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Bacterial taxonomy is the
taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
, i.e. the
rank Rank is the relative position, value, worth, complexity, power, importance, authority, level, etc. of a person or object within a ranking, such as: Level or position in a hierarchical organization * Academic rank * Diplomatic rank * Hierarchy * ...
-based classification, of
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
. In the
scientific classification Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
established by
Carl Linnaeus Carl Linnaeus (; 23 May 1707 – 10 January 1778), also known after his Nobility#Ennoblement, ennoblement in 1761 as Carl von Linné#Blunt, Blunt (2004), p. 171. (), was a Swedish botanist, zoologist, taxonomist, and physician who formalise ...
, each species has to be assigned to a genus ( binary nomenclature), which in turn is a lower level of a hierarchy of ranks (family, suborder, order, subclass, class, division/phyla, kingdom and domain). In the currently accepted classification of life, there are three domains ( Eukaryotes,
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
and Archaea), which, in terms of taxonomy, despite following the same principles have several different conventions between them and between their subdivisions as they are studied by different disciplines (botany, zoology, mycology and microbiology). For example, in zoology there are type specimens, whereas in microbiology there are type strains.


Diversity

Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. The various species differ amongst each other based on several characteristics, allowing their identification and classification. Examples include: * Phylogeny: All bacteria stem from a common ancestor and diversified since, and consequently possess different levels of evolutionary relatedness (see
Bacterial phyla 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 s ...
and
Timeline of evolution The timeline of the evolutionary history of life represents the current scientific theory outlining the major events during the development of life on planet Earth. Dates in this article are consensus estimates based on scientific evidence, main ...
) * Metabolism: Different bacteria may have different metabolic abilities (see
Microbial metabolism Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other ...
) * Environment: Different bacteria thrive in different environments, such as high/low temperature and salt (see
Extremophiles An extremophile (from Latin ' meaning "extreme" and Greek ' () meaning "love") is an organism that is able to live (or in some cases thrive) in extreme environments, i.e. environments that make survival challenging such as due to extreme tempe ...
) * Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bilayers) or bilayer composition (see Bacterial cellular morphologies,
Bacterial cell structure The bacterium, despite its simplicity, contains a well-developed cell structure which is responsible for some of its unique biological structures and pathogenicity. Many structural features are unique to bacteria and are not found among archaea o ...
)


History


First descriptions

Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens
microscope A microscope () is a laboratory instrument used to examine objects that are too small to be seen by the naked eye. Microscopy is the science of investigating small objects and structures using a microscope. Microscopic means being invisi ...
of his own design. He called them "
animalcules Animalcule ('little animal', from Latin ''animal'' + the diminutive suffix ''-culum'') is an old term for microscopic organisms that included bacteria, protozoans, and very small animals. The word was invented by 17th-century Dutch scientist A ...
" and published his observations in a series of letters to the
Royal Society The Royal Society, formally The Royal Society of London for Improving Natural Knowledge, is a learned society and the United Kingdom's national academy of sciences. The society fulfils a number of roles: promoting science and its benefits, re ...
. Early described genera of bacteria include ''
Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Being highly salt tolerant and unable to survive ...
'' and '' Monas'', by O. F. Müller (1773, 1786), then classified as
Infusoria Infusoria are minute freshwater life forms including ciliates, euglenoids, protozoa, unicellular algae and small invertebrates. Some authors (e.g., Bütschli) used the term as a synonym for Ciliophora. In modern formal classifications, the term ...
(however, many species before included in those genera are regarded today as protists); '' Polyangium'', by H. F. Link (1809), the first bacterium still recognized today; ''
Serratia ''Serratia'' is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria of the family Yersiniaceae. According to the List of Prokaryotic names with Standing Nomenclature (LPSN), there are currently 19 species of ''Serratia'' that a ...
'', by Bizio (1823); and '' Spirillum, Spirochaeta'' and ''
Bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were amon ...
'', by Ehrenberg (1838).Murray, R.G.E., Holt, J.G. (2005). The history of ''Bergey's Manual''. In: Garrity, G.M., Boone, D.R. & Castenholz, R.W. (eds., 2001). ''Bergey's Manual of Systematic Bacteriology'', 2nd ed., vol. 1, Springer-Verlag, New York, p. 1-14
link
ee p. 2./ref> The term ''Bacterium'', introduced as a genus by Ehrenberg in 1838, became a catch-all for rod-shaped cells.


