Classification, taxonomy and systematics of prokaryotes (bacteria): Introduction
See also the following files:
- Classification of domains and phyla - Hierarchical classification of prokaryotes
- Classification of Cyanobacteria
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).
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 file Number of published names.
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 are provided in the following table.
| Taxonomic rank | Suffix [reference] |
| Subtribe* | -inae [2] |
| Tribe* | -eae [2] |
| Subfamily* | -oideae [2] |
| Family | -aceae [2] |
| Suborder | -ineae [2] |
| Order | -ales [2] |
| Subclass | Proposed suffix -idae [3] |
| Class | Proposed suffix -ia [3] |
| Division or phylum** | - |
| Domain or empire** | - |
*Taxonomic category not in current use.
**Taxonomic category not covered by the Rules.
In contrast to eukaryotic 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 file 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], and/or Taxonomic Outlines for Volumes 3 and 4 of Bergey's Manual of Systematic Bacteriology (Second Edition) [13, 14], and/or "The All-Species Living Tree Project" [15]. 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 (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.
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.
http://dx.doi.org/10.1099/00207713-47-2-479
4. SNEATH (P.H.A.) and BRENNER (D.J.): "Official" nomenclature lists. ASM News, 1992, 58, 175.
Sneath-Brenner.html
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.
http://www.bergeys.org/outlines/bergeysoutline_1_2001.pdf
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.
http://www.bergeys.org/outlines/bergeysoutline_2_2002.pdf
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.
http://www.bergeys.org/outlines/bergeysoutline_3_2002.pdf
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.
http://www.bergeys.org/outlines/bergeysoutline_4_2003.pdf
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.
http://www.bergeys.org/outlines/bergeysoutline_5_2004.pdf
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://dx.doi.org/10.1601/TOBA7.7
12. NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION: NCBI Taxonomy Browser - Credits: Mikhail Domrachev, Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov, Richard Sternberg, Sean Turner.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Root
13. LUDWIG (W.), SCHLEIFER (K.H.) and WHITMAN (W.B.): Taxonomic outline of the phylum Firmicutes.
http://www.bergeys.org/outlines/Bergeys_Vol_3_Outline.pdf
14. LUDWIG (W.), EUZÉBY (J.) and WHITMAN (W.B.): Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes.
http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf
15. YARZA (P.), RICHTER (M.), PEPLIES (J.), EUZEBY (J.), AMANN (R.), SCHLEIFER (K.H.), LUDWIG (W.), GLÖCKNER (F.O.) and ROSSELLÓ-MÓRA (R.): The All-Species Living Tree Project.
https://www.arb-silva.de/projects/living-tree/
See also the following files:
