Glossary

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 and the separate pages on taxonomy and systematics and on etymology.

Readers are asked to report inaccurate, outdated and missing information as well as malfunctioning links to the LPSN authors.

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
conj.
conjunction
dim.
diminutive
fem.
feminine [gender]
gen.
genitive [case]
Gr.
ancient Greek (the word is transliterated into the Latin alphabet and the original Greek spelling is not given or given on mouse-over like a tooltip)
ind.
indicative
inf.
infinitive
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.
numeral
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, non-tight underlining irrespective of whether the original content was confirmed or was corrected. Known grammatical errors (such as mismatches between the gender of the genus name and the gender of an adjectival epithet) are indicated by the word sic in parentheses.

If the mouse pointer is placed on a tightly underlined word, additional information is displayed:

  • The spelling of a Greek word in the Greek alphabet is given, e.g. πλάσμα for plasma.
  • The declension of an adjective or participle is shown, e.g. tepidus - tepida - tepidum.
  • The stem of a noun is shown, e.g. ferr- for ferrum (iron).
  • The components of a compound word are shown, e.g. Marini + bacterium (the connecting vowel may be attached to one of the components, i.e. not Marin + i + bacterium).

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)
dom. nov.
appropriate abbreviation for dominium novum (new domain)
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.
appropriate abbreviation for phylum novum (new phylum)
pro synon.
appropriate abbreviation for pro synonymon (as synonym)
regn. nov.
appropriate abbreviation for regnum novum (new kingdom)
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.

Note that LPSN creates potentially permanent placeholders as well as temporary stubs.

ICN
International Code of Nomenclature for algae, fungi, and plants (also known as Botanical Code)
ICNP
International Code of Nomenclature of Prokaryotes
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
LPSN
List of Prokaryotic names with Standing in Nomenclature (mentioned here for the sake of completeness)
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 may or may not be a synonym of subspecies but, this term has no standing in nomenclature since the publication of the Bacteriological Code (1990 Revision); under the ICN it is a category separate from subspecies

Acronyms of culture collections are found on the LPSN collection page.

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 (1)]. The rejection of names or epithets is not a means of solving taxonomic controversies. Examples: "Aerobacter" Beijerinck 1900, nom. rejic. (Opinion 46). "Pseudomonas denitrificans" (Christensen 1903) Bergey et al. 1923, nom. rejic. (Opinion 54); "Mycobacterium aquae" Jenkins et al. 1972, nom. rejic. (Opinion 55).

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

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]. See also: Nomen approbatum.

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]. Other errors are cited on the "List of Prokaryotic names with Standing in Nomenclature". See also the "Indexes of the bacterial and yeast nomenclatural changes".

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 LR, Skerman VBD, Sneath PHA. 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 JP. 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 JP. 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 was strongly recommended in previous editions of LPSN: "This inexpensive book is published by the American Society for Microbiology, 1752 N. Street, N.W. Washington, DC 20036-2804, USA."

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 the Bacteriological Code (1990 Revision [2]). The category phylum was added in 2021.

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. Similarly, in the case of not validly published names of parent taxa that have been replaced by a parent taxon with a validly published name, the cited publication may be the one that proposed the validly published name. 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.

To ease browsing the classification, especially for connecting child and parent taxa which would otherwise be unlinked, LPSN creates temporary stubs and potentially permanent placeholders.

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.

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 DSMZ-internal database which also powers LPSN. LPSN in turn links to BacDive. All of these services are provided by the Leibniz Institute DSMZ.

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.

Original name of a new combination or original name of a nomen novum. Basonyms are earlier homotypic synonyms.

The ICNP only briefly defines the term "basonym" and uncertainty is obvious in the taxonomic literature as regards its meaning. But it is clear from the usage of the term "original" in Rule 34a as well as from the link to the citation of authors in Rule 34b that the basonym is the name within which the epithet to be reused in a new combination was originally proposed. That is, the basonym is only one of the names within a series of homotypic synonyms, and the basonym itself has no basonym.

Similar provisions are found in article 6.10 of the ICN (Shenzhen code). Basonyms are called "basionyms" in the ICN.

Examples:

  • New combination: Haemophilus pleuropneumoniae Shope 1964 (Approved Lists 1980) is the basonym of Actinobacillus pleuropneumoniae (Shope 1964) Pohl et al. 1983 comb. nov.
  • New combination: Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov.; Flavobacterium heparinum Payza and Korn 1956 (Approved Lists 1980) is the basonym and Cytophaga heparina (Payza and Korn 1956) Christensen 1980 and Sphingobacterium heparinum (Payza and Korn 1956) Takeuchi and Yokota 1993 are additional homotypic synonyms, which have the same basonym.
  • Nomen novum: Microbispora viridis Miyadoh et al. 1985 is the basonym of Actinomadura rugatobispora Miyadoh et al. 1991.

Reference: Tindall BJ. Rule 27 of the International Code of Nomenclature of prokaryotes: the basonym is not enough. Int J Syst Evol Microbiol 2016; 66:4897-4899.

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. (The Candidatus names actually proposed nowadays do have a taxonomic category and thus a 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].

On 29 July 2002, the Judicial Commission decided that the concept of "Candidatus" should be mentioned in the main body of the Code, despite the fact that such names have no standing in nomenclature and proposed that this will be done in Rule 18a and/or 18f as a note indicating that "The concept of Candidatus is defined in Minute 11 of the ICSB (now ICSP) meeting in IJSB 47 (1997) 597-600 as recommended in IJSEM 52 (2002) 1043-1047" [6].