Early formal classifications

Bacteria were first classified as
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae exclu ...
s constituting the class ''Schizomycetes'', which along with the ''Schizophyceae'' (blue green algae/''Cyanobacteria'') formed the phylum ''Schizophyta''. Haeckel in 1866 placed the group in the phylum '' Moneres'' (from μονήρης: simple) in the kingdom '' Protista'' and defines them as completely structureless and homogeneous organisms, consisting only of a piece of plasma. He subdivided the phylum into two groups: * (no envelope) ** ''Protogenes'' – such as ''Protogenes primordialis'', now classed as a eukaryote and not a bacterium ** ''Protamaeba'' – now classed as a eukaryote and not a bacterium ** ''
Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Being highly salt tolerant and unable to survive ...
'' – a genus of comma shaped bacteria first described in 1854) ** ''
Bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were amon ...
'' – a genus of rod shaped bacteria first described in 1828, that later gave its name to the members of the Monera, formerly referred to as "a moneron" (plural "monera") in English and ""(fem. pl. "") in German ** ''
Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...
'' – a genus of spore-forming rod shaped bacteria first described in 1835Ehrenberg, C. G. (1835). "Dritter Beitrag zur Erkenntniss grosser Organisation in der Richtung des kleinsten Raumes". ''Physikalische Abhandlungen der Koeniglichen Akademie der Wissenschaften zu Berlin aus den Jahren 1833-1835'', pp. 143-336. ** '' Spirochaeta'' – thin spiral shaped bacteria first described in 1835 ** '' Spirillum'' – spiral shaped bacteria first described in 1832 ** etc. * (with envelope) ** ''Protomonas'' – now classed as a eukaryote and not a bacterium. The name was reused in 1984 for an unrelated genus of Bacteria ** '' Vampyrella'' – now classed as a eukaryote and not a bacterium The classification of Ferdinand Cohn (1872) was influential in the nineteenth century, and recognized six genera: '' Micrococcus'', ''
Bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were amon ...
'', ''
Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...
'', ''
Vibrio ''Vibrio'' is a genus of Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Being highly salt tolerant and unable to survive ...
'', '' Spirillum'', and '' Spirochaeta''. The group was later reclassified as the '' Prokaryotes'' by Chatton. The classification of '' Cyanobacteria'' (colloquially "blue green algae") has been fought between being algae or bacteria (for example, Haeckel classified '' Nostoc'' in the phylum Archephyta of Algae). in 1905, Erwin F. Smith accepted 33 valid different names of bacterial genera and over 150 invalid names, and Vuillemin, in a 1913 study, concluded that all species of the ''Bacteria'' should fall into the genera '' Planococcus'', ''
Streptococcus ''Streptococcus'' is a genus of gram-positive ' (plural ) or spherical bacteria that belongs to the family Streptococcaceae, within the order Lactobacillales (lactic acid bacteria), in the phylum Bacillota. Cell division in streptococci occurs ...
'', ''
Klebsiella ''Klebsiella'' is a genus of Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide-based capsule. ''Klebsiella'' species are found everywhere in nature. This is thought to be due to distinct sublineages developi ...
'', '' Merista'', ''Planomerista'', ''
Neisseria ''Neisseria'' is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that colonize humans, only two are pathogens, '' N. meningitidis'' and ''N. gonorrhoeae''. ''Neisseria'' species are Gram-negativ ...
'', ''
Sarcina The ''sarcina'' was the marching pack carried by Roman legionaries, the heavy infantry of the Roman legions. Most of a legionary's equipment other than his arms and armour would, in early times, have been consigned to a baggage train and b ...
'', '' Planosarcina'', '' Metabacterium'', '' Clostridium'', ''
Serratia ''Serratia'' is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria of the family Yersiniaceae. According to the List of Prokaryotic names with Standing Nomenclature (LPSN), there are currently 19 species of ''Serratia'' that a ...
'', ''
Bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were amon ...
'', and '' Spirillum''. Cohn recognized four
tribes The term tribe is used in many different contexts to refer to a category of human social group. The predominant worldwide usage of the term in English is in the discipline of anthropology. This definition is contested, in part due to confli ...
: Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil recognized the kingdom Monera with two phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae (three orders), Myxobacteriae (one order), and Spirochetae (one order). Bisset distinguished 1 class and 4 orders: Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales.
Walter Migula Emil Friedrich August Walter (or Walther) Migula (born 1863 in Żyrowa, Poland; died 1938 in Eisenach, Germany) was a Poland-born German botanist. In 1890, he was habilitated for botany at Karlsruhe Institute of Technology, where he spent sev ...
's system, which was the most widely accepted system of its time and included all then-known species but was based only on morphology, contained the three basic groups Coccaceae, Bacillaceae, and Spirillaceae, but also Trichobacterinae for filamentous bacteria. Orla-Jensen established two orders: Cephalotrichinae (seven families) and Peritrichinae (presumably with only one family). Bergey et al. presented a classification which generally followed the 1920 Final Report of the Society of American Bacteriologists Committee (Winslow et al.), which divided class Schizomycetes into four orders: Myxobacteriales, Thiobacteriales, Chlamydobacteriales, and Eubacteriales, with a fifth group being four genera considered intermediate between bacteria and protozoans: ''Spirocheta'', ''Cristospira'', ''Saprospira'', and ''Treponema''. However, different authors often reclassified the genera due to the lack of visible traits to go by, resulting in a poor state which was summarised in 1915 by Robert Earle Buchanan. By then, the whole group received different ranks and names by different authors, namely: * ''Schizomycetes'' (Naegeli 1857) * ''Bacteriaceae'' (Cohn 1872 a) * ''Bacteria'' (Cohn 1872 b) * ''Schizomycetaceae'' (DeToni and Trevisan 1889) Furthermore, the families into which the class was subdivided changed from author to author and for some, such as Zipf, the names were in German and not in Latin. The first edition of the Bacteriological Code in 1947 sorted out several problems. A. R. Prévot's system) had four subphyla and eight classes, as follows: *Eubacteriales (classes Asporulales and Sporulales) *Mycobacteriales (classes Actinomycetales, Myxobacteriales, and Azotobacteriales) *Algobacteriales (classes Siderobacteriales and Thiobacteriales) *Protozoobacteriales (class Spirochetales)


