Bacterial taxonomy
Encyclopedia
Bacterial taxonomy is the taxonomy
, i.e. the rank
-based classification, of bacteria
.
In the scientific classification established by Carl von Linné, 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
and Archaea
), which, in terms of taxonomy, despite following the same principles have several different conventions between them and between their subdivisions as 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.
of his own design. He called them "animalcules" and published his observations in a series of letters to the Royal Society
. The name "bacterium" was introduced much later, by Christian Gottfried Ehrenberg
in 1838.
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:
The group was later reclassified as the Prokaryotes by Chatton.
It should be noted that 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 in 1913 Vuillemin in a study concluded that all species of the Bacteria should fall into the genera Planococcus, Streptococcus
, Klebsiella
, Merista, Planomerista, Neisseria
, Sarcina, Planosarcina, Metabacterium
, Clostridium
, Serratia
, Bacterium
and Spirillum
.
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
Furthermore the families into which the class was subdivided, changed from author to author and for some such as Zipf the names where in German and not in Latin
The first edition of the Bacteriological Code in 1947 sorted several problems out.
results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Prokaryotae was divided into four divisions, A classification scheme still formally followed by Bergey's manual of systematic bacteriology for tome order
es and archaea began relationships approximately two billion years ago, and that co-evolution
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 prokaryotes 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 (erroneous) believed to be relics of ancient bacteria thus Carl Woese
, 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 This scheme is still followed today.
(SSU) sequences, which with several additions are still used today.
One prominent scientist which opposes the three domain system is Thomas Cavalier-Smith, which 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 molecular biology community (c.f. reviewers' comments on, e.g. Eric Bapteste is "agnostic" regarding the conclusions) and are often not even mention in reviews (e.g.), due to the subjective nature of the assumptions made for logical arguments.
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
of other groups.
LPSN is an online database which currently contains over two thousand accepted names with their references, etymologies and various notes.
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 it's 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 Projecthttp://rdp.cme.msu.edu/, 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 it http://www.arb-silva.de/documentation/background/.
Several identification methods exists:
") therefore the concept of species which works best for animals, becomes entirely a matter of judgement.
The number of species of bacteria and archaea (approximately 5000) 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
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 threshhold 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 Primates would be a single species
family of the class Gammaproteobacteria
, the species in the genus Shigella
(S. dysenteriae, S. flexneri
, S. boydii
, S. sonnei
) by an evolutionary point of view are strains of the species Escherichia coli
(polyphyletic), but due to genetic differences cause different medical conditions in the case of the pathogenic strains., it should be noted that Escherichia coli
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.
) 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.
is in effect a strain of Yersinia pseudotuberculosis
, but with a pathogenicity island that confer a drastically different pathology (Black plague and tuberculosis-like symptoms respectively) which arose 15,000 to 20,000 years ago.
, the genus Azotobacter
and the species Azomonas macrocytogenes are actually members of the genus Pseudomonas
, but were misclassified due to nitrogen fixing capabilities and the large size of the genus Psuedomonas which renders classification problematic. This will probably rectified in the close future.
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 translitterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be translitterated into the Latin alphabet.
When compound words 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 consult LPSN.
If a new or amended species is placed in new ranks, according to Rule 9 of the Bacteriologocal 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 reccomendation 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
, Aquificae
and Chlamydiae
, the male plurals Chloroflexi
, Bacilli
and Deinococci and the greek plurals Spirochaetes, Gemmatimonadetes
and Chrysiogenetes).
For the Archaea the suffix -archaeota is used. For bacterial phyla
it was proposed that the suffix -bacteria be used for phyla.
Consequently for main phyla the name of the phyla is the same as the first described class:
Whereas for others where the -ia suffix for class is used regardless of grammar they differ:
An exception is the phylum Deinococcus-Thermus
, which bears a hyphenated pair of genera —only non accented latin letters are accepted for valid names, but phyla are not officially recognised.
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.
). 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.
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
as an English common noun (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.
Customs are present for centain names, such as those ending in -monas
are converted into -monad (one pseudomonad, two aeromonads and not -monades).
Bacteria which are the etiological cause
for a 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 cholera) or Lyme disease spirochete (Borrelia burgdorferi
) , note also rickettsialpox (Rickettsia akari
) (for more see ).
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).
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:
Linnaean taxonomy
Linnaean taxonomy can mean either of two related concepts:# the particular form of biological classification set up by Carl Linnaeus, as set forth in his Systema Naturæ and subsequent works...
, i.e. the rank
Taxonomic rank
In biological classification, rank is the level in a taxonomic hierarchy. Examples of taxonomic ranks are species, genus, family, and class. Each rank subsumes under it a number of less general categories...
-based classification, of bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
.
In the scientific classification established by Carl von Linné, 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
Biological classification
Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
of Life, there are three domains
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...
(Eukaryotes, Bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
), which, in terms of taxonomy, despite following the same principles have several different conventions between them and between their subdivisions as 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, consequently possess different levels of evolutionary relatedness (see Bacterial phylaBacterial phylaThe bacterial phyla are the major lineages of the domain Bacteria.In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species , which is a lower level of a hierarchy of ranks...
and Timeline of evolutionTimeline of evolutionThis timeline of evolution of life outlines the major events in the development of life on planet Earth since it first originated until the present day. In biology, evolution is any change across successive generations in the heritable characteristics of biological populations...
) - Metabolism: Different bacteria may have different metabolic abilities (see Microbial metabolismMicrobial metabolismMicrobial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics...
) - Environment: Different bacteria thrive in different environments, such as high/low temperature and salt (see Extremophiles)
- Morphology: There are many structural differences between bacteria, such as cell shape, Gram stain (number of lipid bylayers) or bilayer composition (see Bacterial cellular morphologiesBacterial cellular morphologiesBacteria are classified by direct examination with the light microscope through its morphology and aggregation.The basic forms are spheres and round-ended cylinders . But there may be others such as helically-twisted cylinders , cylinders curved in one plane and unusual morphologies...
, Bacterial cell structureBacterial cell structureBacteria, despite their simplicity, contain a well-developed cell structure which is responsible for many of their unique biological properties. Many structural features are unique to bacteria and are not found among archaea or eukaryotes...
) - Pathogenicity: Some bacteria are pathogenic to plants or animals (see Pathogenic bacteriaPathogenic bacteriaPathogenic bacteria are bacteria that cause bacterial infection. This article deals with human pathogenic bacteria.Although the vast majority of bacteria are harmless or beneficial, quite a few bacteria are pathogenic...
)
Classification history
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscopeMicroscope
A microscope is an instrument used to see objects that are too small for the naked eye. The science of investigating small objects using such an instrument is called microscopy...
of his own design. He called them "animalcules" and published his observations in a series of letters to the Royal Society
Royal Society
The Royal Society of London for Improving Natural Knowledge, known simply as the Royal Society, is a learned society for science, and is possibly the oldest such society in existence. Founded in November 1660, it was granted a Royal Charter by King Charles II as the "Royal Society of London"...
. The name "bacterium" was introduced much later, by Christian Gottfried Ehrenberg
Christian Gottfried Ehrenberg
Christian Gottfried Ehrenberg , German naturalist, zoologist, comparative anatomist, geologist, and microscopist, was one of the most famous and productive scientists of his time.- Early collections :...
in 1838.
Placement
Bacteria were first classified as plantPlant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
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
Monera
Monera is a superseded kingdom that contains unicellular organisms without a nucleus , such as bacteria....
(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:
- die Gymnomoneren (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
- VibrioVibrioVibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form...
— a genus of comma shaped bacteria first described in 1854) - BacteriumBacterium (genus)The genus Bacterium was a taxon described in 1828 by Christian Gottfried Ehrenberg. The type species was later changed from Bacterium triloculare to Bacterium coli as it was lost...
— 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 "eine Moneren"(fem. plural "Moneres") in German - BacillusBacillusBacillus is a genus of Gram-positive, rod-shaped bacteria and a member of the division Firmicutes. Bacillus species can be obligate aerobes or facultative anaerobes, and test positive for the enzyme catalase. Ubiquitous in nature, Bacillus includes both free-living and pathogenic species...
— a genus of spore-forming rod shaped bacteria first described in 1835 - Spirochaeta — thin spiral shaped bacteria first described in 1835
- SpirillumSpirillumSpirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is the third distinct bacterial cell shape type besides coccus and bacillus cells.-Taxonomic:...
— spiral shaped bacteria first described in 1832 - etc.
- die Lepomoneren (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 group was later reclassified as the Prokaryotes by Chatton.
It should be noted that the classification of Cyanobacteria (colloquially "blue green algae") has been fought between being algae or bacteria (for example, Haeckel classified Nostoc
Nostoc
Nostoc is a genus of cyanobacteria found in a variety of environmental niches that forms colonies composed of filaments of moniliform cells in a gelatinous sheath.The name "Nostoc" was invented by Paracelsus...
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 in 1913 Vuillemin in a study concluded that all species of the Bacteria should fall into the genera Planococcus, Streptococcus
Streptococcus
Streptococcus is a genus of spherical Gram-positive bacteria belonging to the phylum Firmicutes and the lactic acid bacteria group. Cellular division occurs along a single axis in these bacteria, and thus they grow in chains or pairs, hence the name — from Greek στρεπτος streptos, meaning...
, Klebsiella
Klebsiella
Klebsiella is a genus of non-motile, Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide-based capsule. It is named after the German microbiologist Edwin Klebs...
, Merista, Planomerista, Neisseria
Neisseria
The Neisseria is a large genus of commensal 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 often cause asymptomatic infections, a commensal-like behavior...
, Sarcina, Planosarcina, Metabacterium
Metabacterium
Metabacterium polyspora is an unusual multiple endospore-producing bacterium isolated from the cecum of guinea pigs. This bacterium is physically similar to the phylogenetically related surgeonfish intestinal symbiont Epulopiscium fishelsoni....
, Clostridium
Clostridium
Clostridium is a genus of Gram-positive bacteria, belonging to the Firmicutes. They are obligate anaerobes capable of producing endospores. Individual cells are rod-shaped, which gives them their name, from the Greek kloster or spindle...
, Serratia
Serratia
Serratia is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria of the Enterobacteriaceae family. The most common species in the genus, S. marcescens, is normally the only pathogen and usually causes nosocomial infections. However, rare strains of S. plymuthica, S. liquefaciens,...
