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Chlamydial taxonomy since 1999

Dr Karin D Everett

Introduction

Since the last major reclassification of the Chlamydiales [Everett et al., 1999] and Dr Everett's previous presentation on this site, a lot of new chlamydial species have been proposed with varying degrees of validity. Some of the rules of bacterial taxonomy have also changed. I therefore invited Dr Karin Everett, lead author of the 1999 classification, to contribute her thoughts on chlamydial taxonomy post 1999. The result was an extensive and thoughtful overview which is interesting and which sharply delineates some of the current dilemmas. The following, adapted to the web, are Karin's notes.

[MEW] April 2008.

Chlamydial species described since 1999

As at March 2008, the following new chlamydial agents have been described since 1999:

* footnote: no name for these symbionts was proposed, but they are so intriguing that they have been included in this table

Most of these publications were quite well done.  Based on the rules in place in 1999, only 4 of them could be fully valid species: Candidatus Protochlamydia amoebophila, Neochlamydia hartmannellae, Waddlia malaysiensis, and Criblamydia sequanensis.  This is because these are isolates and can be deposited in culture collections.  Indeed, both P. amoebophila and N. hartmannellae were deposited in ATCC, so under 1999 rules should be full-fledged species.  Nearly all chlamydial species are deposited in the ATCC collection only, which is a problem under the new taxonomic rules, see below.

Rule changes and associated events since 1999.

Following the 1999 reclassification, an unfortunate sequence of events (for chlamydial taxonomy) occurred.

• 1999 August: Bacteriological Code Rules modified by Judicial Commission. It required new species to be deposited in a minimum of 2 culture collections in a minimum of 2 countries.
   
• 2000 May: Neochlamydia hartmannellae gen. nov., sp. nov. proposal in the journal Microbiology
   
• 2000 December: ICSB (ICSP) votes in favour of the Rule changes.
   
• 2001 January: Rule change takes effect. To be valid all subsequent new species must be deposited in 2 culture collections in 2 different countries.
   
• 2001 July: Neochlamydia appears in IJSEM Validation list 81
   
• 2004 January: Euzeby & Tindall (2004) write that Neochlamydia must be deposited in 2 culture collections to be valid because it was validated after August 1999 (206 other species must also be fixed).
   
• 2005 September: Protochlamydia amoebophila published as 'Candidatus'; IJSEM editor Peter Kämpfer argues that it must be 'Candidatus' because it has only been deposited in one culture collection and because it was based 'only' on the genome sequence. Nevertheless Neochlamydia hartmanella is cited without a quarrel by IJSEM.

Publishing requirements for a fully validated new species

• There must be a formal description paragraph (protologue) for the new species
   
• Deposit in 2 publicly accessible culture collections in different countries
   
• Meet all requirements posted at http://ijs.sgmjournals.org/misc/ifora.shtml
   
• Publication of the name in IJSEM
  *In IJSEM, publication of full manuscripts for new species are immediately valid and appear in the IJSEM 'Notification lists'
  *IJSEM has special status. In other journals the quality of publication must be such that the new name can be reproduced in an IJSEM Validation List. However only one chlamydial species has ever been validly published outside of IJSEM (Neochlamydia gen. nov. and Neochlamydia harmannellae sp. nov., Microbiology May 2000). This genus and species were formally validated when they appeared in Validation List 81 in IJSEM in July 2001.

The 2 culture collection in 2 countries requirement means that, in practice, there will never be a fully validated new chlamydial species or family until the rules change or until chlamydiologists can find a culture collection outside the ATCC and the US, which will be prepared to accept and distribute chlamydiae. This is not only a chlamydial problem.  There are, for example, over 200 Candidatus Rickettsia species in PubMed. 

When the term Candidatus was developed in the 1990’s, it was intended only to facilitate the organization of new, uncultivated organisms.  Systematic taxonomists have long mistaken the differences between  ‘unculturable,’ ‘cultivated,’ ‘not isolated,’ ‘intracellular,’ and ‘not alive.’ According to Euzéby's website (a key web source of validated species lists), a name included in the category Candidatus cannot be validly published, and cannot be designated sp. nov., gen. nov., etc. because the category Candidatus is not covered by the Rules of the Bacteriological Code. Paradoxically the same site later reports that the Judicial Commission decided that the concept of "Candidatus" should be mentioned in the main section of the Bacteriological Code, despite the fact that "such names have no standing in nomenclature", see also De Vos et al., 2005. The situation is therefore unclear.

