Naming bacterial species

and 16S rRNA gene sequences for type strains

Naming bacteria

Back to Identification of micro-organisms
See also the following articles :

Introduction   usefull web sites   Candidatus   Precisions by Euzeby   16S sequences

Introduction.

With the use of molecular methods, the identification of micro-organisms (bacteria, archea, virus, fungi and all kinds of protists) has seen a revolution, in particular with the help of phylogenetic analyses of ubiquitous genes (often the SSU rRNA gene sequences).
This revolution was particularly helpful for Bacteria (and Archea), since an international body checks and publish valid names, ensuring that the same organisms is not published twice under different names (an awful situation often encountered for fungi !) and that the name's spelling is correct (according to the "rules).
Nevertheless, the situation is not always clear :
What should be known :
Since January 1980, priority is assessed according to the "APPROVED LISTS OF BACTERIAL NAMES" (Skerman et al., 1980). Presently this list contains about 2 000 described species (see Euzeby site and also a condensed list). However, not every culture collection follows strictly the rule (see this list).
My own experience after ordering hundreds of type strain from a major collection (ATCC) showed that a few percent of their strains are in fact contaminants. Do sequence the 16S rRNA gene and use a phylogenetic analysis to make sure you got the proper species before running serious work on it.

Names which are not in this list are not validly approved names, however these strains may be in collections (Pasteur, DSMZ, ATCC, ...) and be widely used in important industrial applications. Simply, nobody took the burden to describe them approprietly !

Updates of this list are published in the  "INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY" (IJSEM),  by validation of descriptions published in the same journal or elsewhere.
Jean Euzeby  extracts from these lists all new names, combinations or modifications and publishes everything as a web site. This is an enormous work that allows every microbiologist to easily know the current names without having to go to IJSEM and find out in which issue is the final change !
Alternatively you may go to the  DSMZ  or the "collection Pasteur" and of course ATCC. BUT : you should know that their web pages are much less precise than the work of J Euzeby (not up to date, many errors...).
I have collected the abstracts of IJSEM and extracted titles and accession numbers (see top of this page). In preparation : a page with direct access to the 16S rRNA gene sequence for every validly published Bacteria.

Non valid names you be spelled with "" (i.e. "Genus name") but this rule is very rarely in effect aside from bacterial taxonomy publications.

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Some reference web sites for bacterial taxonomy.

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See also :
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Why not ?

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See also :

The "candidatus".

In 1994, Murray et Schleifer proposed for organisms not yet properly described (see Euzeby's comments).
It concerns mostly bacteria known only from their sequences, or species that have been unstable in culture and therefore lost after their description.
The point of view of the bioinformatician.
This naming in the form  "Candidatus Genus species" is really a mess. It does not follow the Linean rule, and renders parsing of files very difficult. I wonder why the description as Candidatus was not simply included in the fields that allow description of the taxonomy in the EMBL/GenBank entries ?

Euzeby's precisions (translated by me, sorry for possible errors).

There are no "valid species", only bacterial species that have been validly described.

The code of nomenclature only keeps the concept of species validly published and more generaly that of taxa validly published.
For taxa published before 1980 January 1rst, a taxon is valid if cited in the Approved Lists of Bacterial Names. It is important to note that these Lists are a record of the situation at this date, and that they are closed: no new name can be added to these Lists.
There are two lists of approved names : a first list for taxa above the genus rank and a list for the Genus name denominations.

For taxa published afterwards, the naming is valid if published in extenso in IJSEM (previously IJSB) or if published elsewhere if validated in a special section of tis journal.

Validation rules .

Priority rules are in fact more complex than described above  (see a more complete description, in french  in "Date de validation et priorité de publication" : http://www.bacterio.cict.fr/bacdico/systematique/nomenclature.html.)
see also:
More informations available also in "Glossaire de nomenclature bactérienne" (http://www.bacterio.cict.fr/bacdico/glossaire.html). Both in French.
Finally see Euzeby's page on why many described species are not valid (but often used).

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Richard Christen. June 2006.