, Bacterium
Bacterium (genus)
The genus Bacterium was a taxon described in 1828 by Christian Gottfried Ehrenberg. The type species was later changed from Bacterium triloculare to Bacterium coli as it was lost...
and Spirillum
Spirillum
Spirillum in microbiology refers to a bacterium with a cell body that twists like a spiral. It is the third distinct bacterial cell shape type besides coccus and bacillus cells.-Taxonomic:...
.
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,)
- Bacteria (Cohn 1872b,)
- 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 where in German and not in Latin
The first edition of the Bacteriological Code in 1947 sorted several problems out.
Subdivisions based on Gram staining
Despite there being little agreement on the major subgroups of the Bacteria, Gram stainingGram staining
Gram staining is a method of differentiating bacterial species into two large groups ....
results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Prokaryotae was divided into four divisions, A classification scheme still formally followed by Bergey's manual of systematic bacteriology for tome order
- Gracilicutes (gram negative)
- Photobacteria (photosynthetic): class Oxyphotobacteriae (water as electron acceptor, 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 [sic] (gram positive, subsequently corrected to Fimicutes)
- 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)
"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 virusVirus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es and archaea began relationships approximately two billion years ago, and that co-evolution
Co-evolution
In biology, coevolution is "the change of a biological object triggered by the change of a related object." Coevolution can occur at many biological levels: it can be as microscopic as correlated mutations between amino acids in a protein, or as macroscopic as covarying traits between different...
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 prokaryotes 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 (erroneous) believed to be relics of ancient bacteria thus Carl Woese
Carl Woese
Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1977,...
, 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 This scheme is still followed today.
Subdivisions
In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
(SSU) sequences, which with several additions are still used today.
Opposition
Some authors have opposed the three domain due to various reasons, often in favour of more traditional anthropocentric classifications.One prominent scientist which opposes the three domain system is Thomas Cavalier-Smith, which proposed that the Archaea and the Eukaryotes (the Neomura
Neomura
Neomura is a clade composed of the two domains of life of Archaea and Eukaryota. The group was first proposed by Thomas Cavalier-Smith and its name means "new walls"; so called because it is thought to have evolved from Bacteria, and one of the major changes was the replacement of peptidoglycan...
) 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 molecular biology community (c.f. reviewers' comments on, e.g. Eric Bapteste is "agnostic" regarding the conclusions) and are often not even mention in reviews (e.g.), due to the subjective nature of the assumptions made for logical arguments.
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
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 contain general considerations, principles, rules and various notes and advises in a similar fashion to the nomenclature codesNomenclature Codes
Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms...
of other groups.
Classification authorities
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 on online version of the taxonomic outline of bacteria and archaea is available http://www.taxonomicoutline.org/.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:| Collection Acronym | Name | Location |
|---|---|---|
| ATCC | American Type Culture Collection American Type Culture Collection The American Type Culture Collection is a private, not-for-profit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the... |
Manassas, Virginia Virginia The Commonwealth of Virginia , is a U.S. state on the Atlantic Coast of the Southern United States. Virginia is nicknamed the "Old Dominion" and sometimes the "Mother of Presidents" after the eight U.S. presidents born there... |
| NCTC | National Collection of Type Cultures National Collection of Type Cultures National Collection of Type Cultures is one of the four organizations that constitutes the HPA Culture Collections. It is a non-profit culture collection repository located in UK. NCTC maintains over 5000 bacterial cultures, over 100 mycoplasmas and more than 500 plasmids, host strains,... |
Health Protection Agency Health Protection Agency The Health Protection Agency, or, in Welsh, Yr Asiantaeth Diogelu Iechyd is a statutory corporation. It is an independent UK organisation that was set up by the government in 2003 to protect the public from threats to their health from infectious diseases and environmental hazards... , United Kingdom United Kingdom The United Kingdom of Great Britain and Northern IrelandIn the United Kingdom and Dependencies, other languages have been officially recognised as legitimate autochthonous languages under the European Charter for Regional or Minority Languages... |
| BCCM | Belgium Coordinated Collection of Microorganism Belgian Co-ordinated Collections of Micro-organisms The Belgian Co-ordinated Collections of Micro-organisms is a Belgian government funded consortium of four scientific institutions, who manage and exploit a collection of fungi, bacteria and plasmids... |
Ghent Ghent Ghent is a city and a municipality located in the Flemish region of Belgium. It is the capital and biggest city of the East Flanders province. The city started as a settlement at the confluence of the Rivers Scheldt and Lys and in the Middle Ages became one of the largest and richest cities of... , Belgium Belgium Belgium , officially the Kingdom of Belgium, is a federal state in Western Europe. It is a founding member of the European Union and hosts the EU's headquarters, and those of several other major international organisations such as NATO.Belgium is also a member of, or affiliated to, many... |
| CIP | Collection d'Institut Pasteur | Paris Paris Paris is the capital and largest city in France, situated on the river Seine, in northern France, at the heart of the Île-de-France region... , France France The French Republic , The French Republic , The French Republic , (commonly known as France , is a unitary semi-presidential republic in Western Europe with several overseas territories and islands located on other continents and in the Indian, Pacific, and Atlantic oceans. Metropolitan France... |