What is clear is that the IJSEM is the major journal from the viewpoint of validating a new prokaryotic taxon.

Publishing Requirements for Candidatus Species.

In IJSEM, publication of full manuscripts for new Candidatus species are immediately valid and appear in the IJSEM ‘Notification Lists’.  For Candidatus status:

•           A formal description paragraph is necessary
•           No deposit of a species or strain in a culture collection is required.
•           Publication requirements are flexible, but generally resemble those on http://ijs.sgmjournals.org/misc/ifora.shtml
•           The new name appears in an IJSEM Notification List.

In other journals:

•           Chlamydial Candidatus species published outside of IJSEM have never been validated by reproduction in IJSEM Validation Lists.
•           No formal description process exists, although responsible editors and reviewers emulate the IJSEM requirements.
•           No formal validation process for these species currently exists.

With essentially no validation process in place for chlamydiae named outside of IJSEM, few names published outside of IJSEM will be retained in the historical literature.

Other categories

Criteria for near-Chlamydiae relatives

It is debatable whether there is or is not a relationship between Planctomycetes, Verrucomicrobia and Chlamydiae.  The opinion of Ward  et al., 2000 differs from that of Griffiths & Gupta, 2007.  See also Wagner & Horn 2006, and Pilhofer  et al., 2008.  Naomi Ward is the Craig-Ventner Institute's point person on the Verrucomicrobium genome sequence, which project should help to sort the issue out in the next few years. [See comment 4 below].

Creation of the class Chlamydiae

Cavalier-Smith, volume 52, part 1 IJSEM 2002.  In 1987, C-S created the division Planctobacteria  divisio nov.  In 1997, Hedlund created Verrucomicrobia div. nov.  In 2002, C-S moved Verrucomicrobia down to the status of a class in the Planctobacteria division.  At the same time, C-S created two additional classes in this division:  Planctomyceae classis nov. and Chlamydiae classis nov.  C-S had one single reason for this:  his speculation that the three groups had protein-based cell walls due to their evolutionary closeness.  However, he presented no evidence to support this.

Creation of the Order Chlamydiales

Storz J & Page LA, 1971. Taxonomy of the chlamydiae:  reasons for classifying organisms of the genus Chlamydia family Chlamydiaceae in a separate order, Chlamydiales ord. nov. IJSB 21, 332-334.

Creation of the Family Chlamydiaceae

Rake GW, 1957 Family II. Chlamydiaceae Rake, Fam. Nov. In Bergey’s Manual of Systematic Bacteriology, 7th edn. Pp 957-968.  Ed. RS Breed, EGD Murray, NR Smith.  Baltimore: Williams & Wilkin

Creation of the Families Parachlamydiaceae, Simkaniaceae and Waddliaceae

Each of these families is a genetically coherent group of obligately intracellular bacteria that has a chlamydia-like developmental cycle of replication.  This cycle includes infectious EBs and metabolically active RBs.  The sizes of these EBs and RBs are comparable to those of Chlamydiaceae.  The bacteria undergo binary fission in inclusions within eukaryotic cells.  Distinct phenotypic and genotypic differences among the 4 Chlamydiales families have been  reported in prestigious scientific journals, and include 16S and 23S rRNA sequence data [Everett et al., 1999; Rurangirwa et al., 1999].

Minimum Criteria for a New Family in any Order

There must be a validly proposed species (i.e. not just Candidatus).

Validation of a Species:  is it important?

Yes.  In 1980 all invalid species were discarded (thousands of prior species).  Only those chosen were retained.  Today there are 3 reasons to force bacteria into the category Candidatus:  (1) not cultivated or isolated, (2) not properly described, (3) not deposited in 2 culture collections in 2 countries.  It seems wrong for whole lineages to be essentially invalidated by making them 'Candidatus' because of reason 3.

The Rules of the Bacteriological Code governing the deposit of type strains in culture collections were modified on 14 August 1999 by the Judicial Commission (De Vos & Trüper, 2000).  The International Committee on Systematic Bacteriology (ICSB now ICSP) voted unanimously in favour of these changes (Labeda, 2000).  The revised Rules 27(3) and 30 took effect 1 January 2001.

In 2004, IJSEM published the names of 207 species that were deemed not to be in accordance with the revised Rules 27(3) and 30.   Solutions whereby they might be validly published were described [Euzéby and Tindall, 2004].

