Chlamydophila

Chlamydophila is a controversial bacterial genus belonging to the family Chlamydiaceae.[2]

Chlamydophila
Chlamydophila psittaci
Scientific classification
Domain: Bacteria
Phylum: Chlamydiota
Class: Chlamydiia
Order: Chlamydiales
Family: Chlamydiaceae
Genus: Chlamydophila
Everett, Bush & Andersen 1999
Type species
Chlamydophila psittaci
(Lillie 1930) Everett, Bush & Andersen 1999
Species[1]
Synonyms
  • "Microbacterium" Levinthal 1930 non Orla-Jensen 1919

Taxonomy
See also: Chlamydia psittaci § Taxonomy

All Chlamydiota are anaerobic bacteria with a biphasic developmental lifecycle that depends on obligately intracellular growth in eukaryotic host cells.

Chlamydophila was recognized by a number of scientists in 1999,[3] with six species in Chlamydophila and three in the original genus, Chlamydia. This was immediately seen as controversial.[4] In 2015 the Chlamydophila species were reclassified as Chlamydia.[4] The history of the classification and reclassification is as follows.

Earlier criteria for differentiation of chlamydial species did not always work well. For example, at that time genus C. psittaci was distinguished from C. trachomatis by sulfadiazine resistance, although not all strains identified as C. psittaci at the time were resistant, and C. pneumoniae was classified by its appearance under electron microscopy (EM) and its ability to infect humans, although the EM appearance may differ from one research group to the next, and many of these species infected humans.

The systematic taxonomy established for Chlamydiota (formerly Chlamydiae) in 1999 used DNA-DNA reassociation, 16S and 23S ribosomal RNA gene similarity, sequence similarity clustering of protein coding genes, and genome size as criteria for classification. Supporting criteria such as antigen detection,[5] glycogen staining, host association, and EM morphology were also employed, depending on applicability and availability.

Comparative genomic analyses in 2006 identified a number of signature proteins that were uniquely present in species from the genera Chlamydia and Chlamydophila, which supported the distinctness of Chlamydophila.[6] This view was challenged three years later by newer whole genome analysis techniques leading to a proposal to "reunite the Chlamydiaceae into a single genus, Chlamydia".[7] By the 2010s this reclassification "was not wholly accepted or adopted"[8] among microbiologists, which "resulted in a reversion to the single, original genus Chlamydia, which now encompasses all 9 species including Chlamydia psittaci."[8] As of 2013, Chlamydophila was still mentioned in some databases, but controversial.[9] The merger of the genus Chlamydophila back into the genus Chlamydia is now generally accepted.[10][11][12][13]

Chlamydophila differentiation

According to the authors of the 1999 study, the mean DNA-DNA reassociation difference distinguishing Chlamydophila from Chlamydia is 10.1%, an accepted value for genus separation. Although the 16S ribosomal RNA gene sequences of the two are close to 95% identical, unlike the other previously established genera, the authors considered a less than 95% similarity only a guideline for establishing new genera in chlamydial families. In the study, the authors used the similarity of the locations of coding for protein and ribosomal RNA genes in the genome (gene clusters) to help distinguish Chlamydophila from Chlamydia. Also, the full-length 23S ribosomal RNA genes of the species of the two genera were less than 95% identical.

Some Molecular Criteria Distinguishing Chlamydiaceae Genera
GenusApproximate Genome Size (million DNA base pairs)Detectable GlycogenNumber of Ribosomal Operons
Chlamydophila 1.2No1
Chlamydia 1.0Yes2

Phylogeny
16S rRNA based LTP_01_2022[14][15][16] 120 marker proteins based GTDB 07-RS207[17][18][19]
 
 

Chlamydophila pneumoniae

 
 
 
 

Chlamydophila pecorum

 
 

Chlamydia

 
 
Chlamydophila
 

C. felis

 
 
 
 

C. caviae

 
 

Chlamydia poikilotherma Staub et al. 2022

 
 
 
 
 

Chlamydia avium

 
 

Chlamydia gallinacea

 
 
 
 

C. abortus

 
 

C. psittaci

 
 
 
 
 
 
 
 
 
 

C. pecorum (Fukushi and Hirai 1992) Everett et al. 1999

 
 
 

"Ca. Chlamydia coralla" corrig. Taylor-Brown et al. 2017

 
 

