|Class:||Chlamydiae Cavalier-Smith 2002|
|Order:||Chlamydiales Storz and Page 1971 emend. Everett et al. 1999|
Chlamydiae is a bacterial phylum and class whose members are obligate intracellular pathogens. Many chlamydiae coexist in an asymptomatic state within specific hosts, and it is widely believed that these hosts provide a natural reservoir for these species.
All known chlamydiae only grow by infecting eukaryotic host cells. They are as small or smaller than many viruses. Chlamydiae replicate inside the host cells and are termed intracellular. Most intracellular chlamydiae are located in an inclusion body or vacuole. Outside of cells they survive only as an extracellular infectious form. Chlamydiae can grow only where their host cells grow. Therefore, chlamydiae cannot be propagated in bacterial culture media in the clinical laboratory. Chlamydiae are most successfully isolated while still inside their host cell.
Chlamydia-like disease affecting the eyes of people was first described in ancient Chinese and Egyptian manuscripts. A modern description of chlamydia-like organisms was provided by Halberstaedrrter and von Prowazek in 1907. Chlamydial isolates cultured in the yolk sacs of embryonating eggs were obtained from a human pneumonitis outbreak in the late 1920s and early 1930s, and by the mid-20th Century isolates had been obtained from dozens of vertebrate species. The term 'chlamydia' (a cloak) appeared in the literature in 1945, although other names continued to be used, including Bedsonia, Miyagawanella, ornithosis-, TRIC-, and PLT-agents.
In 1966, chlamydiae were recognized as bacteria and the genus Chlamydia was validated. The Order Chlamydiales was created by Storz and Page in 1971. Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae was established in Bergey's Manual of Systematic Bacteriology.
By 2006, genetic data for over 350 chlamydial lineages had been reported, four chlamydial families had been recognized (Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, and Waddliaceae), and another family had been proposed (Rhabdochlamydiaceae).
Chlamydiae is a unique bacterial evolutionary group that separated from other bacteria approximately a billion years ago. The species from this group can be distinguished from all other bacteria by the presence of conserved indels in a number of proteins such as RNA polymerase alpha subunit, Gyrase B, Elongation factor-Tu and Elongation factor-P, and by large numbers of signature proteins that are uniquely present in different chlamydiae species. Reports have varied as to whether Chlamydiae is related to Planctomycetales or Spirochaetes. Genome sequencing, however, indicates that 11% of the genes in Candidatus Protochlamydia amoebophila UWE25 and 4% in Chlamydiaceae are most similar to chloroplast, plant, and cyanobacterial genes. However, phylogeny and shared presence of conserved indels in proteins such as RNA polymerase Beta subunit and lysyl-tRNA synthetase indicate that Verrucomicrobia are the closest free-living relatives of these parasitic organisms. Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiae. The unique status of Chlamydiae has enabled the use of DNA analysis for chlamydial diagnostics.
There are three described species of chlamydiae that commonly infect humans:
- Chlamydia trachomatis, which causes the eye-disease trachoma and the sexually transmitted infection chlamydia;
- Chlamydia pneumoniae, which causes a form of pneumonia;
- Chlamydia psittaci, which causes psittacosis.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)  and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project 
♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN) ♥ Strains not lodged at National Center for Biotechnology Information (NCBI) and or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
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- Griffiths E, Petrich AK, Gupta RS (August 2005). "Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification". Microbiology (Reading, Engl.) 151 (Pt 8): 2647–57. doi:10.1099/mic.0.28057-0. PMID 16079343.
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- Ward N, Rainey F, Hedlund B, Staley J, Ludwig W, Stackebrandt E (2000). "Comparative phylogenetic analyses of members of the order Planctomycetales and the division Verrucomicrobia: 23S rRNA gene sequence analysis supports the 16S rRNA gene sequence-derived phylogeny". Int J Syst Evol Microbiol 50 (6): 1965–72. doi:10.1099/00207713-50-6-1965. PMID 11155969.
- Teeling H, Lombardot T, Bauer M, Ludwig W, Glöckner F (2004). "Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees". Int J Syst Evol Microbiol 54 (Pt 3): 791–801. doi:10.1099/ijs.0.02913-0. PMID 15143026.
- Griffiths E, Gupta RS (August 2007). "Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae". Microbiology (Reading, Engl.) 153 (Pt 8): 2648–54. doi:10.1099/mic.0.2007/009118-0. PMID 17660429.
- Corsaro D, Greub G (2006). "Pathogenic Potential of Novel Chlamydiae and Diagnostic Approaches to Infections Due to These Obligate Intracellular Bacteria". Clin Microbiol Rev 19 (2): 283–97. doi:10.1128/CMR.19.2.283-297.2006. PMC 1471994. PMID 16614250.
- See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from the "Chlamydiae". Retrieved 2013-03-20.
- See the All-Species Living Tree Project . Data extracted from the "16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.
- Chlamydiae.com, a comprehensive information source from Dr. Michael Ward (Professor of Medical Microbiology in the University of Southampton)