In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall.
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane.
Pseudomonadota is a major phylum of Gram-negative bacteria. The renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use the earlier name Proteobacteria, of long standing in the literature. The phylum Proteobacteria includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Yersinia, Legionella, and many others. Others are free-living (non-parasitic) and include many of the bacteria responsible for nitrogen fixation.
In biology, a kingdom is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.
The three-domain system is a biological classification introduced by Carl Woese, Otto Kandler, and Mark Wheelis in 1990 that divides cellular life forms into three domains, namely Archaea, Bacteria, and Eukaryota. The key difference from earlier classifications such as the two-empire system and the five-kingdom classification is the splitting of Archaea from bacteria as completely different organisms. It has been challenged by the two-domain system that divides organisms into Bacteria and Archaea only, as Eukaryotes are considered as one group of Archaea.
The Thermoproteota are prokaryotes that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified characteristic Thermoproteota environmental rRNA indicating the organisms may be the most abundant archaea in the marine environment. Originally, they were separated from the other archaea based on rRNA sequences; other physiological features, such as lack of histones, have supported this division, although some crenarchaea were found to have histones. Until recently all cultured Thermoproteota had been thermophilic or hyperthermophilic organisms, some of which have the ability to grow at up to 113 °C. These organisms stain Gram negative and are morphologically diverse, having rod, cocci, filamentous and oddly-shaped cells.
Euryarchaeota is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes, which generally live at temperatures between 41 and 122 °C. They are separated from the other archaeans based mainly on rRNA sequences and their unique DNA polymerase.
The Aquificota phylum is a diverse collection of bacteria that live in harsh environmental settings. The name Aquificota was given to this phylum based on an early genus identified within this group, Aquifex, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.
The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.
Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.
The Thermoprotei is a class of the Thermoproteota.
Neomura is a possible clade composed of the two domains of life of Archaea and Eukaryota. The group was named by Thomas Cavalier-Smith in 2002. Its name means "new walls", reflecting his hypothesis that it evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan cell walls with other glycoproteins. As of August 2017, the neomuran hypothesis is not accepted by most workers; molecular phylogenies suggest that eukaryotes are most closely related to one group of archaeans and evolved from them, rather than forming a clade with all archaeans, and that Archaea and Bacteria are sister groups.
Gracilicutes is a clade in bacterial phylogeny.
Monera is historically a biological kingdom that is made up of prokaryotes. As such, it is composed of single-celled organisms that lack a nucleus. It has been superseded by the three-domain system.
Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
Bacterial taxonomy is subfield of taxonomy devoted to the classification of bacteria specimens into taxonomic ranks.
There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure, and not based on the molecular evidence.
The initial version of a classification system of life by British zoologist Thomas Cavalier-Smith appeared in 1978. This initial system continued to be modified in subsequent versions that were published until he died in 2021. As with classifications of others, such as Carl Linnaeus, Ernst Haeckel, Robert Whittaker, and Carl Woese, Cavalier-Smith's classification attempts to incorporate the latest developments in taxonomy., Cavalier-Smith used his classifications to convey his opinions about the evolutionary relationships among various organisms, principally microbial. His classifications complemented his ideas communicated in scientific publications, talks, and diagrams. Different iterations might have a wider or narrow scope, include different groupings, provide greater or lesser detail, and place groups in different arrangements as his thinking changed. His classifications has been a major influence in the modern taxonomy, particularly of protists.
Robert George Everitt Murray was an English-Canadian bacteriologist. He is known for his research on bacterial structure and pathology, as well as bacterial taxonomy.