Informal groups based on Gram staining

Despite there being little agreement on the major subgroups of the ''Bacteria'', Gram staining results were most commonly used as a classification tool. Consequently, until the advent of molecular phylogeny, the Kingdom ''Prokaryota'' was divided into four divisions, A classification scheme still formally followed by Bergey's manual of systematic bacteriology for tome orderGeorge M. Garrity: Bergey's manual of systematic bacteriology. 2. Auflage. Springer, New York, 2005, Volume 2: The Proteobacteria, Part B: The Gammaproteobacteria * ''Gracilicutes'' (gram-negative) ** ''Photobacteria'' (photosynthetic): class ''Oxyphotobacteriae'' (water as electron donor, includes the order ''Cyanobacteriales''=blue-green algae, now phylum ''Cyanobacteria'') and class ''Anoxyphotobacteriae'' (anaerobic phototrophs, orders: ''Rhodospirillales'' and ''Chlorobiales'' ** ''Scotobacteria'' (non-photosynthetic, now the ''Proteobacteria'' and other gram-negative nonphotosynthetic phyla) * ''Firmacutes'' ic(gram-positive, subsequently corrected to ''Firmicutes'') **several orders such as ''Bacillales'' and ''Actinomycetales'' (now in the phylum ''Actinobacteria'') * ''Mollicutes'' (gram variable, e.g. ''Mycoplasma'') * ''Mendocutes'' (uneven gram stain, "methanogenic bacteria", now known as the ''Archaea'')


Molecular era


"Archaic bacteria" and Woese's reclassification

Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. However, a few biologists argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...
es and archaea began relationships approximately two billion years ago, and that
co-evolution In biology, coevolution occurs when two or more species reciprocally affect each other's evolution through the process of natural selection. The term sometimes is used for two traits in the same species affecting each other's evolution, as well ...
may have been occurring between members of these groups. It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared only later. Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term ''prokaryote'' only surviving meaning is "not a eukaryote", limiting its value. With improved methodologies it became clear that the methanogenic bacteria were profoundly different and were (erroneously) believed to be relics of ancient bacteria thus
Carl Woese Carl Richard Woese (; July 15, 1928 – December 30, 2012) was an American microbiologist and biophysicist. Woese is famous for defining the Archaea (a new domain of life) in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, ...
, regarded as the forerunner of the molecular phylogeny revolution, identified three primary lines of descent: the ''Archaebacteria'', the ''Eubacteria'', and the ''Urkaryotes'', the latter now represented by the nucleocytoplasmic component of the ''Eukaryotes''. These lineages were formalised into the rank Domain (''regio'' in Latin) which divided Life into 3 domains: the ''Eukaryota'', the ''Archaea'' and the ''Bacteria''.


Subdivisions

In 1987 Carl Woese divided the ''Eubacteria'' into 11 divisions based on
16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rR ...
(SSU) sequences, which with several additions are still used today.


Opposition

While the three domain system is widely accepted, some authors have opposed it for various reasons. One prominent scientist who opposes the three domain system is
Thomas Cavalier-Smith Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford. His research has led to discov ...
, who proposed that the ''Archaea'' and the ''Eukaryotes'' (the '' Neomura'') stem from Gram positive bacteria (''Posibacteria''), which in turn derive from gram negative bacteria (''Negibacteria'') based on several logical arguments, which are highly controversial and generally disregarded by the molecular biology community (''c.f.'' reviewers' comments on, ''e.g.'' Eric Bapteste is "agnostic" regarding the conclusions) and are often not mentioned in reviews (''e.g''.) due to the subjective nature of the assumptions made. However, despite there being a wealth of statistically supported studies towards the rooting of the tree of life between the ''Bacteria'' and the ''Neomura'' by means of a variety of methods, including some that are impervious to accelerated evolution—which is claimed by Cavalier-Smith to be the source of the supposed fallacy in molecular methods—there are a few studies which have drawn different conclusions, some of which place the root in the phylum ''Firmicutes'' with nested archaea. Radhey Gupta's molecular taxonomy, based on conserved signature sequences of proteins, includes a monophyletic Gram negative clade, a monophyletic Gram positive clade, and a polyphyletic Archeota derived from Gram positives. Hori and Osawa's molecular analysis indicated a link between Metabacteria (=Archeota) and eukaryotes. The only cladistic analyses for bacteria based on classical evidence largely corroborate Gupta's results (se
comprehensive mega-taxonomy
.
James Lake James A. Lake (born August 10, 1941, Kearney, Nebraska) is an American evolutionary biologist and a Distinguished Professor of Molecular, Cell, and Developmental Biology and of Human Genetics at UCLA. Lake is best known for the New Animal Phyloge ...
presented a 2 primary kingdom arrangement (Parkaryotae + eukaryotes and eocytes + Karyotae) and suggested a 5 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, Halobacteria, and Eubacteria) based on ribosomal structure and a 4 primary kingdom scheme (Eukaryota, Eocyta, Methanobacteria, and Photocyta), bacteria being classified according to 3 major biochemical innovations: photosynthesis (Photocyta), methanogenesis (Methanobacteria), and sulfur respiration ( Eocyta). He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria.


Authorities

Classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms.


Nomenclature authority

Despite there being no official and complete classification of prokaryotes, the names (nomenclature) given to prokaryotes are regulated by the International Code of Nomenclature of Bacteria ( Bacteriological Code), a book which contains general considerations, principles, rules, and various notes, and advises in a similar fashion to the
nomenclature codes Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms. To an end-user who only deals with names of species, with some awareness that specie ...
of other groups.


Classification authorities

As taxa proliferated, computer aided taxonomic systems were developed. Early non networked identification software entering widespread use was produced by Edwards 1978, Kellogg 1979, Schindler, Duben, and Lysenko 1979, Beers and Lockhard 1962, Gyllenberg 1965, Holmes and Hill 1985, Lapage et al 1970 and Lapage et al 1973. Today the taxa which have been correctly described are reviewed in ''Bergey's manual of Systematic Bacteriology'', which aims to aid in the identification of species and is considered the highest authority. An online version of the taxonomic outline of bacteria and archaea (TOBA) is availabl

''List of Prokaryotic names with Standing in Nomenclature'' (LPSN) is an online database which currently contains over two thousand accepted names with their references, etymologies and various notes.