C. pneumoniae (Grayston et al. 1989) Everett et al. 1999

 
 
 
 
 

"Chlamydia ibidis" Vorimore et al. 2013

 
 
 
 

Chlamydia avium Sachse et al. 2015

 
 

Chlamydia gallinacea Sachse et al. 2015

 
 
 
 

C. felis Everett et al. 1999

 
 
 

C. caviae Everett et al. 1999

 
 
 

"Chlamydia buteonis" Laroucau et al. 2019

 
 
 

C. abortus Everett et al. 1999

 
 

C. psittaci (Lillie 1930) Everett et al. 1999

 
 
 
 
 
 
 
 

See also

References
  1. J.P. Euzéby. "Chlamydophila". List of Prokaryotic names with Standing in Nomenclature. Retrieved 2011-06-11.
  2. Chlamydophila at the US National Library of Medicine Medical Subject Headings (MeSH)
  3. Everett KD, Bush RM, Andersen AA (April 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 Bacteriology. 49 Pt 2 (2): 415–40. doi:10.1099/00207713-49-2-415. PMID 10319462.
  4. Parte, A.C. "Chlamydia". LPSN.
  5. Bush RM, Everett KD (January 2001). "Molecular evolution of the Chlamydiaceae". International Journal of Systematic and Evolutionary Microbiology. 51 (Pt 1): 203–20. doi:10.1099/00207713-51-1-203. PMID 11211261.
  6. Griffiths E, Ventresca MS, Gupta RS (January 2006). "BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species". BMC Genomics. 7: 14. doi:10.1186/1471-2164-7-14. PMC 1403754. PMID 16436211.
  7. Stephens RS, Myers G, Eppinger M, Bavoil PM (March 2009). "Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved". FEMS Immunology and Medical Microbiology. 55 (2): 115–9. doi:10.1111/j.1574-695X.2008.00516.x. PMID 19281563.
  8. Balsamo G, Maxted AM, Midla JW, Murphy JM, Wohrle R, Edling TM, et al. (September 2017). "Compendium of Measures to Control Chlamydia psittaci Infection Among Humans (Psittacosis) and Pet Birds (Avian Chlamydiosis), 2017". Journal of Avian Medicine and Surgery. 31 (3): 262–282. doi:10.1647/217-265. PMID 28891690.
  9. "Chlamydia/Chlamydophila group". NCBI taxonomy database. National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2013-03-26. Given the contentious nature of the issue, the NCBI Taxonomy Database retains both genus names for use by submitters.
  10. Bavoil P, Kaltenboeck B, Greub G (March 2013). "In Chlamydia veritas". Pathogens and Disease. 67 (2): 89–90. doi:10.1111/2049-632X.12026. PMID 23620152.
  11. Bachmann NL, Polkinghorne A, Timms P (August 2014). "Chlamydia genomics: providing novel insights into chlamydial biology". Trends in Microbiology. 22 (8): 464–72. doi:10.1016/j.tim.2014.04.013. PMID 24882432.
  12. Sachse K, Bavoil PM, Kaltenboeck B, Stephens RS, Kuo CC, Rosselló-Móra R, Horn M (March 2015). "Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species". Systematic and Applied Microbiology. 38 (2): 99–103. doi:10.1016/j.syapm.2014.12.004. hdl:10261/123714. PMID 25618261.
  13. Borel N, Polkinghorne A, Pospischil A (May 2018). "A Review on Chlamydial Diseases in Animals: Still a Challenge for Pathologists?". Veterinary Pathology. 55 (3): 374–390. doi:10.1177/0300985817751218. PMID 29310550.
  14. "The LTP". Retrieved 23 February 2022.
  15. "LTP_all tree in newick format". Retrieved 23 February 2022.
  16. "LTP_01_2022 Release Notes" (PDF). Retrieved 23 February 2022.
  17. "GTDB release 07-RS207". Genome Taxonomy Database. Retrieved 20 June 2022.
  18. "bac120_r207.sp_labels". Genome Taxonomy Database. Retrieved 20 June 2022.
  19. "Taxon History". Genome Taxonomy Database. Retrieved 20 June 2022.
  • Chlamydophila genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID
  • Taxonomic Outline of the Procaryotes, Bergey's Manual of Systematic Bacteriology, Second Edition Release 1.0, April c.
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