[KDE] April 2008

Comment

1. The statement in Euzéby's list as at March 2008 that Candidatus is not covered by the rules of the bacteriological code is puzzling, as the Judicial Commission is later reported [De Vos et al., 2005] as having decided on 29 July 2002 to adopt 'Candidatus' in the main body of the Bacteriological Code. I asked Dr Everett to explain this paradox. She replied:  "These words are not mine.  The words ....  come directly from ........ J.P. Euzéby's website. It says these things, and so chances are these are right.  J.P. Euzéby probably attended all the meetings and committees that are listed.  But things have to be published in IJSEM, and I don't know what to think about the discrepancy in his comments.  He lists in this page 'All names proposed in the IJSB/IJSEM and some names proposed outside the IJSB/IJSEM'.  You'll find some familiar 'Candidatus' names there.  But this doesn't make them 'valid'."

2. As the rules stand, 'Candidatus' species can not be used as the basis for establishing new chlamydial families, even though, for example, the Piscichlamydia, the Rhabdochlamydia and the Criblamydia probably belong to new families. Unless: (i) new chlamydial species can be cultivated and; (ii) a second publicly accessible culture collection, outside the USA, willing to distribute chlamydiae can be identified, it looks as if we are going to be stuck with the present classification for a long time.

3. A multi locus typing scheme was recently developed based on seven housekeeping genes of members of the Chlamydiales selected as being: widely separated on the chlamydial chromosome; not adjacent to putative outer membrane, secreted or hypothetical proteins that might be under diversifying selection; and with a similar extent of nucleotide substitutions.  The authors found that C. trachomatis and C. pneumoniae are highly uniform. The difference in genetic diversity between C. trachomatis and C. pneumoniae is in concordance with a later assimilation to the human host of the latter. They concluded their data supported the taxonomy of the order Chlamydiales. See: Pannekoek et al., 2008.

4. In terms of recent understanding of near-chlamydia relatives, Wagner & Horn 2006 include the Chlamydiae in a superphylum along with Planctomyces, Verrucomicrobia, Lentispherae, Poribacteria and OP3. Although the bootstrap evidence for this is comparatively weak, it is pointed out that many members of the superphylum live in close association with eukaryotes and for at least two phyla (Chlamydia and Poribacteria) no free-living members have been described. Most members of the superphylum (except Kuenenia stuttgartiensis) share characteristic nucleotide transporter genes. The Chlamydiae and Planctomycetes lack the bacterial tubulin homologue FtsZ, which is found in almost all other bacterial groups and the Euryarchaeota. However cell division is probably FtsZ-based in the Lentispherae and the Verrucomicrobia [Pilhofer et al., 2008]. Eukaryotic genes are characteristically present in many members of the superphylum, probably as a result of lateral gene transfer due to their close association with eukaryotes. However, neither Planctomycetes nor Chlamydiae are at the root of the bacterial tree. Comprehensive sequence analyses of available genome data of representatives of Verrucomicrobia, Lentisphaerae, Chlamydiae and Planctomycetes strongly indicate that their last common ancestor possessed a conserved, ancestral type of dcw gene cluster and an FtsZ-based cell division mechanism. This implies that Planctomycetes and Chlamydiae may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with Verrucomicrobia [Pilhofer et al., 2008].

[MEW] April 2008

NEXT Chlamydiaceae

References

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Collingro, A., Toenshoff, E. R., Taylor, M. W., Fritsche, T. R., Wagner, M. & Horn, M. (2006). Candidatus Protochlamydia amoebophila', an endosymbiont of Acanthamoeba spp.  Int J Syst Evol Microbiol. 2005 Sep;55(Pt 5):1863-6. Full paper .

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Draghi, A. 2nd., Bebak J., Popov, V. L., Noble, A. C., Geary, S. J., West, A. B., Byrne, P. & Frasca, S Jr. (2007). Characterization of a Neochlamydia-like bacterium associated with epitheliocystis in cultured Arctic charr Salvelinus alpinus. Diseases of aquatic organisms 76(1), 27 - 38.

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Everett, K. D. E., Bush, R. M. & Andersen, A. A. (1999). Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. International Journal of Systematic and Evolutionary Bacteriology 49, 415 - 440.   Full paper  

Everett KDE, Thao M, Horn M, Dyszynski, G. E. & Baumann, P. (2005). Novel chlamydiae in whiteflies and scale insects: endosymbionts 'Candidatus Fritschea bemisiae' strain Falk and 'Candidatus Fritschea eriococci' strain Elm. Int. J. Syst. Evol. Microbiol. 55 (Pt 4), 1581-1587.

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[KDE] March 2008.