Description of new species

The ''International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology'' (IJSB/IJSEM) is a peer reviewed journal which acts as the official international forum for the publication of new prokaryotic taxa. If a species is published in a different peer review journal, the author can submit a request to IJSEM with the appropriate description, which if correct, the new species will be featured in the Validation List of IJSEM.


Distribution

Microbial culture collections are depositories of strains which aim to safeguard them and to distribute them. The main ones being:


Analyses

Bacteria were at first classified based solely on their shape (vibrio, bacillus, coccus etc.), presence of endospores, gram stain, aerobic conditions and motility. This system changed with the study of metabolic phenotypes, where metabolic characteristics were used. Recently, with the advent of molecular phylogeny, several genes are used to identify species, the most important of which is the 16S ribosomal RNA, 16S rRNA gene, followed by 23S, ITS region, gyrB and others to confirm a better resolution. The quickest way to identify to match an isolated strain to a species or genus today is done by amplifying its 16S gene with universal primers and sequence the 1.4kb amplicon and submit it to a specialised web-based identification database, namely either Ribosomal Database Project

which align the sequence to other 16S sequences using infernal, a secondary structure bases global alignment, or ARB SILVA, which aligns sequences via SINA (SILVA incremental aligner), which does a local alignment of a seed and extends i

Several identification methods exists: * Phenotypic analyses ** Fatty acid methyl ester, fatty acid analyses ** Growth conditions (
Agar plate An agar plate is a Petri dish that contains a growth medium solidified with agar, used to culture microorganisms. Sometimes selective compounds are added to influence growth, such as antibiotics. Individual microorganisms placed on the plate wil ...

Biolog multiwell plates
* Genetic analyses ** DNA-DNA hybridization ** DNA profiling ** Sequence ** GC ratios * Phylogenetic analyses ** 16S-based phylogeny ** phylogeny based on other genes ** Multi-gene sequence analysis ** Whole-genome sequence based analysis


New species

The minimal standards for describing a new species depend on which group the species belongs to. ''c.f.''


Candidatus

Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a Bacteriology Culture Collection. It is an interim taxonomic status for noncultivable organisms. e.g. " Candidatus Pelagibacter ubique"


Species concept

Bacteria divide asexually and for the most part do not show regionalisms (" Everything is everywhere"), therefore the concept of species, which works best for animals, becomes entirely a matter of judgement. The number of named species of bacteria and archaea (approximately 13,000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The reason for this is the differences in species concepts between the ''bacteria'' and macro-organisms, the difficulties in growing/characterising in pure culture (a prerequisite to naming new species, ''vide supra'') and extensive
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring (reproduction). H ...
blurring the distinction of species. The most commonly accepted definition is the polyphasic species definition, which takes into account both phenotypic and genetic differences. However, a quicker diagnostic ''ad hoc'' threshold to separate species is less than 70% DNA–DNA hybridisation, which corresponds to less than 97% 16S DNA sequence identity. It has been noted that if this were applied to animal classification, the order
primate Primates are a diverse order of mammals. They are divided into the strepsirrhines, which include the lemurs, galagos, and lorisids, and the haplorhines, which include the tarsiers and the simians ( monkeys and apes, the latter including ...
s would be a single species. For this reason, more stringent species definitions based on whole genome sequences have been proposed.


Pathology vs. phylogeny

Ideally, taxonomic classification should reflect the evolutionary history of the taxa, i.e. the phylogeny. Although some exceptions are present when the phenotype differs amongst the group, especially from a medical standpoint. Some examples of problematic classifications follow.


''Escherichia coli'': overly large and polyphyletic

In the family Enterobacteriaceae of the class Gammaproteobacteria, the species in the genus ''
Shigella ''Shigella'' is a genus of bacteria that is Gram-negative, facultative anaerobic, non-spore-forming, nonmotile, rod-shaped, and genetically closely related to '' E. coli''. The genus is named after Kiyoshi Shiga, who first discovered it in 1 ...
'' ('' S. dysenteriae'', '' S. flexneri'', '' S. boydii'', '' S. sonnei'') from an evolutionary point of view are strains of the species ''
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
'' (polyphyletic), but due to genetic differences cause different medical conditions in the case of the pathogenic strains. Confusingly, there are also ''E. coli'' strains that produce
Shiga toxin Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome of lambdoid prophages. The toxins are named after Kiyoshi Shiga, who first described the bacterial or ...
known as STEC.
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
is a badly classified species as some strains share only 20% of their genome. Being so diverse it should be given a higher taxonomic ranking. However, due to the medical conditions associated with the species, it will not be changed to avoid confusion in medical context.


''Bacillus cereus'' group: close and polyphyletic

In a similar way, the ''Bacillus'' species (=phylum ''
Firmicutes The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...
'') belonging to the "''B. cereus'' group" ('' B. anthracis'', '' B. cereus'', '' B . thuringiensis'', '' B. mycoides'', '' B. pseudomycoides'', '' B. weihenstephanensis'' and '' B. medusa'') have 99-100% similar 16S rRNA sequence (97% is a commonly cited adequate species cut-off) and are polyphyletic, but for medical reasons (anthrax ''etc.'') remain separate.


