Chlamydiota

The Chlamydiota, also called Chlamydiae, form a bacterial phylum and class with a wide range of lifestyles. They include species that cause disease in humans and animals, others that live as symbionts inside common protozoa, and newly discovered forms from deep-sea sediments that are still poorly understood. For decades, all known Chlamydiota were obligate intracellular bacteria, meaning they could only survive and reproduce inside a host cell. In 2020, many additional Chlamydiota were found on the ocean floor, and it remains unclear whether all of these require hosts.

Among the Chlamydiota that cause human illness, the two most significant are Chlamydia pneumoniae, responsible for a form of pneumonia, and Chlamydia trachomatis, which causes the sexually transmitted infection chlamydia. Chlamydia is the most common bacterial STI in the United States, with about 2.86 million infections reported each year.

In terms of biology, all Chlamydiota known for a long time grow only by infecting eukaryotic host cells. They are as small as or smaller than many viruses, ovoid in shape, and stain Gram-negative. They depend entirely on replication inside host cells, so some are called obligate intracellular pathogens, while others are symbionts of widespread protozoa.

Most of these intracellular Chlamydiota live inside a vacuole or inclusion body. Inside a cell, they exist 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 only grow where their host cells grow, following a characteristic two-phase developmental cycle. As a result, clinically important Chlamydiota cannot be grown in standard bacterial culture media in a lab; they are best isolated while still inside their host cells. The 2020 discovery of ocean-floor Chlamydiota raises the question of whether all of them have hosts.

Peptidoglycan

Regarding peptidoglycan, scientists have long known that Chlamydiota are vulnerable to antibiotics that block peptidoglycan production, such as penicillin, yet for many years they could not find any peptidoglycan in their cell walls. In 2013, Protochlamydia amoebophila was shown to have a sacculus made of peptidoglycan, while Simkania negevensis does not. Neither species has the FtsZ gene, which was once thought essential for cell division when peptidoglycan is present. In 2014, the human pathogen Chlamydia trachomatis was found to contain peptidoglycan during its intracellular stage, forming ring-like structures.

By 2016, more data clarified the role of peptidoglycan in Chlamydia: it does not form a complete sacculus around the cell like typical bacteria or Protochlamydia, but instead produces a thin ring of peptidoglycan at the division site during cell division. The protein MreB controls the formation of this ring, taking over the role that FtsZ would normally play. This explains why penicillin is bacteriostatic (stops growth) rather than bactericidal (kills outright) in Chlamydia. The elementary bodies of Chlamydia have a tough cell wall, but this wall is not made of peptidoglycan; it consists of a network of proteins.

History

Historically, a chlamydia-like eye disease was described in ancient Chinese and Egyptian manuscripts. A modern description of chlamydia-like organisms came from Halberstaedter and von Prowazek in 1907.

In the late 1920s and early 1930s, chlamydial isolates were cultured in the yolk sacs of embryonated eggs from a human pneumonitis outbreak, and by the mid-20th century, isolates had been obtained from dozens of vertebrate species. The term "chlamydia" (meaning a cloak) appeared in the literature in 1945, though other names like Bedsonia, Miyagawanella, ornithosis-, TRIC-, and PLT-agents were also used. In 1956, Chlamydia trachomatis was first cultured by Tang Fei-fan, though it was not yet recognized as a bacterium.

Nomenclature

In terms of nomenclature, Chlamydiota were recognized as bacteria in 1966, 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. The discovery of ocean-floor forms in 2020 involved new clades. In 2022, the phylum was renamed Chlamydiota.

Taxonomy and molecular signatures

Taxonomically, the Chlamydiota currently contain eight validly named genera and 14 genera total. The phylum consists of two orders (Chlamydiales and Parachlamydiales) and nine families within a single class (Chlamydiia). Only four of these families are validly named: Chlamydiaceae, Parachlamydiaceae, Simkaniaceae, and Waddliaceae. Five are described as families: Clavichlamydiaceae, Criblamydiaceae, Parilichlamydiaceae, Piscichlamydiaceae, and Rhabdochlamydiaceae.

The order Chlamydiales as recently described includes the families Chlamydiaceae and Clavichlamydiaceae, while the new order Parachlamydiales contains the remaining seven families. This division is supported by two distinct phylogenetic clades that warrant taxonomic ranks above the family level. Molecular signatures in the form of conserved indels and conserved signature proteins are uniquely shared by each order, providing a way to distinguish the clades and supporting the shared ancestry of families within each order.

The distinctness of the two orders is also supported by the fact that no such signatures were found among any other combination of families. Molecular signatures exclusive to the family Chlamydiaceae have also been identified. The Chlamydiaceae originally consisted of one genus, Chlamydia, but in 1999 was split into two genera, Chlamydophila and Chlamydia. Since 2015, the genera have been reunited, with species belonging to the group.