| DSMZ | Deutsche Sammlung von Mikroorganismen und Zellkulturen Deutsche Sammlung von Mikroorganismen und Zellkulturen The Deutsche Sammlung von Mikroorganismen und Zellkulturen - DSMZ - GmbH was founded 1969 as the national culture collection in Germany... |
Braunschweig Braunschweig Braunschweig , is a city of 247,400 people, located in the federal-state of Lower Saxony, Germany. It is located north of the Harz mountains at the farthest navigable point of the Oker river, which connects to the North Sea via the rivers Aller and Weser.... , Germany Germany Germany , officially the Federal Republic of Germany , is a federal parliamentary republic in Europe. The country consists of 16 states while the capital and largest city is Berlin. Germany covers an area of 357,021 km2 and has a largely temperate seasonal climate... |
| JCM | Japan Collection of Microorganisms Japan Collection of Microorganisms Japan Collection of Microorganisms is a culture collection of microorganisms in Japan. It is a semi-governmental collection maintained by RIKEN BioResource Center and it is located in Saitama Prefecture. JCM was initiated in 1980 with the purpose of serving as a repository of microorganisms... |
Saitama Saitama, Saitama ' is the capital and the most populous city of Saitama Prefecture in Japan, situated in the south-east of the prefecture. Its area incorporates the former cities of Urawa, Ōmiya, Yono and Iwatsuki. It is a city designated by government ordinance... , Japan Japan Japan is an island nation in East Asia. Located in the Pacific Ocean, it lies to the east of the Sea of Japan, China, North Korea, South Korea and Russia, stretching from the Sea of Okhotsk in the north to the East China Sea and Taiwan in the south... |
| NCCB | Netherlands Culture Collection of Bacteria | Utrecht Utrecht Utrecht is a city in the Netherlands.The name may also refer to:* Utrecht , of which Utrecht is the capital* Utrecht , including the city of Utrecht* Bishopric of Utrecht* Roman Catholic Archdiocese of Utrecht... , Netherlands Netherlands The Netherlands is a constituent country of the Kingdom of the Netherlands, located mainly in North-West Europe and with several islands in the Caribbean. Mainland Netherlands borders the North Sea to the north and west, Belgium to the south, and Germany to the east, and shares maritime borders... |
| NCIMB | National Collection of industrial, Marine and food bacteria | Aberdeen Aberdeen Aberdeen is Scotland's third most populous city, one of Scotland's 32 local government council areas and the United Kingdom's 25th most populous city, with an official population estimate of .... , Scotland Scotland Scotland is a country that is part of the United Kingdom. Occupying the northern third of the island of Great Britain, it shares a border with England to the south and is bounded by the North Sea to the east, the Atlantic Ocean to the north and west, and the North Channel and Irish Sea to the... |
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 rRNA16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
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 it's 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 Projecthttp://rdp.cme.msu.edu/, which align the sequence to other 16S sequences using infernal, a secondary structure bases global alignment, or ARB SILVA
ARB Project
The ARB Project is a free software package for phylogenetic analysis of rRNA and other biological sequences.- Introduction :From the authors' own description,The ARB project was initiated almost 10 years ago...
, which aligns sequences via SINA (SILVA incremental aligner), which does a local alignment of a seed and extends it http://www.arb-silva.de/documentation/background/.
Several identification methods exists:
- Phenotypic analyses
- fatty acid analysesFatty acid methyl esterA fatty acid methyl ester can be created by an alkali catalyzed reaction between fats or fatty acids and methanol. The molecules in biodiesel are primarily FAMEs, usually obtained from vegetable oils by transesterification....
- Growth conditions (Agar plateAgar plateAn agar plate is a Petri dish that contains a growth medium used to culture microorganisms or small plants like the moss Physcomitrella patens.Selective growth compounds may also be added to the media, such as antibiotics....
, Biolog multiwell plates)
- fatty acid analyses
- Genetic analyses
- DNA-DNA hybridization
- DNA profiling
- Sequence
- GC ratiosGC-contentIn molecular biology and genetics, GC-content is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine . This may refer to a specific fragment of DNA or RNA, or that of the whole genome...
- Phylogenetic analyses
- 16S16S ribosomal RNA16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
-based phylogeny - phylogeny based on other genes
- Multi-gene sequence analysis
- Whole-genome sequence based analysis
- 16S
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 everywhereEnvironmental microbiology
Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
") therefore the concept of species which works best for animals, becomes entirely a matter of judgement.
The number of species of bacteria and archaea (approximately 5000) 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
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
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 threshhold 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 Primates would be a single species
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 EnterobacteriaceaeEnterobacteriaceae
The Enterobacteriaceae is a large family of bacteria that includes many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis, Klebsiella and Shigella. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the...
family of the class Gammaproteobacteria
Gammaproteobacteria
Gammaproteobacteria is a class of several medically, ecologically and scientifically important groups of bacteria, such as the Enterobacteriaceae , Vibrionaceae and Pseudomonadaceae. An exceeding number of important pathogens belongs to this class, e.g...
, the species in the genus Shigella
Shigella
Shigella is a genus of Gram-negative, nonspore forming, non-motile, rod-shaped bacteria closely related to Escherichia coli and Salmonella. The causative agent of human shigellosis, Shigella causes disease in primates, but not in other mammals. It is only naturally found in humans and apes. During...