''Yersinia pestis'': extremely recent species

''
Yersinia pestis ''Yersinia pestis'' (''Y. pestis''; formerly '' Pasteurella pestis'') is a gram-negative, non-motile, coccobacillus bacterium without spores that is related to both ''Yersinia pseudotuberculosis'' and ''Yersinia enterocolitica''. It is a facult ...
'' is in effect a strain of '' Yersinia pseudotuberculosis'', but with a pathogenicity island that confers a drastically different pathology (Black plague and tuberculosis-like symptoms respectively) which arose 15,000 to 20,000 years ago.


Nested genera in ''Pseudomonas''

In the gammaproteobacterial order ''
Pseudomonadales The Pseudomonadales are an order of Pseudomonadota. A few members are pathogens, such as species of ''Pseudomonas'', ''Moraxella'', and ''Acinetobacter'', which may cause disease in humans, animals and plants. ''Pseudomonas'' The bacterial genu ...
'', the genus ''
Azotobacter ''Azotobacter'' is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts (and also has hard crust) and may produce large quantities of capsular slime. They are aerobic, free-living soil microbes that play an impo ...
'' and the species '' Azomonas macrocytogenes'' are actually members of the genus ''
Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able t ...
'', but were misclassified due to nitrogen fixing capabilities and the large size of the genus ''Pseudomonas'' which renders classification problematic. This will probably rectified in the close future.


Nested genera in ''Bacillus''

Another example of a large genus with nested genera is the genus ''Bacillus'', in which the genera ''Paenibacillus'' and ''Brevibacillus'' are nested clades. There is insufficient genomic data at present to fully and effectively correct taxonomic errors in ''Bacillus''.


''Agrobacterium'': resistance to name change

Based on molecular data it was shown that the genus ''Agrobacterium'' is nested in ''Rhizobium'' and the ''Agrobacterium'' species transferred to the genus '' Rhizobium'' (resulting in the following comp. nov.: ''Rhizobium radiobacter'' (formerly known as ''A. tumefaciens)'', ''R. rhizogenes'', ''R. rubi'', ''R. undicola'' and ''R. vitis'') Given the plant pathogenic nature of ''Agrobacterium'' species, it was proposed to maintain the genus ''Agrobacterium'' and the latter was counter-argued


Nomenclature

Taxonomic names are written in italics (or underlined when handwritten) with a majuscule first letter with the exception of epithets for species and subspecies. Despite it being common in zoology,
tautonym A tautonym is a scientific name of a species in which both parts of the name have the same spelling, such as ''Rattus rattus''. The first part of the name is the name of the genus and the second part is referred to as the ''specific epithet'' in ...
s (e.g. ''Bison bison'') are not acceptable and names of taxa used in zoology, botany or mycology cannot be reused for Bacteria (Botany and Zoology do share names). Nomenclature is the set of rules and conventions which govern the names of taxa. The difference in nomenclature between the various kingdoms/domains is reviewed in. For Bacteria, valid names must have a Latin or Neolatin name and can only use basic latin letters (w and j inclusive, see History of the Latin alphabet for these), consequently hyphens, accents and other letters are not accepted and should be transliterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be
transliterated Transliteration is a type of conversion of a text from one script to another that involves swapping letters (thus ''trans-'' + '' liter-'') in predictable ways, such as Greek → , Cyrillic → , Greek → the digraph , Armenian → or L ...
into the Latin alphabet. When
compound words In linguistics, a compound is a lexeme (less precisely, a word or sign) that consists of more than one stem. Compounding, composition or nominal composition is the process of word formation that creates compound lexemes. Compounding occurs when ...
are created, a connecting vowel is needed depending on the origin of the preceding word, regardless of the word that follows, unless the latter starts with a vowel in which case no connecting vowel is added. If the first compound is Latin then the connecting vowel is an -i-, whereas if the first compound is Greek, the connecting vowel is an -o-. For etymologies of names consul
LPSN


Rules for higher taxa

For the ''Prokaryotes'' (''Bacteria'' and ''Archaea'') the rank kingdom is not used (although some authors refer to phyla as kingdoms) If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriological Code the name is formed by the addition of an appropriate suffix to the stem of the name of the type genus. For subclass and class the recommendation from is generally followed, resulting in a neutral plural, however a few names do not follow this and instead keep into account graeco-latin grammar (e.g. the female plurals ''
Thermotogae The Thermotogota are a phylum of the domain (biology), domain Bacteria. The phylum Thermotogota is composed of Gram-negative staining, anaerobic organism, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.Gupta, RS (2014) The Phyl ...
'', '' Aquificae'' and '' Chlamydiae'', the male plurals '' Chloroflexi'', ''
Bacilli Bacilli is a taxonomic class of bacteria that includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens such as ''Bacillus anthracis'' (the cause of anthrax). ''Bacilli'' are almost exclusively gram-positi ...
'' and '' Deinococci'' and the greek plurals ''
Spirochaetes A spirochaete () or spirochete is a member of the phylum Spirochaetota (), (synonym Spirochaetes) which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled (corkscrew-shaped or s ...
'', '' Gemmatimonadetes'' and '' Chrysiogenetes'').


