is crucial that they be made available as sustainably and widely as possible. The best course of action would appear to be to deposit type strains in culture collections which should be able to maintain the distribution of the strain in the future. As from December 14, 2000 (date of the publication of the minutes of the meetings of the Judicial Commission, August 1999, Sydney, Australia [1]), a viable culture of a type strain must be deposited in at least two publicly accessible service collections in different countries from which subcultures must be available [Rule 30 (3b)]. The prerequisite for the valid publication of the name of a species or subspecies is the deposit and free availabilty of the designated type strain in two open collections.
The Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM), and the International Committee on Systematics of Prokaryotes (ICSP), decided in August 2002 that authors of papers in which new names and/or new combinations are proposed provide evidence that types are deposited in two publicly accessible recognized culture collections in two different countries (i.e. documents certifying deposition and public availability of type strains). Papers will not be accepted and new species, new subspecies or new combinations will not be cited in a Validation List without such evidence.
In exceptional cases, such as organisms requiring specialised facilities (e.g. Risk Group/Biological Safety Level 3, high pressure requirements etc.), exceptions may be made to this Rule. Exceptions will be considered on an individual basis, by a committee consisting of the chairman of the ICSP, the chairman of the Judicial Commission, and the editor in chief of the IJSEM. Exceptions will be made known at the time of publication.
The principle behind the deposit of type strains is that of making them easily and widely available for comparative purposes. Clearly, depositing a type strain in such a way that it is difficult to access is counterproductive to that principle. Organisms deposited in such a fashion that access is restricted, such as safe deposits or strains deposited solely for current patent purposes, may not serve as type strains. On 29 July 2002, the Judicial Commission agreed that the use of strains solely deposited for patent purposes or a safe deposit should not serve as type strains and that this be formulated in a ruling, which would be retroactive [2].
If a strain on which the original description was based cannot be found, a neotype strain may be proposed [Rule 18c]. See: Neotype strain.
More information on type strains is given on a separate page.
References:
  1. DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
  2. DE VOS (P.), TRÜPER (H.G.) and TINDALL (B.J.): Judicial Commission of the International Committee on Systematics of Prokaryotes Xth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 28, 29 and 31 July and 1 August 2002, Paris, France. Int. J. Syst. Evol. Microbiol. , 2005, 55 , 525-532.

