TheChlamydiota (synonymChlamydiae) are abacterialphylum andclass whose members are remarkably diverse, includingpathogens of humans and animals,symbionts of ubiquitousprotozoa,[4] and marine sediment forms not yet well understood.[5] All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all havehosts.[5]
Among the Chlamydiota, all of the ones long known to science grow only by infectingeukaryotic host cells. They are as small as or smaller than manyviruses. They are ovoid in shape and stainGram-negative. They are dependent on replication inside the host cells; thus, some species are termed obligateintracellular pathogens and others are symbionts of ubiquitous protozoa. Most intracellular Chlamydiota are located in aninclusion body orvacuole; when growing in a cell, they survive in a metabolically active but noninfectious form called the reticulate body. Outside cells, they survive only as an infectious, spore-like form called the elementary body.
These Chlamydiota can grow only where their host cells grow, and develop according to a characteristic biphasic developmental cycle.[6][7][8] Therefore,clinically relevant Chlamydiotacannot be propagated in bacterial culture media in the clinical laboratory. They are most successfully isolated while still inside their host cells.
In 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all havehosts.[5]
Scientists have long known that Chlamydiota are susceptible to antibiotics that target the production ofpeptidoglycan (PG) such as penicillin, yet have for a long time failed to find any PG in their cell walls.[9] In 2013,Protochlamydia amoebophila was shown to have a sacculus made of PG whileSimkania negevensis does not. There is noFtsZ gene, which is previously believed to be essential for cell division in the presence of PG, in either of them.[10] In 2014, the human pathogenChlamydia trachomatis was shown to contain PG in its intracellular stage, apparently forming rings.[11] In 2016, the role of PG inChlamydia was clarified using more data: it does not make a whole sacculus around the cell like usual bacteria andProtochlamydia do, but instead produces a thin ring of PG down the middle during cell division.MreB controls the production of the ring, taking up the role thatFtsZ would've performed. This explains why penicillin is bacteriostatic and not bacteriocidal toChlamydia.[12]
The elemental bodies ofChlamydiaare characterized by the presence of a tough cell wall. This wall is not made of PG, but instead consists of a network of proteins.[13]
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 andvon Prowazek in 1907.
Chlamydial isolates cultured in the yolk sacs of embryonating eggs were obtained from a humanpneumonitis 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 1956,Chlamydia trachomatis was first cultured byTang Fei-fan, though they were not yet recognized as bacteria.[14]
In 1966, Chlamydiota were recognized as bacteria and the genusChlamydia was validated.[15] The orderChlamydiales was created by Storz and Page in 1971. The classChlamydiia was recently validly published.[16][17][18] Between 1989 and 1999, new families, genera, and species were recognized. The phylum Chlamydiae was established inBergey's Manual of Systematic Bacteriology.[19] By 2006, genetic data for over 350 chlamydial lineages had been reported.[20] Discovery of ocean-floor forms reported in 2020 involves newclades.[5] In 2022 the phylum was renamed Chlamydiota.[3]
The Chlamydiales order as recently described contains the families Chlamydiaceae, and theClavichlamydiaceae, while the new Parachlamydiales order harbors the remaining seven families.[16] This proposal is supported by the observation of two distinct phylogenetic clades that warrant taxonomic ranks above the family level. Molecular signatures in the form ofconserved indels (CSIs) and proteins (CSPs) have been found to be uniquely shared by each separate order, providing a means of distinguishing each clade from the other and supporting the view of shared ancestry of the families within each order.[16][27] The distinctness of the two orders is also supported by the fact that no CSIs were found among any other combination of families.