According to the "Ad Hoc Committee for the re-evaluation of the species definition in bacteriology" [7], microbiologists are encouraged to use the "Candidatus" concept for well characterized but as yet uncultured organisms.

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. [8].

"List of Prokaryotic names with Standing in Nomenclature" provides names included in the category Candidatus; see the advanced search page.

References:

  1. Murray RG, Schleifer KH. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int J Syst Bacteriol 1994; 44:174-176.
  2. Judicial Commission. Minutes of the Meetings, 2 and 6 July 1994, Prague, Czech Republic. Int. J. Syst. Bacteriol. 1995; 45:195-196.
  3. Murray RG, 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. VIIIth 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. 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.
  7. 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.
  8. 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.

The IJSEM publishes lists of names of Candidatus taxa. The occurrence of a name in such a list does not render that name validly published but the Candidatus lists provide an overview on the published Candidatus names and allow for orthographical and grammatical corrections.

When a genus is lowered in rank to a 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.

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.

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 (see: New combination) 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.

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 nomenclatural type of the taxon) is chosen by the rule of priority of publication of the names of the taxa [Rules 38 and 42]. For instance, 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 generic name [Rule 44].

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 no type species is placed in the genus, a new generic name must be proposed and the 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 the type species of one 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 name of a 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).

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, 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. See also: Minimal standards.

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.

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).

The term "clade" is not a nomenclatural term but is of taxonomic importance. A clade is a monophyletic group. A rooted phylogenetic tree is needed for determining whether or not a group of organisms is monophyletic. Accordingly, whether or not a group of organisms is a clade is conditional upon a specific phylogenetic hypothesis. A phylogenetic tree is a hypothesis rather than a fact.

The purpose of a phylogenetic tree is to represent the genealogical relationships between organisms. A monophyletic group is a group of organisms that includes the last common ancestor of these organisms and also includes all descendants of this ancestor. The organisms that belong to a monophyletic group thus share a common ancestor not shared with any organism placed outside the group. Monophyletic groups are the units of evolutionary history.

As emphasized in phylogenetic systematics, if and only if a taxon corresponds to a monophyletic group according to the phylogenetic tree from which it was derived, this taxon is logically consistent with the tree. For this reason, it can be called a natural taxon (as opposed to an artificial taxon, which corresponds to a paraphyletic or polyphyletic group in the tree from which it was supposed to be derived). A classification comprising only natural taxa is a natural classification. In phylogenetic systematics, other classifications are artificial classifications. In contrast, phenetics groups according to overall similarity. But if so, the resulting classifications are not derived from a phylogenetic tree at all.

Classification is the arrangement of objects into groups. The classification of things in general, or of organisms such as prokaryotes, may use numbers or names for the resulting groups. If suitable names are used, a classification comprises taxa and becomes a taxonomic classification. The far more general term "classification" is not even bound to organisms.

Distinct forms of classification may have different goals. As regards organisms, they 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). If a group of organisms has a name, it is taxon, and if this group also actually exists in nature as a result of evolution, it is a natural taxon. A classification containing only natural taxa is a natural classification. Other classifications are artificial classifications. This distinction must not be confused with the distinction between validly published names and other names.

If the groups that comprise a classification are to be named, 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.
  2. Wiley EO, Siegel-Causey D, Brooks DR, Funk VA. The compleat cladist. University of Kansas Museum of Natural History, Lawrence, KS, 1991.

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]. In addition to names (of subgenera, genera, or taxa above genus rank), epithets can also be conserved.

Only the Judicial Commission can place names on the list of conserved names (nomina conservanda), and epithets on the list of conserved epithets [Rules 23a Note 4 (i) and 56b Note 2].

A conserved name (nomen conservandum), if conserved over other names, 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]. The same holds for conserved epithets. In Opinion 80, the "Judicial Commission noted [...] that a name (epithet) can only be conserved over another name (epithet) or in combination with a particular circumscription." Opinions issued after 1980 were indeed restricted to these two situations. The conservation of names or epithets is not a means of solving taxonomic controversies.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

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).

On LPSN, conserved names can be obtained via the advanced search.

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.

Principle 8 and Rule 23a indicate that each taxon with a given circumscription, position, and rank (as defined in Principle 8 Note 2) can have only one correct name. This correct name is usually the earliest one that is validly published and legitimate; the sole exceptions are conserved and rejected names. The question whether or not a certain taxon should have a certain circumscription, position, and rank is an issue of taxonomy, on which the ICNP does not rule [Principle 1(4)]. That question must not be confused with the purely nomenclatural question whether a certain name is the correct name of a taxon, given its circumscription, position, and rank. For this reason, it is inappropriate to criticize other authors for using an "incorrect" name if these other authors merely expressed a distinct taxonomic opinion but chose a name in accordance with the ICNP.

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.

Accordingly, by far the most frequent taxonomic status in LPSN is "correct name", followed by the "synonym" status. Type subspecies obtain the status "synonym of its species (division into subspecies abandoned)" if the currently preferred taxonomic solution is to not divide the species into subspecies. Illegitimate and rejected names obtain the special status "in need of a replacement" if a legitimate synonym is not available. How big this need actually is in practice heavily depends on the name.