Phyla endings

Until 2021, phyla were not covered by the Bacteriological code, so they were named informally. This resulted in a variety of approaches to naming phyla. Some phyla, like Firmicutes, were named according to features shared across the phylum. Others, like Chlamydiae, were named using a class name or genus name as the stem (e.g., ''Chlamydia''). In 2021, the decision was made to include names under the Bacteriological Code. Consequently, many phylum names were updated according to the new nomenclatural rules. The higher taxa proposed by
Cavalier-Smith Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford. His research has led to disc ...
are generally disregarded by the molecular phylogeny community (''e.g''.) ( ''vide supra''). Under the new rules, the name of a phylum is derived from the type genus: * '' Acidobacteriota'' (from '' Acidobacterium'') * ''
Actinomycetota The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...
'' (from ''
Actinomyces ''Actinomyces'' is a genus of the Actinomycetia class of bacteria. They all are gram-positive. ''Actinomyces'' species are facultatively anaerobic and they grow best under anaerobic conditions. ''Actinomyces'' species may form endospores, an ...
'') * ''
Aquificota 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'' (“water maker”), whic ...
'' (from ''
Aquifex ''Aquifex'' is a bacterial genus, belonging to phylum Aquificota. There is one species of ''Aquifex'' with a validly published name – '' A. pyrophilus'' – but "'' A. aeolicus''" is sometimes considered as species though it has no standing as ...
'') * ''
Armatimonadota ''Armatimonadota'' is a phylum of gram-negative bacteria. History ''Armatimonadota'' was originally described solely on the basis of environmental 16S rRNA gene clone sequences, and was temporarily titled candidate phylum OP10. However, in 20 ...
'' (from '' Armatimonas'') * '' Atribacterota'' (from '' Atribacter'') * ''
Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...
'' (from ''
Bacillus ''Bacillus'' (Latin "stick") is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum '' Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural ''Bacill ...
'') * '' Bacteroidota'' (from ''
Bacteroides ''Bacteroides'' is a genus of Gram-negative, obligate anaerobic bacteria. ''Bacteroides'' species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unus ...
'') * ''
Balneolota ''Balneolales'' is an order of bacteria. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information The National Center for Biot ...
'' (from '' Balneola'') * ''
Bdellovibrionota Bdellovibrionota is a phylum of bacteria. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the National Center for Biotechnology Information (NCBI). See also * Li ...
'' (from '' Bdellovibrio'') * '' Caldisericota'' (from '' Caldisericum'') * '' Calditrichota'' (from '' Caldithrix'') * ''
Campylobacterota Campylobacterota are a phylum of bacteria. All species of this phylum are Gram-negative. The Campylobacterota consist of few known genera, mainly the curved to spirilloid ''Wolinella'' spp., ''Helicobacter'' spp., and ''Campylobacter'' spp. Most ...
'' (from '' Campylobacter'') * '' Chlamydiota'' (from ''
Chlamydia Chlamydia, or more specifically a chlamydia infection, is a sexually transmitted infection caused by the bacterium '' Chlamydia trachomatis''. Most people who are infected have no symptoms. When symptoms do appear they may occur only several we ...
'') * '' Chlorobiota'' (from ''
Chlorobium ''Chlorobium'' is a genus of green sulfur bacteria. They are photolithotrophic oxidizers of sulfur and most notably utilise a noncyclic electron transport chain to reduce NAD+. Photosynthesis is achieved using a Type 1 Reaction Centre using b ...
'') * '' Chloroflexota'' (from ''
Chloroflexus Chloroflexales is an order of bacteria in the class Chloroflexia. Taxonomy The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI). * ...
'') * '' Chrysiogenota'' (from '' Chrysiogenes'') * ''
Coprothermobacterota ''Coprothermobacterota'' is a phylum of nonmotile, rod-shaped bacteria. Its members are strictly anaerobic and thermophilic, growing at optimal temperatures between 55 °C and 70 °C. The name of this phylum is based on an early genus ...
'' (from '' Coprothermobacter'') * '' Deferribacterota'' (from '' Deferribacter'') * ''
Deinococcota ''Deinococcota'' (synonym, ''Deinococcus-Thermus'') 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 ...
'' (from '' Deinococcus'') * ''
Dictyoglomota ''Dictyoglomus'' is a genus of bacterium, given its own Phylum, called the Dictyoglomi. This organism is extremely ''thermophilic'', meaning it thrives at extremely high temperatures. It is ''chemoorganotrophic'', meaning it derives energy by met ...
'' (from '' Dictyoglomus'') * ''
Elusimicrobiota The phylum Elusimicrobiota, previously known as "Termite Group 1", has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils, and toxic wastes. The high abundance of Elusimicrobio ...
'' (from '' Elusimicrobium'') * '' Fibrobacterota'' (from '' Fibrobacterota'') * ''
Fusobacteriota Fusobacteriota are obligately anaerobic non-sporeforming Gram-negative bacilli. Since the first reports in the late nineteenth century, various names have been applied to these organisms, sometimes with the same name being applied to different ...
'' (from ''
Fusobacterium ''Fusobacterium'' is a genus of anaerobic, Gram-negative, non-sporeforming bacteria belonging to Gracilicutes. Individual cells are slender, rod-shaped bacilli with pointed ends. Strains of ''Fusobacterium'' cause several human diseases, includi ...
'') * ''
Gemmatimonadota The Gemmatimonadota are a phylum of bacteria established in 2003. The phylum contains two classes Gemmatimonadetes and Longimicrobia. Species The type species '' Gemmatimonas aurantiaca'' strain T-27T was isolated from activated sludge in a sewa ...
'' (from '' Gemmatimonas'') * '' Ignavibacteriota'' (from '' Ignavibacterium'') * '' Kiritimatiellota'' (from '' Kiritimatiella'') * '' Lentisphaerota'' (from '' Lentisphaera'') * ''
Mycoplasmatota Mycoplasmatota is a phylum of bacteria that contains the class Mollicutes. The phylum was originally named "Tenericutes" (''tener cutis'': soft skin). Notable genera include ''Mycoplasma'', ''Spiroplasma'', ''Ureaplasma'', and ''Candidatus'' Phyt ...
'' (from '' Mycoplasma'') * ''
Myxococcota The Myxococcota are a phylum of bacteria known as the fruiting gliding bacteria. All species of this group are Gram-negative. They are predominantly aerobic genera that release myxospores in unfavorable environments. Phylogeny The currently acce ...
'' (from '' Myxococcus'') * '' Nitrospinota'' (from '' Nitrospina'') * ''
Nitrospirota Nitrospirota is a phylum of bacteria. It includes multiple genera, such as '' Nitrospira'', the largest. The first member of this phylum, '' Nitrospira marina'', was discovered in 1985. The second member, '' Nitrospira moscoviensis'', was discove ...
'' (from ''
Nitrospira ''Nitrospira'' (from Latin: nitro, meaning "nitrate" and Greek: spira, meaning "spiral") translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was d ...
'') * ''
Planctomycetota The Planctomycetota are a phylum of widely distributed bacteria, occurring in both aquatic and terrestrial habitats. They play a considerable role in global carbon and nitrogen cycles, with many species of this phylum capable of anaerobic ammoniu ...
'' (from '' Planctomyces'') * '' Pseudomonadota'' (from ''
Pseudomonas ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able t ...
'') * '' Rhodothermota'' (from ''
Rhodothermus ''Rhodothermus'' is a genus of bacteria. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information The National Center for Bio ...
'') * '' Spirochaetota'' (from '' Spirochaeta'') * ''
Synergistota The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape. Although Synergistota have a diderm cell envelope,Gupta, R. S. (2011) Origin of Diderm (Gram-negative) Bacteria: Antibiotic Sel ...
'' (from '' Synergistes'') * ''
Thermodesulfobacteriota The Thermodesulfobacteriota are a phylum of thermophilic sulfate-reducing bacteria. A pathogenic intracellular thermodesulfobacteriote has recently been identified. Phylogeny The phylogeny is based on phylogenomic Phylogenomics is the interse ...
'' (from '' Thermodesulfobacterium'') * '' Thermomicrobiota'' (from '' Thermomicrobium'') * ''
Thermotogota The Thermotogota are a phylum of the domain Bacteria. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-10 ...
'' (from '' Thermotoga'') * ''
Verrucomicrobiota Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated speci ...
'' (from '' Verrucomicrobium'')