Molecular signatures have also been found that are exclusive for the family Chlamydiaceae.[16][27] The Chlamydiaceae originally consisted of one genus,Chlamydia, but in 1999 was split into two genera,Chlamydophila andChlamydia. The genera have since 2015 been reunited where species belonging to the genus Chlamydophila have been reclassified as Chlamydia species.[28][29]
However, CSIs and CSPs have been found specifically forChlamydophila species, supporting their distinctness from Chlamydia, perhaps warranting additional consideration of two separate groupings within the family. CSIs and CSPs have also been found that are exclusively shared by allChlamydia that are further indicative of a lineage independent fromChlamydophila, supporting a means to distinguishChlamydia species from neighbouringChlamydophila members.[16][27]
The Chlamydiota form a unique bacterial evolutionary group that separated from other bacteria about a billion years ago, and can be distinguished by the presence of several CSIs and CSPs.[16][27][32][8] The species from this group can be distinguished from all other bacteria by the presence of conservedindels in a number of proteins and by large numbers of signature proteins that are uniquely present in different Chlamydiae species.[33][34]
The Chlamydiota is interesting in that the order Chlamydiales (which contains all validly-published members before 2010) have no known free-living members. Considering most bacteria are free-living, there has to be some point when the lineage branched off into being intracellular. Identifying where that branch had happened and the original host remains somewhat controversial.[35]
As of 2003 it was commonly believed that Chlamydiota shares acommon ancestor withcyanobacteria, the group containing theendosymbiont ancestor to thechloroplasts of modernplants.[36] This was due to studies showing specific genes, later entire genomic contents, to be most similar to cyanobacteria and land plants. A 2004 study found that 11% of the genes inProtochlamydia amoebophila UWE25 and 4% in the Chlamydiaceae are most similar tochloroplastic,plant, andcyanobacterial genes.[8] In 2006, an article notedL,L-diaminopimelate aminotransferase as remarkably similar to the plant and cyanobacterial versions.[37] An alternative, no less unusual interpretation from 2008 is that aChlamydia might have been an endosymbioant of an ancestral plant, having transferring away some of its genes to the host before being lost.[36]
Before the cyanobacterial hypothesis there were competing hypotheses involvingPlanctomycetota orSpirochaetota. The Planctomycetota theory has been present since 1987 withCavalier-Smith's Planctobacteria.[38] This view was almost killed off by a 2000 study showing no significant link in 23S rRNA (just like earlier 16S rRNA analyses did).[39]James W. Molder, writing in 2003, believed that this represented the end of the Planctomycetes theory.[40] However, growing evidence points to an actual link between these two phyla in what has since been known as thePVC superphylum.[41][42][43] Phylogeny and shared presence of CSIs in proteins that are lineage-specific indicate that theVerrucomicrobiota are the closest free-living relatives of these parasitic organisms as of 2007.[44]
Comparison ofribosomal RNA genes has provided aphylogeny of known strains within Chlamydiota.[20] Trees have since been built using more loci. See§ Phylogeny below.
The unique physiological status of the Chlamydiota including their biphasic lifecycle and obligation to replicate within a eukaryotic host has enabled the use of DNA analysis for chlamydial diagnostics.[51]Horizontal transfer of genes is evident and complicates this area of research. In one extreme example, two genes encoding histone-like H1 proteins of eukaryotic origin have been found in the prokaryotic genome of C. trachomatis, an obligateintracellular pathogen.
^Horn M. (2010). "Class I.Chlamydiia class. nov.". In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL, Ludwig W, Whitman WB (eds.).Bergey's Manual of Systematic Bacteriology. Vol. 4 (2nd ed.). New York, NY: Springer. p. 844.doi:10.1007/978-0-387-68572-4.ISBN978-0-387-95042-6.
^abcdefgGupta RS, Naushad S, Chokshi C, Griffiths E, Adeolu M (September 2015). "A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: Proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia".Antonie van Leeuwenhoek.108 (3):765–781.doi:10.1007/s10482-015-0532-1.PMID26179278.S2CID17099157.
^Kuo C-C, Horn M, Stephens RS (2011) Order I. Chlamydiales. In: Bergey's Manual of Systematic Bacteriology, vol. 4, 2nd ed. pp. 844-845. Eds Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W. Springer-: New York.
^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.Bibcode:2015SyApM..38...99S.doi:10.1016/j.syapm.2014.12.004.hdl:10261/123714.PMID25618261.
^Oren A, Garrity GM (2015). "List of new names and new combinations previously effectively, but not validly, published".Int J Syst Evol Microbiol.65 (7):2017–2025.doi:10.1099/ijs.0.000317.PMID28056215.
^Chlamydiota inLPSN;Freese, H. M.; Meier-Kolthoff, J. P.; Sardà Carbasse, J.; Afolayan, A. O.; Göker, M. (29 October 2025). "TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity".Nucleic Acids Research.53:D1–D12.doi:10.1093/nar/gkaf1110.
^abGupta, Radhey S.; Naushad, Sohail; Chokshi, Chirayu; Griffiths, Emma; Adeolu, Mobolaji (September 2015). "A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia".Antonie van Leeuwenhoek.108 (3):765–781.doi:10.1007/s10482-015-0532-1.PMID26179278.
^Gupta RS, Griffiths E (December 2006). "Chlamydiae-specific proteins and indels: novel tools for studies".Trends in Microbiology.14 (12):527–535.doi:10.1016/j.tim.2006.10.002.PMID17049238.
^Wagner, M.; Horn, M. (2006). "The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance".Current Opinion in Biotechnology.17 (3):241–249.doi:10.1016/j.copbio.2006.05.005.PMID16704931.