The special status "orphaned ..." is used for names whose currently assigned parent taxon is not regarded as the correct name. This includes names of subspecies that lack an according new combination while a new combination for their species names is regarded as the correct name. It also includes names of species whose genus name is currently regarded as a synonym of another genus name but for which a new combination including this other genus name has not (yet) been proposed. Such subspecies and species names are conditionally illegitimate according to the second sentence in Rule 51a. Orphaned names in LPSN also include names of taxa of higher rank that are in the course of being explicitly or implicitly reclassified. For instance, the recorded literature reference for the assignment to a parent taxon may be outdated because a not validly published name of a parent taxon became validly published. Such status values are usually temporary.

For names that are not validly published and are not reduced to synonyms, LPSN uses the status "preferred name". This should be distinguished from the status "correct name". The taxonomic status of synonyms that are not validly published indicates that they have no standing in nomenclature.

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.

The subspecies is the category of the lowest rank covered by the ICNP. Traditionally, subspecies delineation was based on phenotypic characters. 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." This comment paves the way for switching from subspecies delineation mainly based on the phenotype to delineation mainly based on the genotype, as in the case of species.

Meier-Kolthoff et al. (2014) indeed proposed a digital DNA:DNA hybridization threshold for delineating subspecies that can be used in analogy to the threshold used for species. The method is implemented in the TYGS and available online.

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 TRÜPER (H.G.): Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol., 1987, 37, 463-464.
  3. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, et al. Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2.

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. Diacritic signs are used, of course, when Greek words are shown in their original spelling in the Greek alphabet.

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. An updated list of names above phylum rank is given by Göker and Oren (2023).

The taxonomic category domain or empire has until 2023 not been covered by the Rules of the ICNP. In 2023 the ICSP approved the inclusion of the categories domain (or dominion) and kingdom in the ICNP (Oren 2023). Names of domains do not have a rank-specific suffix in the ICNP. They are formed as the nominative plural of a single component that also occurs as the last component of the name of one of the genera included in the domain at the time the name is proposed.

References:

  1. Göker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73:5650.
  2. Oren A. Emendation of Principle 8, Rules 5b, 8, 15, 33a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes to include the categories of kingdom and domain. Int J Syst Evol Microbiol 2023; 73:6123.
  3. Trüper HG. 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.
  4. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 1990; 87:4576-4579.

A doubtful name (nomen dubium) is a name whose application is uncertain. This happens, for instance, if the description of the name does not match any known organism. Such a name should be rejected [Rule 56a (2)]. Example: Methanosarcina methanica (Smit 1930) Kluyver and van Niel 1936 (Approved Lists 1980), nom. rejic. (Opinion 63).

A nomen dubium is often also a nomen confusum. In the case of "Peptococcus anaerobius" (Hamm) Douglas 1957 (Opinion 56) the Request for an Opinion proposed the rejection of the name as nomen confusum while Opinion 56 rejected it as nomen dubium (it is also a nomen perplexum). In the case of Citrobacter diversus corrig. (Burkey 1928) Werkman and Gillen 1932 (Approved Lists 1980), nom. rejic. (Opinion 67) the name may rather be treated as a nomen ambiguum because it was used distinctly by Ewing and Davis (1972) compared to Werkman and Gillen (1932). The rejection of names or epithets is not a means of solving taxonomic controversies.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

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.

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.

See domain.

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.

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. The names of bacterial genera which end in -bacter should be regarded as having the masculine gender [Judicial Opinion 3].
  • 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.
  • Some Latin or Greek components do not have a fixed gender but are in common gender and the authors have the right of choice. This also holds for genus names derived from present participles.
  • If the last component is a Greek word, the gender can be masculine, feminine, masculine/feminine, or neuter.

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. Further examples: A-C, D-J, K-N, O-S, T-Z.

The gender of each genus name is given on the LPSN pages for single names. See also the page on etymology and the links therein.

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)... Many more examples are given on separate pages, see the page on etymology and the links therein.

Names of subclasses, orders, suborders, families, subfamilies, tribes, and subtribes are in the feminine gender [Rule 7]. Names of classes and phyla are in the neuter gender.

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 earlier (senior) homonym and any later published name as a later (junior) homonym. 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. The later homonym is almost always an illegitimate name.

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.

The correct name of a taxon is based upon legitimacy [Principle 6], among other criteria. A validly published 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 later (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 the Prokaryotic Code. 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).

While there are certain aspects of legitimacy that apply under all conditions, legitimacy of a taxon name may also depend on the taxonomic position of the taxon [Rule 51a].

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.

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 were 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:

Taxa below the rank of subspecies (infrasubspecific subdivisions) are not covered by the Rules of the Prokaryotic Code [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.).

The ingroup is the group of interest in a taxonomic study. It is supposed to be a clade but it may or may not be a taxon.

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. See also: TYGS.

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.

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 Prokaryotic 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, as stipulated in its Statutes.

The International Committee on Systematics of Prokaryotes (ICSP) has published answers to Frequently Asked Questions (FAQ) about its purpose and its activities. Consulting the last version of this FAQ document is highly recommended.

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.

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.

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, Tindall BJ. 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, Tindall BJ. 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.

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.

Names used in prokaryotic nomenclature are Latin or Latinized words and such names are usually printed in italics (or underlined in manuscripts). The Bacteriological Code (1990 Revision) and its successors set 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.