Names after people

Several species are named after people, either the discoverer or a famous person in the field of microbiology, for example ''Salmonella'' is after D.E. Salmon, who discovered it (albeit as "Bacillus typhi"). For the generic epithet, all names derived from people must be in the female nominative case, either by changing the ending to -a or to the diminutive -ella, depending on the name. For the specific epithet, the names can be converted into either adjectival form (adding -nus (m.), -na (f.), -num (n.) according to the gender of the genus name) or the genitive of the Latinised name.


Names after places

Many species (the specific epithet) are named after the place they are present or found (e.g. Thiospirillum jenense). Their names are created by forming an adjective by joining the locality's name with the ending -ensis (m. or f.) or ense (n.) in agreement with the gender of the genus name, unless a classical Latin adjective exists for the place. However, names of places should not be used as nouns in the genitive case.


Vernacular names

Despite the fact that some hetero/homogeneus colonies or biofilms of bacteria have names in English (e.g.
dental plaque Dental plaque is a biofilm of microorganisms (mostly bacteria, but also fungi) that grows on surfaces within the mouth. It is a sticky colorless deposit at first, but when it forms tartar, it is often brown or pale yellow. It is commonly found be ...
or Star jelly), no bacterial species has a vernacular/trivial/common name in English. For names in the singular form, plurals cannot be made ( singulare tantum) as would imply multiple groups with the same label and not multiple members of that group (by analogy, in English, chairs and tables are types of furniture, which cannot be used in the plural form "furnitures" to describe both members), conversely names plural form are pluralia tantum. However, a partial exception to this is made by the use of vernacular names. However, to avoid repetition of taxonomic names which break the flow of prose, vernacular names of members of a genus or higher taxa are often used and recommended, these are formed by writing the name of the taxa in sentence case roman ("standard" in MS Office) type, therefore treating the
proper noun A proper noun is a noun that identifies a single entity and is used to refer to that entity (''Africa'', ''Jupiter'', '' Sarah'', ''Microsoft)'' as distinguished from a common noun, which is a noun that refers to a class of entities (''continent, ...
as an English
common noun A proper noun is a noun that identifies a single entity and is used to refer to that entity (''Africa'', ''Jupiter'', ''Sarah'', ''Microsoft)'' as distinguished from a common noun, which is a noun that refers to a class of entities (''continent, ...
(e.g. the salmonellas), although there is some debate about the grammar of plurals, which can either be regular plural by adding -(e)s (the salmonellas) or using the ancient Greek or Latin plural form ( irregular plurals) of the noun (the salmonellae); the latter is problematic as the plural of - bacter would be -bacteres, while the plural of myces (N.L. masc. n. from Gr. masc. n. mukes) is mycetes.R. E. BUCHANAN, Taxonomy, Annu. Rev. Microbiol. 1955.9:1-20. http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.09.100155.000245 Customs are present for certain names, such as those ending in
-monas The suffix -monas is used in microbiology for many genera and is intended to mean "unicellular organism". Meaning The suffix -monas found in many genera in microbiology is similar in usage to -bacter, -bacillus, -coccus or -spirillum. The gener ...
are converted into -monad (one pseudomonad, two aeromonads and not -monades). Bacteria which are the etiological cause for a disease are often referred to by the disease name followed by a describing noun (bacterium, bacillus, coccus, agent or the name of their phylum) e.g. cholera bacterium (''
Vibrio cholerae ''Vibrio cholerae'' is a species of Gram-negative, facultative anaerobe and comma-shaped bacteria. The bacteria naturally live in brackish or saltwater where they attach themselves easily to the chitin-containing shells of crabs, shrimps, and oth ...
'') or Lyme disease spirochete (''
Borrelia burgdorferi ''Borrelia burgdorferi'' is a bacterial species of the spirochete class in the genus '' Borrelia'', and is one of the causative agents of Lyme disease in humans. Along with a few similar genospecies, some of which also cause Lyme disease, it mak ...
''), note also rickettsialpox ('' Rickettsia akari'') (for more seeftp://ftp.ncbi.nih.gov/pub/taxonomy/). '' Treponema'' is converted into treponeme and the plural is treponemes and not treponemata. Some unusual bacteria have special names such as Quin's oval ('' Quinella ovalis'') and Walsby's square (''
Haloquadratum walsbyi ''Haloquadratum walsbyi'' is of the genus ''Haloquadratum,'' within the archaea domain known for its square halophilic nature. First discovered in a brine pool in the Sinai peninsula of Egypt, ''H. walsbyi'' is noted for its flat, square-shaped ...