(S. dysenteriae, S. flexneri
Shigella flexneri
Shigella flexneri is a species of Gram-negative bacteria in the genus Shigella that can cause diarrhea in humans. There are several different serogroups of Shigella; S. flexneri belongs to group B. S. flexneri infections can usually be treated with antibiotics although some strains have become...
, S. boydii
Shigella boydii
Shigella boydii is a Gram-negative bacteria of the genus Shigella. Like other member of the genus, S. boydii is a non-motile, non-sporeforming, rod-shaped bacteria which can cause dysentery in humans through fecal-oral contamination....
, S. sonnei
Shigella sonnei
Shigella sonnei is a species of Shigella. Together with Shigella flexneri, it is responsible for 90% of shigellosis. Shigella sonnei is named for the Danish bacteriologist Carl Olaf Sonne....
) by an evolutionary point of view are strains of the species Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
(polyphyletic), but due to genetic differences cause different medical conditions in the case of the pathogenic strains., it should be noted that Escherichia coli
Escherichia coli
Escherichia coli is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls...
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 FirmicutesFirmicutes
The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
) belonging to the "B. cereus group" (B. anthracis
Bacillus anthracis
Bacillus anthracis is the pathogen of the Anthrax acute disease. It is a Gram-positive, spore-forming, rod-shaped bacterium, with a width of 1-1.2µm and a length of 3-5µm. It can be grown in an ordinary nutrient medium under aerobic or anaerobic conditions.It is one of few bacteria known to...
, B. cereus, B . thuringiensis
Bacillus thuringiensis
Bacillus thuringiensis is a Gram-positive, soil-dwelling bacterium, commonly used as a biological pesticide; alternatively, the Cry toxin may be extracted and used as a pesticide. B...
, B. mycoides
Bacillus mycoides
Bacillus mycoides is a bacterium of the genus Bacillus.Gram positiveRhizoid formationimmobileCasein breakdown positive Gelatin breakdown positiveCatalase positiveGlucose fermentation positiveLactose fermentation negative...
, B. pseudomycoides, B. weihenstephanensis
Bacillus weihenstephanensis
Bacillus weihenstephanensis is a soil-dwelling, Gram-positive, rod-shaped, beta hemolytic bacterium. It is differentiated by its psychrotolerant growth . -Pathogenisis:...
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 specie
Yersinia pestisYersinia pestis
Yersinia pestis is a Gram-negative rod-shaped bacterium. It is a facultative anaerobe that can infect humans and other animals....
is in effect a strain of Yersinia pseudotuberculosis
Yersinia pseudotuberculosis
Yersinia pseudotuberculosis is a Gram-negative bacterium that causes Pseudotuberculosis disease in animals; humans occasionally get infected zoonotically, most often through the food-borne route.-Pathogenesis:In animals, Y...
, but with a pathogenicity island that confer 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 PseudomonadalesPseudomonadales
The Pseudomonadales are an order of Proteobacteria. A few members are opportunistic pathogens, such as species of Pseudomonas, Moraxella, and Acinetobacter, which may cause pneumonia.-Pseudomonas:...
, the genus Azotobacter
Azotobacter
Azotobacter is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime. They are aerobic, free-living soil microbes which play an important role in the nitrogen cycle in nature, binding atmospheric nitrogen, which is...
and the species Azomonas macrocytogenes are actually members of the genus Pseudomonas
Pseudomonas
Pseudomonas is a genus of gammaproteobacteria, belonging to the family Pseudomonadaceae containing 191 validly described species.Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the...
, but were misclassified due to nitrogen fixing capabilities and the large size of the genus Psuedomonas 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 Bacillus genus, 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 in nested in rhizobium and the Agrobacterium species transferred to the Rhizobium genus (resulting in the following comp. nov.: Rhizobium radiobacter in turn 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 conter-arguedNomenclature
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, tautonymTautonym
-In biology :In biology, tautonym is an informal term to indicate a scientific name of a species in which both parts of the name have the same spelling, for example Bison bison...
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
History of the Latin alphabet
The Latin alphabet is the main writing system in use in the Western world and is the most widely used alphabet writing system in the world. Being the standard script of the English language it is often referred to simply as "the alphabet" in English...
for these), consequently hyphens, accents and other letters are not accepted and should be translitterated correctly (e.g. ß=ss). Ancient Greek being written in the Greek alphabet, needs to be translitterated into the Latin alphabet.
When compound words 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 consult 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 Bacteriologocal 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 reccomendation 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
Thermotogae
Thermotogae is a phylum of the domain "Bacteria". This phylum comprises merely the class "Thermotogae", with the order "Thermotogales" and the family "Thermotogaceae"....
, Aquificae
Aquificae
The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of...
and Chlamydiae
Chlamydiae
Chlamydiae is a bacterial phylum and class whose members are obligate intracellular pathogens. Many Chlamydiae coexist in an asymptomatic state within specific hosts, and it is widely believed that these hosts provide a natural reservoir for these species....
, the male plurals Chloroflexi
Chloroflexi
Chloroflexi is one of four classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes....