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 used to consist 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. Nowadays the Judicial Commission consists of the aforementioned twelve members only.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

Some functions of the Judicial Commission used to be 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.

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) or its successors [formerly Article 8c (2) of the Statutes of the International Committee on Systematic Bacteriology].

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

Outdated version. 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.

Names and epithets may be: (i) legitimate: in accordance with the Rules; (ii) illegitimate: contrary to the Rules [Rule 23a Note 5]. The wording of Rule 23b and other Rules implies that the question of legitimacy can only sensibly be applied to validly published names. Since names that are not validly published have do not have a status under the Rules [Principle 7], only validly published names can be legitimate or illegitimate.

LPSN provides stable Uniform Resource Locators (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 text stubs and placeholders are not regarded as stable and should not be linked to. LPSN also provides stable numeric IDs for all names except for stubs and placeholders.

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.

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.

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). A nomen confusum is often also a nomen dubium. The rejection of names or epithets is not a means of solving taxonomic controversies.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

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. This is permitted for names of classes validly published prior to 2012 since an ICSP decision in 2022 made Rule 8 non-retroactive. A separate LPSN page provides on overview on the real composition of the names of classes. A Request for an Opinion published in 2022 detected the scheme used for forming the deviating names of class and asked the Judicial Commision to correct the remaining ones.

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].

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)...

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).

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 a 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 kingdoms were not regulated by the ICNP until 2023. As of 2023, the name of a kingdom is a Latin or latinized word. The name of a kingdom is in the masculine gender, the plural number and written with an initial capital letter. The name is formed by the addition of the suffix -ati to the stem of the name of the type genus of the kingdom [Rule 8].

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 were not regulated by the ICNP until 2021. The ending -aeota had been proposed in the literature to standardize the formation of phylum names. As of 2021, the name of a phylum is a Latin or latinized word. The name of a phylum 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 -ota to the stem of the name of the type genus of the phylum [Rule 8].

Some complaints about the so-called "replacement" of the old phylum names such as "Proteobacteria" by the new, validly published ones were issued on platforms such as Twitter and potentially on other social media. The complaints also yielded two flawed but potentially highly visible publications which criticised the ICSP but were ill-informed. The ICSP has already responded to one of them. The phylum names formed according to the scheme implemented in Rule 8 have a variety of advantages over the older names, which were never validly published.

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 nomenclatural 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: Trüper HG, Imhoff JF. International Committee on Systematic Bacteriology - Subcommittee on the taxonomy of 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.

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].

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. The 2022 Revision of the ICNP has removed this category.

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.

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].

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 nomenclatural 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 later (junior) homonym of urealyticus used in the name Staphylococcus capitis subsp. urealyticus corrig. Bannerman and Kloos 1991.

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. The 2022 Revision of the ICNP has removed this category.

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.

If a strain on which the original description was based (because the strain served as the nomenclatural type) 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.

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 [there may be other instances]. 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 Prokaryotic 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.

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.

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.

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]. Among the representatives of a taxon, the nomenclatural type is the representative with which the name of the taxon is permanently associated, irrespective of whether the nomenclatural type is regarded as a correct name or as a later heterotypic synonym [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 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.

The Greek K and Z and the Medieval Latin J (for consonantic I) should be maintained to avoid confusion [Recommendation 6 (7)]. Diacritic signs must be replaced.

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 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, taxonomic terminology employed by the respective study, and misprints of taxon names occurring in the literature.

As far as possible LPSN also determines taxonomists whose publications recently focused on a certain group of organisms. Such taxonomists may be suitable as reviewers for taxonomic manuscripts related to the respective group of organisms. However, editors are advised to use additional criteria.

In 2021 LPSN has also introduced an experimental feature, the so-called phylogenomic assignment score, based on comparisons of type-strain genomes. A strongly negative score (say, -0.05 or lower) indicates that the taxon may better be assigned to another parent taxon.

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 of the International Committee on Systematic Bacteriology. Minutes of the Meeting, 14 September 1990, Osaka, Japan. Int. J. Syst. Bacteriol. 1991; 41:185-187.

Bacteriologists who are willing to acquire nomenclatural literacy or who are about to describe and/or name prokaryotes, should read the LPSN pages on etymology and the following literature sources.

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 main principles of orthography under the ICNP are as follows:

  • 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)]. Diacritic signs must be replaced.
  • 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).

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
  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.

The old regulations for spelling corrections were as follows:

  • 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.
  • 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).

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.

As of 2022, the ICNP behaves more like the ICN regarding orthographic and grammatical corrections. The sentence in the ICNP that was directed against such corrections (unless they were conducted as described above) got removed. The resulting Rule 61 still argues against a correction ‘especially if the change affects the first syllable and above all the first letter of the name or epithet’, in analogy to Article 60.3 of the ICN. Apart from that, the 2022 revision of the ICNP permits orthographic grammatical corrections by any author in any kind of publication.

While an effective publication is a prerequisite for the valid publication of a name under the ICNP, the ICNP does not also define such a prerequisite for spelling corrections. This implies that spelling corrections can also be conducted in databases.