Valid publication

A name has no status and no claim to recognition unless it is validly published [Principle 7]. The correct name of a taxon is based upon valid publication [Principle 6]. According to Rule 27, a name of a new taxon, or a new combination for an existing taxon, is validly published if the following criteria are met.
(i) The name is cited in the Approved Lists of Bacterial Names, or it is published in papers in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology (and conforms to requirements laid down in the Bacteriological Code), or the name is validly published by announcement in a Validation List.
(ii) The type of the taxon is designated. In the case of species or subspecies the culture collections numbers of at least two publicly accessible service collections in different countries where a subculture of the type strain has been deposited must be indicated. On 29 July 2002, the Judicial Commission confirmed this decision, although rare exceptions can be accepted in those cases where maintenance conditions for the culture are so exceptional (e.g. obligate barophiles or extremely virulent pathogens) that not more than one culture collection can be found which is able to maintain the strain. See also: Type of a species or subspecies.
References:
The Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM), and the International Committee on Systematics of Prokaryotes (ICSP), decided in August 2002 that authors of papers in which new names and/or new combinations are proposed provide evidence that types are deposited in two publicly accessible recognized culture collections in two different countries (i.e. documents certifying deposition and public availability of type strains). Papers will not be accepted and new species, new subspecies or new combinations will not be cited in a Validation List without such evidence.
(iii) The derivation ( etymology) of a new name (and if necessary of a new combination) is given [Rule 27(2) b]. Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
When a new species or a new combination results in the proposal of a new genus, both the genus name and the new species name or new combination must be validly published [Rule 27 Note 2]. Valid publication of the new species or new combination alone does not constitute valid publication of the new genus [Rule 27 Note 2]. Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244. Example: The species Crinalium epipsammum De Winder et al. 1991 appears on the Validation List no. 38 but the genus Crinalium does not. So, genus name Crinalium is not validly published.
If the initial proposal of the new name or the new combination or the nomen novum is not published in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology, the author should announce the name in a Validation List ("Validation of the publication of new names and new combinations previously effectively published outside the IJSB or the IJSEM") published regularly in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology [Rule 27].
The date of valid publication is that of publication in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology [Rules 23b and 27].
The name of a species or subspecies is not validly published if the description is demonstrably ambiguous and cannot be critically identified for purposes of the precise application of the name of a taxon. Reference: DE VOS (P.) and TRÜPER (H.G.): Judicial Commission of the International Committee on Systematic Bacteriology. IXth International (IUMS) Congress of Bacteriology and Applied Microbiology. Minutes of the meetings, 14, 15 and 18 August 1999, Sydney, Australia. Int. J. Syst. Evol. Microbiol. 2000, 50, 2239-2244.
A name or epithet is neither validly published, notably, in the following circumstances:
  • The name or epithet is not published in the body of an article in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology or does not appear in a Validation List [Rule 27].
  • A nomenclatural type (see: Nomenclatural type) is not designated for a new taxon, or cited for a new combination [Rule 27 (3)]. Example: Clostridium piliforme (ex Tyzzer 1917) Duncan et al. 1993 is not validly published because no type strain is designated.
  • The name or epithet was not accepted at the time of publication by the author who published it [Rule 28b (1)].
  • The name or epithet was merely proposed in anticipation of the future acceptance of the taxon concerned [Rule 28b (2)].
  • The name or epithet was mentioned incidentally (see: Incidental mention) [Rule 28b (3)].
Taxon names that are not validly published are placed in quotation marks.
Validly published names of Cyanobacteria are mostly validly published under International Code of Nomenclature for algae, fungi, and plants (ICN).

Validation Lists

The Validation Lists ("Validation of the publication of new names and new combinations previously effectively published outside the IJSB or outside the IJSEM") are lists published regularly since 1977 in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology, validating bacterial names effectively published elsewhere [Rule 27].
The contents of the Validation Lists depend on the submission of reprints by authors (or other individuals) who propose new names that appear in journals other than the International Journal of Systematic Bacteriology or other than the International Journal of Systematic and Evolutionary Microbiology.
Announcement in a Validation List is primarily the responsibility of the author(s) of the new names or new combinations [Rule 27 Note]. However, other individuals may also submit a new name or new combination for valid publication, provided it conforms to the rules of the code. Scientists wishing to have new names and/or combinations included in a list should send the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office. Authors and other individuals wishing to have new names and/or combinations included in a Validation List should send the pertinent reprint or a photocopy thereof, or an electronic copy of the published paper to the Editorial Office of the International Journal of Systematic and Evolutionary Microbiology.
Citation in a Validation List is not automatic! Papers will be reviewed by an IJSEM Editor and by the Lists Editor.
The Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM), and the International Committee on Systematics of Prokaryotes (ICSP), decided in August 2002 that authors of papers in which new names and/or new combinations are proposed provide evidence that types are deposited in two publicly accessible recognized culture collections in two different countries (i.e. documents certifying deposition and public availability of type strains). Papers will not be accepted and new species, new subspecies or new combinations will not be cited in a Validation List without the certificates. On 29 July 2002, the Judicial Commission confirmed this decision, although rare exceptions can be accepted in those cases where maintenance conditions for the culture are so exceptional (e.g. obligate barophiles or extremely virulent pathogens) that not more than one culture collection can be found which is able to maintain the strain.
If two names are validly published by announcement on the same Validation List in the International Journal of Systematic Bacteriology or in the International Journal of Systematic and Evolutionary Microbiology, priority is established by the sequence number on the list (the sequence number reflects the date of receipt on the validation request in the form that is accepted for publication) [Rule 24b (2), Note 1].

Variety

Variety is a synonym of subspecies. After publication of the Bacteriological Code (1990 Revision), the use of the term variety has no standing in nomenclature [Rule 5c].