, Bacilli
Bacilli
Bacilli refers to a taxonomic class of bacteria. It includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens like Bacillus anthracis .-Ambiguity:...
and Deinococci and the greek plurals Spirochaetes, Gemmatimonadetes
Gemmatimonadetes
The Gemmatimonadetes are a family of bacteria, given their own phylum . The first member of this phylum was discovered in 2003 in activated sludge in a sewage treatment system. The bacteria was named Gemmatimonas aurantiaca and is a gram-negative rod-shaped aerobe that appears to replicate by...
and Chrysiogenetes).
| Rank | Suffix | Example |
|---|---|---|
| Genus | Elusimicrobium | |
| Subtribe (disused) | |
(Elusimicrobiinae) |
| Tribe (disused) | |
(Elusimicrobiieae) |
| Subfamily | |
(Elusimicrobioideae) |
| Family | |
Elusimicrobiaceae |
| Suborder | |
(Elusimicrobineae) |
| Order | |
Elusimicrobiales |
| Subclass | |
(Elusimicrobidae) |
| Class | |
Elusimicrobia |
| Phylum | see text | Elusimicrobia |
Phyla endings
Phyla are not covered by the Bacteriological code, however, the scientific community generally follows the Ncbi and Lpsn taxonomy, where the name of the phylum is generally the plural of the type genus, with the exception of the Firmicutes, Cyanobacteria and Proteobacteria, whose names do not stem from a genus name. The higher taxa proposed by Cavalier-Smith are generally disregarded by the molecular phylogeny community (e.g.) (vide supra).For the Archaea the suffix -archaeota is used. For bacterial phyla
Bacterial phyla
The bacterial phyla are the major lineages of the domain Bacteria.In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species , which is a lower level of a hierarchy of ranks...
it was proposed that the suffix -bacteria be used for phyla.
Consequently for main phyla the name of the phyla is the same as the first described class:
- AcidobacteriaAcidobacteriaAcidobacteria are a newly devised phylum of Bacteria, whose members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture....
(from Acidobacterium) - ActinobacteriaActinobacteriaActinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
(from ActinomycesActinomycesActinomyces from Greek "actino" that means mucus and fungus, is a genus of the actinobacteria class of bacteria. They are all Gram-positive and are characterized by contiguous spread, suppurative and granulomatous inflammation, and formation of multiple abscesses and sinus tracts that may...
) - Caldisericia (from CaldisericumCaldisericumCaldisericum exile is a species of bacteria sufficiently distinct from other bacteria to be placed in its own family, order, class and phylum. It is the first member of the candidate phylum OP5 to be cultured and described....
) - ElusimicrobiaElusimicrobiaThe phylum Elusimicrobia previosuly known as 'Termite Group 1' has been shown to be widespread in different ecosystems like marine environment, sewage sludge, contaminated sites and soils...
(from Elusimicrobium) - FusobacteriaFusobacteriaFusobacteria 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 species...
(from FusobacteriumFusobacteriumFusobacterium is a genus of filamentous, anaerobic, Gram-negative bacteria, similar to Bacteroides.Fusobacterium contribute to several human diseases, including periodontal diseases, Lemierre's syndrome, and topical skin ulcers...
) - ThermodesulfobacteriaThermodesulfobacteriaThe Thermodesulfobacteria are a phylum of thermophilic sulfate-reducing bacteria.-Phylogeny:The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project...
(from Thermodesulfobacterium) - ThermotogaeThermotogaeThermotogae is a phylum of the domain "Bacteria". This phylum comprises merely the class "Thermotogae", with the order "Thermotogales" and the family "Thermotogaceae"....
(from ThermotogaThermotogaThermotoga is a genus of the phylum Thermotogae. Members of Thermotoga are hyperthermophilic bacteria whose cell is wrapped in an unique sheath-like outer membrane, called a "toga"....
) - AquificaeAquificaeThe Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. Members of the genus Aquifex, for example, are productive in water between 85 to 95 °C. They are the dominant members of...
(from Aquifica) - ChlamydiaeChlamydiaeChlamydiae is a bacterial phylum and class whose members are obligate intracellular pathogens. Many Chlamydiae coexist in an asymptomatic state within specific hosts, and it is widely believed that these hosts provide a natural reservoir for these species....
(from ChlamydiaChlamydia (bacterium)Chlamydia is a genus of bacteria that are obligate intracellular parasites. Chlamydia infections are the most common bacterial sexually transmitted infections in humans and are the leading cause of infectious blindness worldwide....
) - ChloroflexiChloroflexiChloroflexi is one of four classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes....
(from Chloroflexus) - Chrysiogenetes (from ChrysiogenesChrysiogenesChrysiogenes arsenatis is a species of bacterium given its own phylum, called the Chrysiogenetes. It has a unique lifestyle and biochemistry. Instead of respiring with oxygen, it respires using the most oxidized form of arsenic, arsenate. It uses arsenate as its terminal electron acceptor....
) - GemmatimonadetesGemmatimonadetesThe Gemmatimonadetes are a family of bacteria, given their own phylum . The first member of this phylum was discovered in 2003 in activated sludge in a sewage treatment system. The bacteria was named Gemmatimonas aurantiaca and is a gram-negative rod-shaped aerobe that appears to replicate by...