This raises the question on how to correctly spell a variety of prokaryotic names, particularly older ones. In 2022, LPSN has chosen a careful approach. We directly conduct grammatical corrections, i.e. we adapt the gender of an epithet to the one of its genus name where necessary. We also directly correct inaccurate stems of genus names within names of taxa above genus rank. Other orthographic corrections are not conducted by LPSN during the 2022/2023 period. Instead, we merely compile a list of such names or epithets. These could be of use later for providing general guidelines. We also care about marking such instances in the public LPSN etymologies, as a precaution against the usage of inaccurately formed names or epithets as exemplars.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

In a taxonomic study, an outgroup is any group except for the ingroup. One to several outgroups are needed for comparative purposes, usually for rooting and sometimes for determining which character states are ancestral and which are derived. The most important outgroup is often the sister group. The choice of one to several outgroups relies on assumptions about phylogenetic relationships.

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 (5)]. Importantly, Rule 56a (5) Note 1 restricts the application of the term "perilous name" to situations in which it is concluded that a "taxon be maintained as a separate [nomen]species, without prejudice to the recognition or acceptance of its genetic relatedness to another taxon." The rejection of names or epithets is not a means of solving taxonomic controversies. Each of the two known examples for nomina periculosa involved an epithet that was rejected in order to allow to other epithets to be conserved against each other.

Examples:

  • Yersinia pseudotuberculosis subsp. pestis (Lehmann and Neumann 1896) Bercovier et al. 1981 was placed on the list of nomina rejicienda in Judicial Opinion 60 because of practical concerns about human welfare (nomen periculosum). The "Judicial Commission decided that Yersinia pestis and Yersinia pseudotuberculosis should be maintained as separate nomenclatural species." The purpose of the rejection of Yersinia pseudotuberculosis subsp. pestis (van Loghem) Bercovier et al. 1981 was to enable this.
  • Opinion 69 concluded that the "name Clostridium putrificum is rejected while Clostridium botulinum is conserved for toxigenic strains and Clostridium sporogenes is conserved for non-toxigenic strains."

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

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 (4)]. Examples: "Mycobacterium marianum" Penso 1953, nom. rejic. (Opinion 53) because of its orthographic similarity to Mycobacterium marinum Aronson 1926; "Peptococcus anaerobius" (Hamm 1912) Douglas 1957, nom. rejic. (Opinion 56) because it could easily be confused with Peptostreptococcus anaerobius (Natvig 1905) Kluyver and van Niel 1936.

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]. Note that, the rejection of names or epithets is not a means of solving taxonomic controversies.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

The species was long held to be 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: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.

There is a terminological problem with "phylogenetic" species definitions. The phrasing is based on the traditional but inappropriate use of the term "phylogenetic data" for sequence data. Since a DNA:DNA hybridization does not involve a phylogenetic tree, how should a species definition based on DDH be phylogenetic? The approach may better be called "genomic" or "genotypic" species definition.

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."

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"). Meier-Kolthoff and Göker (2019) argued that the technique implemented in the TYGS and previously in the GGDC work best in this regard.

DNA:DNA hybridization and its bioinformatic follow-up techniques are not the only genome sequence based methods for species delineation. For instance, Meier-Kolthoff et al. (2014) claimed that the difference in G+C content is at most 1% within species if based on genome sequencing. However, the reverse is not true, as distinct species may also differ at most 1% in G+C content.

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. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182.
  5. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352-356.
  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. 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.

This is not a nomenclatural but a taxonomic term. Its meaning is somewhat obscured in microbiology because of the frequent confusion of "sequence data" with "phylogenetic data". But phylogenetic relationships cannot sensibly be defined based on the characters from which they are inferred. Instead, the term "phylogenetic relationship" refers to the genealogical relationship between groups of organisms (which may be taxa). In the course of organismal evolution, species give rise to daughter species through a series of consecutive speciation events. These successive instances of descent of offspring from parents yield hierarchical relationships that can be reconstructed using phylogenetic inference either from sequence data or other data.

Two groups of organisms A and B are phylogenetically more closely related to each other than to another group of organisms C if and only if A and B share a common ancestor in the given phylogenetic tree that is not an ancestor of C. That is, A and B belong to a clade to which C does not belong. Taxonomic relationships can analogously be defined as follows. Two taxa X and Y are taxonomically more closely related to each other than to another taxon Z if and only if X and Y share a parent taxon in the given taxonomic classification that is not a parent taxon of Z.

In phylogenetic systematics, taxonomic relationships must reflect phylogenetic relationships. That is, each taxon must correspond to a clade. In other approaches to taxonomic classification "relationship" has a different meaning. For instance, two groups of organisms U and V are phenetically more closely related to each other than to another group of organisms W if and only if U and V are more similar to each other than to W. But more similar organisms are not necessarily more closely related phylogenetically.

Priority means that among a set of names for a taxon with a given circumscription, position, and rank the name first validly published and in accordance with the Rules is the correct name, or epithet, for the taxon [Principles 6-8]. The correct name of a taxon is thus based on priority of publication but names that differ in circumscription, position, or rank do not compete for priority.

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 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).

As indicated in Rule 23a, a species name in a given position can bear only one correct epithet, namely the earliest legitimate epithet. As clarified in Rule 23a Note 1, the priority of a species epithet is independent of the priority of its genus name. As indicated in Rule 23a Note 2, the priority of a subspecies epithet is independent of the priority of its species epithet. This is of practical relevance particularly regarding heterotypic synonyms, last but not least heterotypic synonyms that make use of distinct genus names. Importantly, Rule 15 indicates that the nomenclatural type of a taxon remains the nomenclatural type of this taxon even if treated as younger heterotypic synonym.

