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Phylum of bacteria

The Chlamydiota (synonym Chlamydiae) are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. 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 have hosts. Among the Chlamydiota, all of the ones long known to science grow only by infecting eukaryotic host cells. They are as small as or smaller than many viruses. They are ovoid in shape and stain Gram negative. They are dependent on replication inside the host cells; thus, some species are termed obligate intracellular pathogens and others are symbionts of ubiquitous protozoa. Most intracellular Chlamydiota are located in an inclusion body or vacuole. Outside cells, they survive only as an extracellular infectious form. These Chlamydiota can grow only where their host cells grow, and develop according to a characteristic biphasic developmental cycle. Therefore, clinically relevant Chlamydiota cannot be propagated in bacterial culture media in the clinical laboratory. They are most successfully isolated while still inside their host cells. Of various Chlamydiota that cause human disease, the two most important species are Chlamydia pneumoniae, which causes a type of pneumonia, and Chlamydia trachomatis, which causes chlamydia. Chlamydia is the most common bacterial sexually transmitted infection in the United States, and 2.86 million chlamydia infections are reported annually.

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 1956, Chlamydia trachomatis was first cultured by Tang Fei fan, though they were not yet recognized as bacteria.

In 1966, Chlamydiota were recognized as bacteria and the genus Chlamydia was validated. The order Chlamydiales was created by Storz and Page in 1971. The class Chlamydiia was recently validly published. 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. Discovery of ocean floor forms reported in 2020 involves new clades. The phylum presently consist of two orders (Chlamydiales, Parachlamydiales) and nine families within a single class (Chlamydiia). while five are described as families (Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae). The Chlamydiales order as recently described contains the families Chlamydiaceae, and the Clavichlamydiaceae, while the new Parachlamydiales order harbors the remaining seven families. 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. However, CSIs and CSPs have been found specifically for Chlamydophila species, supporting their distinctness from Chlamydia, perhaps warranting additional consideration of two separate groupings within the family. Reports have varied as to whether the Chlamydiota are related to the Planctomycetota or Spirochaetota. Genome sequencing, however, indicates that 11% of the genes in Protochlamydia amoebophila UWE25 and 4% in the Chlamydiaceae are most similar to chloroplast, plant, and cyanobacterial genes. Comparison of ribosomal RNA genes has provided a phylogeny of known strains within Chlamydiota. 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 obligate intracellular pathogen.