Classification of prokaryotes (bacteria): Introduction
- ️J.P. Euzeby
- ️Thu Jan 01 1998
Updated: May 03, 2007
Classification of prokaryotes (bacteria): Introduction
See also the following files:
. Classification of domains and phyla - Hierarchical classification of prokaryotes
. Classification of genera List A - C, List D - L, List M - R, List S - Z - List of genera included in families - List of genera included in orders - List of genera included in suborders
. Classification of families - List of families included in suborders - List of families included in orders
. Classification of suborders - Classification of orders - List of orders and suborders included in classes - List of orders and suborders included in subclasses
. Classification of classes - Classification of subclasses
. Classification of Cyanobacteria
. Introduction à la taxonomie des procaryotes (In French)
WARNING: There is no official classification of prokaryotes (see below)!
By definition, each prokaryotic species must be included in a genus (binary nomenclature established by Carl von Linné [1]). A genus is theorically a member of successively higher ranks: subtribe, tribe, subfamily, family, suborder, order, subclass, class, division (or phylum) and domain (or empire).
No name is included in the categories subtribe and subfamily.
The rank subtribe and tribe fall into disuse.
The categories division (or phylum) and domain (or empire) are not covered by the Rules of Bacteriologocal Code (1990 Revision) [2].
It is important to note that "there is considerable reluctance among many contemporary systematic procaryotic biologists to place new species and genera into higher taxa, especially at the intermediate levels (family, order, and class) because of uncertainty of phylogenetic models" (see Garrity et al. 2004).
According to Rule 9 of the Bacteriologocal Code (1990 Revision) [2], the name of a taxon between genus and class is formed by the addition of an appropriate suffix to the stem of the name of the type genus. In 1997, E. Stackebrandt et al. [3] proposed suffixes to denote classes and subclasses.
The suffixes and the number of names published in the Approved Lists of Bacterial Names and in the International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology (IJSB/IJSEM) are provided in the following table.
|
Taxonomic rank |
Suffixe [reference] |
Number of names published in the Approved Lists of Bacterial Names and in the IJSB/IJSEM |
| Subtribe | -inae [2] |
0 |
| Tribe* | -eae [2] |
24 |
| Subfamily | -oideae [2] |
0 |
| Family | -aceae [2] |
231 |
| Suborder | -ineae [2] |
17 |
| Order | -ales [2] |
104 |
| Subclass | Proposed suffix -idae [3] |
6 |
| Class | Proposed suffix -ia [3] |
66 |
| Division or phylum** | - |
24 + 4*** |
| Domain or empire** | - |
2 |
* Taxonomic category not in current use.
** Taxonomic category not covered by the Rules.
*** Four phyla not cited in the IJSB/IJSEM.
In contrast to prokaryotic nomenclature, there is no such thing as an official classification of prokaryotes because taxonomy remains a matter of scientific judgment and general agreement [4].
The closest approximation to an "official" classification of prokaryotes would be one that is widely accepted by the community of microbiologists [5].
The most widely accepted classification is the "Taxonomic Outline of the Prokaryotes" initiated in the early 1990s in the editorial office of Bergey's Manual Trust as a preliminary step in organizing the content of the second edition of Bergey's Manual of Systematic Bacteriology.
The latest "Taxonomic Outline", now known as "Taxonomic Outline of the Bacteria and Archaea" (TOBA) [11]" (current through the September 2006 issue of the IJSEM), and older archive versions [6, 7, 8, 9, 10] of the document are available online.
The files Classification of genera: List A - C, Classification of genera: List D - L, Classification of genera: List M - R, Classification of genera: List S - Z, List of genera included in families, List of genera included in orders, List of genera included in suborders, Classification of families, List of families included in suborders, List of families included in orders, Classification of suborders, Classification of orders, List of orders and suborders included in classes, List of orders and suborders included in subclasses, Classification of classes, Classification of subclasses, and Classification of domains and phyla - Hierarchical classification of prokaryotes present a hierachical classification of taxa.