(from Gemmatimonas) - Deferribacteres (from DeferribacterDeferribacterDeferribacter is a genus in the phylum Deferribacteres .-Etymology:The name Deferribacter derives from:Latin pref. de-, from; Latin noun ferrum, iron; New Latin masculine gender noun , a rodbacter, nominally meaning "a rod", but in effect meaning a bacterium, rod; New Latin masculine gender noun...
)
Whereas for others where the -ia suffix for class is used regardless of grammar they differ:
- phylum BacteroidetesBacteroidetesThe phylum Bacteroidetes is composed of three large classes of bacteria that are widely distributed in the environment, including in soil, in sediments, sea water and in the guts and on the skin of animals....
vs. class Bacteroidia from BacteroidesBacteroidesBacteroides is a genus of Gram-negative, bacillus bacteria. Bacteroides species are non-endospore-forming, anaerobes, and may be either motile or non-motile, depending on the species. The DNA base composition is 40-48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids... - phylum Chlorobi vs. class Chlorobia from ChlorobiumChlorobiumChlorobium 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+...
- phylum VerrucomicrobiaVerrucomicrobiaVerrucomicrobia is a recently described phylum of bacteria. This phylum contains only a few described species . The species identified have been isolated from fresh water and soil environments and human feces...
vs. class Verrucomicrobiae from Verrucomicrobium (anomalous class name) - phylum Dictyoglomi versus class Dictyoglomia from DictyoglomusDictyoglomusDictyoglomus 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 metabolizing organic molecules...
- phylum FibrobacteresFibrobacteresFibrobacteres is a small bacterial phylum which includes many of the major rumen bacteria, allowing for the degradation of plant-based cellulose in ruminant animals. Members of this phylum were categorized in other phyla...
versus class Fibrobacteria from Fibrobacter (c.f. the suffix -bacter-bacter-Meaning:Bacter is a Neolatin term coined from bacterium, which in turn derives from the Greek βακτήριον, meaning small staff...
, note the difference with Deferribacteres) - phylum LentisphaeraeLentisphaeraeLentisphaerae is a phylum of bacteria closely related to Chlamydiae and Verrucomicrobia.It includes two monotypic orders Lentisphaerales and Victivallales. Phylum members can be aerobic or anaerobic and fall under two distinct phenotypes. One consists of terrestrial gut microbiota from mammals...
versus class Lentisphaeria from Lentisphaera - phylum Nitrospira or NitrospiraeNitrospiraeNitrospira is a genus of bacteria in the phylum Nitrospirae. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. The second member of this genus was discovered in 1995 from a corroded iron pipe in a Moscow...
versus class Nitrospira from Nitrospira - phylum Spirochaetes versus class Spirochaetae from Spirochaeta
- phylum SynergistetesSynergistetesSynergistetes is a phylum of bacteria. Members are Gram-negative,rod-shaped obligate anaerobes. Species within this phylum have been implicated in periodontal disease, gastrointestinal infections and soft tissue infections.- Phylogeny:...
versus class Synergistetia from Synergistes - phylum PlanctomycetesPlanctomycetesPlanctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, and marine and fresh water. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, called the stalk, at the nonreproductive end that helps them to attach to each other...
versus Planctomycea from Planctomyces
An exception is the phylum Deinococcus-Thermus
Deinococcus-Thermus
The Deinococcus-Thermus are a small group of bacteria composed of cocci highly resistant to environmental hazards.There are two main groups.* The Deinococcales include two families, with three genera, Deinococcus and Truepera, the former with several species that are resistant to radiation; they...
, which bears a hyphenated pair of genera —only non accented latin letters are accepted for valid names, but phyla are not officially recognised.
Names after people
Manynumber? 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. Borrelia burgdorferiBorrelia burgdorferi
Borrelia burgdorferi is a species of Gram negative bacteria of the spirochete class of the genus Borrelia. B. burgdorferi is predominant in North America, but also exists in Europe, and is the agent of Lyme disease....
). 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 plaqueDental plaque
Dental plaque is a biofilm, usually a pale yellow, that develops naturally on the teeth. Like any biofilm, dental plaque is formed by colonizing bacteria trying to attach themselves to a smooth surface...
or Star jelly
Nostoc
Nostoc is a genus of cyanobacteria found in a variety of environmental niches that forms colonies composed of filaments of moniliform cells in a gelatinous sheath.The name "Nostoc" was invented by Paracelsus...
), 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
Proper noun
A proper noun or proper name is a noun representing a unique entity , as distinguished from a common noun, which represents a class of entities —for example, city, planet, person or corporation)...
as an English common noun (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.
Customs are present for centain names, such as those ending in -monas
-monas
The suffix -monas is used in microbiology for many genera and is intended to mean "unicellular organism".-Meaning:The suffix -monas is used in microbiology for many genera in a similar way to -bacter, -bacillus, -coccus or -spirillum...
are converted into -monad (one pseudomonad, two aeromonads and not -monades).
Bacteria which are the etiological cause
Etiology
Etiology is the study of causation, or origination. The word is derived from the Greek , aitiologia, "giving a reason for" ....
for a 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 cholera) or Lyme disease spirochete (Borrelia burgdorferi
Borrelia burgdorferi
Borrelia burgdorferi is a species of Gram negative bacteria of the spirochete class of the genus Borrelia. B. burgdorferi is predominant in North America, but also exists in Europe, and is the agent of Lyme disease....