Examples: If Microbacterium liquefaciens (Collins et al. 1983) Takeuchi and Hatano 1998 and Microbacterium maritypicum corrig. (ZoBell and Upham 1944) Takeuchi and Hatano 1998 were to be treated as heterotypic synonyms, the epithet in Microbacterium maritypicum corrig. (ZoBell and Upham 1944) Takeuchi and Hatano 1998 had priority although the new combination Microbacterium maritypicum corrig. (ZoBell and Upham 1944) Takeuchi and Hatano 1998 was proposed on page 981 of IJSEM volume 48 whereas the new combination Microbacterium liquefaciens (Collins et al. 1983) Takeuchi and Hatano 1998 was proposed already on page 745 of the same volume. Similarly, if Borreliella garinii (Baranton et al. 1992) Adeolu and Gupta 2015 and Borreliella bavariensis (Margos et al. 2013) Adeolu and Gupta were to be treated as heterotypic synonyms, the epithet in Borreliella garinii (Baranton et al. 1992) Adeolu and Gupta 2015 had priority even though both new combinations appeared with the same sequence number in the same validation list.

Further examples:

  1. Bacillus axarquiensis Ruiz-García et al. 2005, Bacillus malacitensis Ruiz-García et al. 2005 and Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) were suggested to be heterotypic synonyms by Dunlap et al. (2016), who also proposed the use of the name Bacillus axarquiensis Ruiz-García et al. 2005. However, this proposal contravenes Rule 23a of the ICNP because the epithet in Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) has priority over the epithet in Bacillus axarquiensis Ruiz-García et al. 2005. To express the affiliation of Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) to the genus Bacillus it was necessary to create the new combination Bacillus halotolerans (Delaporte and Sasson 1967) Tindall 2017. Bacillus axarquiensis Ruiz-García et al. 2005 and Bacillus malacitensis Ruiz-García et al. 2005 can then be treated as younger heterotypic synonyms of Bacillus halotolerans (Delaporte and Sasson 1967) Tindall 2017.
  2. Marinobacterium georgiense González et al. 1997 and Pseudomonas iners Iizuka and Komagata 1964 (Approved Lists 1980) were suggested to be heterotypic synonyms by Satomi et al. (2002), who proposed the use of the name Marinobacterium georgiense González et al. 1997. However, this proposal contravenes Rule 23a of the ICNP because the epithet in Pseudomonas iners Iizuka and Komagata 1964 (Approved Lists 1980) has priority over the epithet in Marinobacterium georgiense González et al. 1997. To express the affiliation of Pseudomonas iners Iizuka and Komagata 1964 (Approved Lists 1980) to the genus Marinobacterium it was necessary to generate the new combination Marinobacterium iners (Iizuka and Komagata 1964) Tindall 2020. Marinobacterium georgiense González et al. 1997 can then be treated as younger heterotypic synonym of Marinobacterium iners (Iizuka and Komagata 1964) Tindall 2020.
  3. Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 and Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980) were suggested to be heterotypic synonyms by Spröer et al. (1998), who proposed to use the name Marinobacter hydrocarbonoclasticus Gauthier et al. 1992. However, this proposal contravenes Rule 23a of the ICNP because the epithet in Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980) has priority over the epithet in Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 although Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 is the nomenclatural type of the genus Marinobacter Gauthier et al. 1992. To express the affiliation of Pseudomonas nautica Baumann et al. 1972 (Approved Lists 1980) to the genus Marinobacter it was necessary to generate the new combination Marinobacter nauticus (Baumann et al. 1972) Tindall 2020. Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 can then be treated as younger heterotypic synonym of Marinobacter nauticus (Baumann et al. 1972) Tindall 2020 and at the same time remain the nomenclatural type of the genus Marinobacter Gauthier et al. 1992.

References:

  1. Tindall BJ. The consequences of Bacillus axarquiensis Ruiz-Garcia et al. 2005, Bacillus malacitensis Ruiz-Garcia et al. 2005 and Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) being treated as heterotypic synonyms. Int J Syst Evol Microbiol 2017; 67:175-176.
  2. Tindall BJ. Marinobacterium iners (Iizuka and Komagata 1964) comb. nov. arising from the synonymy of Marinobacterium georgiense Gonzalez et al. 1997 and Pseudomonas iners Iizuka and Komagata 1964 (Approved Lists 1980). Curr Microbiol 2019; 76:1128-1129.
  3. Tindall BJ. Marinobacter nauticus (Baumann et al. 1972) comb. nov. arising from instances of synonymy and the incorrect interpretation of the International Code of Nomenclature of Prokaryotes. Arch Microbiol 2020; 202:657-663.

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) [originally defined in 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.*

Each revision supersedes all previous editions. For instance, the 1999 revision shall be cited as Bacteriological Code (1990 Revision) and will apply from the date of publication (1992) [Rule 1a] until the publication of the next revision. The 2008 revision was finally published in 2019 as Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1-S111. The 2022 revision was finally published in 2023.

Current revision: Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R, Sutcliffe IC. International Code of Nomenclature of Prokaryotes (2022 Revision) Preprint. Zenodo 2023; 0:0.

The Bacteriological Code or Prokaryotic Code (1990 revision and later revisions) 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. 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: Phylum, Class, Subclass, Order, Suborder, Family, Tribe, 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]. Subfamily and Subtribe were removed in 2022.