''). Before the advent of molecular phylogeny, many higher taxonomic groupings had only trivial names, which are still used today, some of which are polyphyletic, such as Rhizobacteria. Some higher taxonomic trivial names are: * Blue-green algae are members of the phylum " Cyanobacteria" * Green non-sulfur bacteria are members of the phylum Chloroflexota * Green sulfur bacteria are members of the Chlorobiota * Purple bacteria are some, but not all, members of the phylum Pseudomonadota * Purple sulfur bacteria are members of the order Chromatiales * low G+C Gram-positive bacteria are members of the phylum
Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earl ...
, regardless of GC content * high G+C Gram-positive bacteria are members of the phylum
Actinomycetota The ''Actinomycetota'' (or ''Actinobacteria'') are a phylum of all gram-positive bacteria. They can be terrestrial or aquatic. They are of great economic importance to humans because agriculture and forests depend on their contributions to s ...
, regardless of GC content * Rhizobia are members of various genera of Pseudomonadota * Lactic acid bacteria are members of the order
Lactobacillales Lactobacillales are an order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped (bacilli) or spherical (cocci) bacteria that share common metabolic and physiological characteristics. These bact ...
* Coryneform bacteria are members of the family Corynebacteriaceae * Fruiting gliding bacteria or myxobacteria are members of the phylum
Myxococcota The Myxococcota are a phylum of bacteria known as the fruiting gliding bacteria. All species of this group are Gram-negative. They are predominantly aerobic genera that release myxospores in unfavorable environments. Phylogeny The currently acce ...
* Enterics are members of the order
Enterobacteriales Enterobacterales is an order of Gram-negative, non-spore forming, facultatively anaerobic, rod-shaped bacteria with the class Gammaproteobacteria. The type genus of this order is ''Enterobacter.'' The name Enterobacterales is derived from the ...
(although the term is avoided if they do not live in the intestines, such as '' Pectobacterium'') * Acetic acid bacteria are members of the family Acetobacteraceae


Terminology

* The abbreviation for species is sp. (plural spp.) and is used after a generic epithet to indicate a species of that genus. Often used to denote a strain of a genus for which the species is not known either because has the organism has not been described yet as a species or insufficient tests were conducted to identify it. For example ''Halomonas'' sp. GFAJ-1 * If a bacterium is known and well-studied but not culturable, it is given the term ''
Candidatus In prokaryote nomenclature, ''Candidatus'' (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured. Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide m ...
'' in its name * A basonym is original name of a new combination, namely the first name given to a taxon before it was reclassified * A synonym is an alternative name for a taxon, i.e. a taxon was erroneously described twice * When a taxon is transferred it becomes a new combination (comb. nov.) or new name (nom. nov.) * paraphyly,
monophyly In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic gro ...
, and polyphyly


See also

* Branching order of bacterial phyla (Woese, 1987) * Branching order of bacterial phyla (Gupta, 2001) * Branching order of bacterial phyla (Cavalier-Smith, 2002) * Branching order of bacterial phyla (Rappe and Giovanoni, 2003) * Branching order of bacterial phyla (Battistuzzi et al.,2004) * Branching order of bacterial phyla (Ciccarelli et al., 2006) * Branching order of bacterial phyla after ARB Silva Living Tree * Branching order of bacterial phyla (Genome Taxonomy Database, 2018) *
Bacterial phyla 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 s ...
, a complicated classification * List of Archaea genera * List of Bacteria genera * List of bacterial orders * List of Latin and Greek words commonly used in systematic names * List of sequenced archaeal genomes *
List of sequenced prokaryotic genomes A ''list'' is any set of items in a row. List or lists may also refer to: People * List (surname) Organizations * List College, an undergraduate division of the Jewish Theological Seminary of America * SC Germania List, German rugby unio ...
* List of clinically important bacteria * Species problem *
Evolutionary grade A grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit. Definition An evolutionary grade is a group of sp ...
*
Cryptic species complex In biology, a species complex is a group of closely related organisms that are so similar in appearance and other features that the boundaries between them are often unclear. The taxa in the complex may be able to hybridize readily with each oth ...
* Synonym (taxonomy) *
Taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
*
LPSN List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomica ...
, list of accepted bacterial and archaeal names * Cyanobacteria, a phylum of common bacteria but poorly classified at present *
Human microbiome project The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on ...
*
Microbial ecology Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viru ...


References

{{DEFAULTSORT:Bacterial Taxonomy Biological nomenclature