) , note also rickettsialpox (Rickettsia akari
Rickettsia akari
Rickettsia akari is a species of Rickettsia which causes rickettsialpox.After a 1946 outbreak of a rickettsial-type disease at an apartment complex in Kew Gardens, Queens, an investigation was performed to identify the source of the infections...
) (for more see ).
Treponema
Treponema
Treponema is a bacterial genus. The major species is Treponema pallidum, whose subspecies are responsible for diseases such as syphilis and yaws.The species Treponema hyodysenteriae and Treponema innocens have been reclassified into Serpula....
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).
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 ChloroflexiChloroflexiChloroflexi is one of four classes of bacteria in the phylum Chloroflexi, known as filamentous green non-sulfur bacteria. They produce energy from light and are named for their green pigment, usually found in photosynthetic bodies called chlorosomes....
- Green sulfur bacteria are members of the Chlorobi
- Purple bacteria are some, but not all, members of the phylum ProteobacteriaProteobacteriaThe Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
- Purple sulfur bacteria are members of the order Chromatiales
- low G+C Gram-positive bacteria are members of the phylum FirmicutesFirmicutesThe Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and Zymophilus, have a porous pseudo-outer-membrane that causes them to stain Gram-negative...
, regardless of GC content - high G+C Gram-positive bacteria are members of the phylum ActinobacteriaActinobacteriaActinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
, regardless of GC content - Rhizobacteria are members of various genera of proteobacteria
- Rhizobia are members of the order RhizobialesRhizobialesRhizobiales is an order of alpha proteobacteria. They are gram-negative.The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families here. The Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae are the four families that contain...
- Lactic streptococci are members of the genus LactococcusLactococcusLactococcus is a genus of lactic acid bacteria that were formerly included in the genus Streptococcus Group N1. They are known as homofermentors meaning that they produce a single product, lactic acid in this case, as the major or only product of glucose fermentation...
- Coryneform bacteria are members of the family Corynebacteriaceae
- Fruiting gliding bacteria or myxobacteria are members of the order Myxococcales
- Enterics are members of the order Enterobacteriales, 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-1GFAJ-1GFAJ-1 is a strain of rod-shaped bacterium in the family Halomonadaceae. The extremophile was isolated from the hypersaline and alkaline Mono Lake in eastern California by a research team led by NASA astrobiologist Felisa Wolfe-Simon...
- If a bacterium is known and well studies but not culturable, it is given the term Candidatus in its name
- A basonym is original name of a new combination, namely the first name given to a taxa before it was reclassified
- A synonym is an alternative name for a taxa, i.e. a taxa was erroneusly described twice
- When a taxa is transfer it becomes a new combinations (comb. nov.) or nomina nova (nom. nov.)
- paraphylyParaphylyA group of taxa is said to be paraphyletic if the group consists of all the descendants of a hypothetical closest common ancestor minus one or more monophyletic groups of descendants...
, monophylyMonophylyIn common cladistic usage, a monophyletic group is a taxon which forms a clade, meaning that it contains all the descendants of the possibly hypothetical closest common ancestor of the members of the group. The term is synonymous with the uncommon term holophyly...
and polyphylyPolyphylyA polyphyletic group is one whose members' last common ancestor is not a member of the group.For example, the group consisting of warm-blooded animals is polyphyletic, because it contains both mammals and birds, but the most recent common ancestor of mammals and birds was cold-blooded...
See also
- list of Latin and Greek words commonly used in systematic names
- List of Bacteria genera
- List of bacterial orders
- List of sequenced prokaryotic genomes
- Human microbiome projectHuman microbiome projectThe Human Microbiome Project is a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans . Launched in 2008, it is a five-year project, best characterized as a...
- Environmental microbiologyEnvironmental microbiologyEnvironmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
and Microbial ecologyMicrobial ecologyMicrobial ecology 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 viruses.... - List of clinically important bacteria
- List of sequenced archaeal genomes
- List of Archaea genera
- Species problemSpecies problemThe species problem or species concept is a mixture of difficult, related questions that often come up when biologists identify species and when they define the word "species"....
- Evolutionary gradeEvolutionary gradeIn alpha taxonomy, a grade refers to 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:...
- Cryptic species complexCryptic species complexIn biology, a cryptic species complex is a group of species which satisfy the biological definition of species—that is, they are reproductively isolated from each other—but whose morphology is very similar ....
- Synonym (taxonomy)Synonym (taxonomy)In scientific nomenclature, a synonym is a scientific name that is or was used for a taxon of organisms that also goes by a different scientific name. For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies...
- TaxonomyTaxonomyTaxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
- LPSNLPSNList of Prokaryotic names with Standing in Nomenclature is an online database that maintains and provides accurate name and related information of prokaryotes according to the International Code of Nomenclature of Bacteria , curated by prof...
, list of accepted bacterial and archaeal names - Cyanobacteria, a phyla of common bacteria but poor classified at present
- Bacterial phylaBacterial phylaThe bacterial phyla are the major lineages of the domain Bacteria.In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species , which is a lower level of a hierarchy of ranks...
, a complicated classification