Alterations to the Bacteriological Code (1990 Revision) could 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]. Alterations to the Prokaryotic Code are made after an online debate. 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) and the Prokaryotic Code are retroactive, except where exceptions are specified [Rule 2].

The Code is divided into Principles, Rules, and Recommendations [General Consideration 6], which can have Notes:

  • 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.
  • Notes attached to a Rule form an integral part of that Rule. Notes attached to a Recommendation form an integral part of that Recommendation.

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) included 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.

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.

The 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 nomenclatural 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 the Prokaryotic Code. Example: The name Rhizomonas van Bruggen et al. 1990 is illegitimate because it is a later (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.

The LPSN record number is a numeric identifier for each taxon-name entry. The record number displayed on the page of each taxon name is identical to the record number used in the according row in the LPSN download files, if that taxon name is included in the respective file. For taxon names that were also listed in Prokaryotic Nomenclature Up-To-Date (PNU) the record number is identical to the PNU record number. Note that the relative time of inclusion of an entry into LPSN cannot be inferred from the record numbers. An entry added later on may well have a lower record number than an entry added beforehand.

Users should be aware that negative record numbers are assigned to stubs and placeholders. These are not stable and may be removed at any time. However, positive record numbers are designed to be stable and can be used to link to LPSN pages for individual taxon names or to otherwise unambiguously refer to an LPSN entry. The LPSN download files already contain such links.

A reference strain is a strain that is neither a type strain nor a neotype strain but a strain used in comparative studies, e.g., taxonomic or serological, or for chemical assay [Rule 19].

As for a rejected name (nomen rejiciendum: nom.rej., or nom. rejic.) or epithet, only the Judicial Commission can reject names (nomina rejicienda) or epithets [Rules 23a Note 4 (i) and 56a, b]. The Judicial Commission may place on the list of rejected names (nomina rejicienda) a name or epithet previously published in an Approved List [Rule 24c]. A name or epithet 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)]. The rejection of names or epithets is not a means of solving taxonomic controversies.

Reference: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

On LPSN, rejected names are available via the advanced search.

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]. Exceptions from the Rules are only permitted if these possible exceptions are defined in the Rules themselves. The Judicial Commission cannot overrule the ICNP.

A Request for an Opinion must be published in the International Journal of Systematic Bacteriology or, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology [Appendix 8]. A Request for an Opinion must be accompanied by a fully documented statement of the relevant facts [Appendix 8].

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: Arahal DR, Bull CT, Busse HJ, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Rossello-Mora R, et al. Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion. Int J Syst Evol Microbiol 2023; 73:5782.

Outdated version. 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.

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.

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].

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. One may also wonder whether or not this topic fits to the scope of LPSN. However, users asked for it, and the hazard associated with a certain bacterium is of considerable importance in nomenclature, too, particularly when new combinations are proposed as names of well-known pathogens. Hence, 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.

The LPSN risk-group classification is mainly taken from the German TRBA 466 ["Einstufung von Prokaryonten (Bacteria und Archaea) in Risikogruppen"], downloaded on the date given in the note about the indicated risk group. 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.

Regulations equivalent to the German TRBA classification, such as the "Approved List of biological agents" issued by the British Advisory Committee on Dangerous Pathogens, are considered as far as possible. Importantly, the number shown in the "Risk group" field is the maximum of the classifications included in the LPSN database for the given taxon name. Details are given in the notes.

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.

In a taxonomic study, the sister group is the taxon that is phylogenetically most closely related to the ingroup. Accordingly, the sister group is an outgroup. The sister group is supposed to be a clade but it may or may not be a taxon.

The stem of a Greek or Latin word is found in the singular genitive case of the noun or adjective (Trüper 1999). A Latin or Greek dictionary indicates the singular genitive cases and scientists should be able to identify the stem of a Latin or Greek word.

Reference:

Examples:

Latin nouns and Greek nouns latinized by ancient Romans

  • First declension: the stem of capsa gen. capsae (box) is caps-; of catena gen. catenae (chain) is caten-; of sphaera gen. sphaerae (sphere) is sphaer-; of spira gen. spirae (coil) is spir- etc.
  • Second declension: the stem of ager gen. agri (field) is agr-; of bacillus (or bacillum) gen. bacilli (little staff) is bacill-; of equus gen. equi (horse) is equ-; of oscillum gen. oscilli (swing) is oscill-; of puer gen. pueri (child) is puer-; of vir gen. viri (man) is vir- etc.
  • Third declension: the stem of animal gen. animalis (animal) is animal-; of bos gen. bovis (cow) is bov-; of canis gen. canis (dog) is can-; of caro gen. carnis (flesh) is carn-; of caput gen. capitis (head) is capit-; of corpus gen. corporis (body) is corpor-; of feles (or felis) felis (cat) is fel-; of leo gen. leonis (lion) is leon-; of mare gen. maris (sea) is mar- etc.
  • Fourth declension: the stem of cornu gen. cornus (horn) is corn-; of flexus gen. flexus (a bending, turning) is flex-; of gelus (or gelu) gen. gelus (frost) is gel-; of genu gen. genus (knee) is gen-; of lacus gen. lacus (lake, basin, tank) is lac-; of manus gen. manus (hand) is man- etc.
  • Fifth declension: the stem of dies gen. diei (day) is di-; of facies gen. faciei (face) is faci-; of glacies gen. glaciei (ice) is glaci-; of scabies gen. scabiei (the scab, mange, itch) is scabi- etc.