The data have been drawn up after the original publications, and/or the latest "Taxonomic Outline of the Bacteria and Archaea" [11], and /or the "NCBI Taxonomy Browser" [12]. Of course, this classification is subject to revision following examination of large-scale phylogenetic models.
It is very difficult to avoid unintentional errors and the author would greatly appreciate factual information concerning any errors or corrections for these lists.
References:
1. Von LINNÉ (C.): Systema naturae per regna tria naturae. Online pdf version of this classic work, Gallica, la bibliothèque numérique de la Bibliothèque Nationale de France: Tomus I, Pars I; Tomus I, Pars II; Tomus II; Tomus III).
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.
3. STACKEBRANDT (E.), RAINEY (F.A.) and WARD-RAINEY (N.L.): Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol., 1997, 47, 479-491.
4. SNEATH (P.H.A.) and BRENNER (D.J.): "Official" nomenclature lists. ASM News, 1992, 58, 175. Available on the Internet
5. STALEY (J.T.) and KRIEG (N.R.): Classification of procaryotic organisms: an overview. In: N.R. KRIEG and J.G. HOLT (ed.): Bergey's Manual of Systematic Bacteriology, vol. 1, 1984, The Williams & Wilkins Co., Baltimore, pp. 1-4.
6. GARRITY (G.M.), WINTERS (M.), KUO (A.W.) and SEARLES (D.B.). (2001). Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition., Release 1.0., Springer-Verlag, New York. 320 pages. DOI: 10.1007/bergeysoutline.
http://141.150.157.80/bergeysoutline/main.htm
7. GARRITY (G.M.), WINTERS (M.), KUO (A.W.) and SEARLES (D.B.). (2002). Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition., Release 2.0., Springer-Verlag, New York. 350 pages. DOI: 10.1007/bergeysoutline.
http://141.150.157.80/bergeysoutline/main.htm
8. GARRITY (G.M.), JOHNSON (K.L.), BELL (J.A.) and SEARLES (D.B.). (2002). Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition., Release 3.0., Springer-Verlag, New York. 365 pages. DOI: 10.1007/bergeysoutline200210.
http://141.150.157.80/bergeysoutline/main.htm
9. GARRITY (G.M.), BELL (J.A.) and LILBURN (T.G.). (2003) Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition., Release 4.0., Springer-Verlag, New York. 397 pages. DOI: 10.1007/bergeysoutline200310.
http://141.150.157.80/bergeysoutline/main.htm
10. GARRITY (G.M.), BELL (J.A.) and LILBURN (T.G.). (2004) Taxonomic Outline of the Procaryotes. Bergey's Manual of Systematic Bacteriology, Second Edition., Release 5.0., Springer-Verlag, New York. 401 pages. DOI: 10.1007/bergeysoutline200405.
http://141.150.157.80/bergeysoutline/main.htm
11. Garrity (G.M.), Lilburn (T.G.), Cole (J.R.), Harrison (S.H.), EuzÉby (J.) and Tindall (B.J.): Taxonomic Outline of the Bacteria and Archaea, Release 7.7. Michigan State University Board of Trustees. DOI: 10.1601/TOBA7.7.
http://www.taxonomicoutline.org
12. NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION: NCBI Taxonomy Browser - Credits: Mikhail Domrachev, Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov, Richard Sternberg, Sean Turner.
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Root
See also the following files:
. Classification of domains and phyla - Hierarchical classification of prokaryotes
. Classification of genera List A - C, List D - L, List M - R, List S - Z - List of genera included in families - List of genera included in orders - List of genera included in suborders
. Classification of families - List of families included in suborders - List of families included in orders
. Classification of suborders - Classification of orders - List of orders and suborders included in classes - List of orders and suborders included in subclasses
. Classification of classes - Classification of subclasses
. Classification of Cyanobacteria
. Introduction à la taxonomie des procaryotes (In French)
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