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 gen. chlamydis (coat) is chlamyd-; of coma gen. comae (hair) is com-; of coccus gen. cocci (grain) is cocc-; of hals gen. halis (salt) is hal-; of monas gen. monadis (unit, monad) is monad-; of myces gen. mycetis (fungus) is mycet-; of nema gen. nematis (thread) is nemat-; of ornis gen. ornithis (bird) is ornith-; of plasma gen. plasmatis (form) is plasmat-; of soma gen. somatis (body) is somat-; of thrix gen. trichis (hair) is trich- etc.

Stems of compound bacterial generic names ending in -bacterium, -bacter or -bactrum

According to 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).

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. Stubs neither indicate that the respective taxon name is validly published nor do they indicate that the name is not validly published.

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.; sometimes 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. Nowadays brackets are used to indicate LPSN stubs and placeholders.

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 synonyms validly published later on 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.

When several taxon names are regarded as synonyms of another name, they also have to be regarded as synonyms of each other: if A is supposed to be the same as B and B is supposed to be the same as C, then A is implicitly supposed to be the same as C, too. In order to treat taxon names as not being synonymous to each other, one simply should not treat them as synonym of the same other name. There is no concept of partial synonymy between taxon names in the ICNP. For instance, for some species of Klebsiella new combinations in the genus Raoultella were proposed. If one regards Klebsiella and Raoultella as distinct genera, they are not synonyms; but if they are treated as synonyms (by including the type species of both genera into the same genus), then both genus names become synonyms in their entirety.

In the broad sense, a taxon is a group of organisms that has a name. In the strict sense, a taxon is a group of organisms that has a name that has several or even all of the properties of a name that can be validly published or even legitimate under some code of nomenclature. A taxon can have a category. A taxonomic classification is comprised of taxa.

The relative place of a taxon in the hierarchy of the classification is indicated by its category. By far the most common taxonomic hierarchy is the Linnaean hierarchy. The various codes of nomenclature also define how names of taxa are formed with respect to their category and thus their place in the hierarchy. The rank of each category, i.e. its position in the Linnaean hierarchy, determines how child taxa can be assigned to parent taxa.

According to Rule 5b of the ICNP, the taxonomic categories which are covered by the Rules are as follows (in descending taxonomic rank): domain or dominion (dominium), kingdom (regnum), phylum (phylum), class (classis), subclass (subclassis), order (ordo), suborder (subordo), family (familia), tribe (tribus), 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) empire (imperium), division (divisio), subfamily (subfamilia), subtribe (subtribus), and infrasubspecific subdivisions are not covered by the Rules. Some of them used to be covered by earlier revisions of the ICNP, and some of them are covered by the ICN.

This glossary contains detailed information on how names of classes, domains, families, genera, kingdoms, 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.

Other codes may distinctly treat the categories. For instance, families of animals have names that end in -idae, while plant taxa ranked at the level of the family have names that end in -aceae, as in the ICNP.

Taxonomy may best be understood as a special kind of classification. The terminology used by the ICNP is not consistent with the usage of "taxonomy" as a broad term that encompasses nomenclature.

The ICNP uses "taxonomy" in the narrow sense of classification (of organisms) in many instances:

  • General Consideration 7: when defining "taxonomic group" and "taxonomic category" (these are only used in classification)
  • Principle 1(4): when defining "taxonomic freedom" (studies other than those targetting classification of organisms would not affect their names anyway, hence no need to emphasize freedom other than when referring to classification of organisms)
  • Principle 9: when talking about "taxonomic studies" (studies other than those conducting classification of organisms would not cause a change of a name anyway)
  • Rule 24a Note 2: "taxonomic opinions" (studies other than those conducting classification of organisms would not have an effect on synonymy etc. anyway)
  • Rule 28: "taxonomic doubt" (studies other than those conducting classification of organisms would not cause a change of a name anyway)
  • Rule 37a(1): "taxonomic position" (the example refers to the placement of a species in a genus)
  • Rule 51a: "taxonomic position" (can there be a position unless it is about classification?)

Moreover, the ICNP uses "taxonomy" as separate from "nomenclature". For instance, in Rule 24a Note 2 and Rule 28a Note 3 we find the phrasing "prokaryotic nomenclature and taxonomy". Other usages in the ICNP are neutral. There does not appear to be any instance in the ICNP in which the term "taxonomy" is clearly understood in the broad sense that encompasses nomenclature.

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.

Whenever possible, the nomenclatural 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.

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 all of the following criteria are met.

(i) The name is cited in the Approved Lists of Bacterial Names, or it is published in a publication 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 Prokaryotic Code), or the name is validly published by announcement in a Validation List [Rule 27 (1)]. In contrast, the listing of the name in a Notification List is not a requirement [Rule 27 Note 1].

(ii) The type of the taxon is designated [Rule 27 (3)]. 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 properties of the described taxon are given, the kind of proposal is indicated and 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 Note 1].

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 (1)].
  • 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). In 2021 it was accepted that names of Cyanobacteria validly published under the ICN are also accepted as validly published under the ICNP. LPSN keeps the two kinds of valid publication strictly separate, however, to avoid confusion. Further details are provided on the Cyanobacteria page.

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].

This LPSN page was printed on 2024-03-19 04:16:21