Bacterial phyla
Encyclopedia
The bacterial phyla are the major lineages (phyla
or divisions) of the domain Bacteria
.
In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species (binary nomenclature), which is a lower level of a hierarchy of ranks. Currently, the most accepted mega-classification system is under the three-domain system
, which is based on molecular phylogeny
. In this system bacteria are members of the domain Bacteria and "phylum" is the rank below domain as the rank "kindgom" is disused at present in bacterial taxonomy
.
In this classification scheme Bacteria is (unofficially) subdivided into over 29 phyla with representatives cultured in a lab. Many major clades of bacteria that exist but cannot currently be cultured are known solely via etagenomics] and are called candidate phyla. If these are included the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 52 as of 2003.
Regarding the precise phylogeny at the base of the clade Bacteria, some scientists believe there may be a branching order, whereas other scientists, such as Norman Pace, believe the various Bacterial phyla represent a large hard polytomy
(a simultaneous multiple speciation event).
. The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distored and confusion classification, an examples of which, noted Carl Woese, is Pseudomonas
whose etymology ironically matched its taxonomy, namely "false unit".
In 1987, Carl Woese
, regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA
(SSU) sequences:
The "purple bacteria and relatives" were renamed Proteobacteria
.
The low and high CG content gram positive subdivisions were renamed Actinobacteria
and Firmicutes
divisions, making the number of phyla 12.
Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. The candidate phylum TM7 may be Gram positive. Chloroflexi
however possess a single bilayer, but stain negative (with some exceptions).
"Green non-sulfur bacteria and relatives" was renamed Chloroflexi
.
"Radioresistant micrococci and relatives" are commonly referred to as Deinococcus-Thermus
clade,, although it has been prosed to call the clade Xenobacteria or Hadobacteria (latter is illegitimate).
, which oxidises hydrogen gas. Other non-thermophiles, such as Acidobacteria
, a ubiquitous phyla with divergent physiologies, have been found, some of which are chemolithotrophs, such as Nitrospira (nitrile-oxidising) or Leptospirillum (Fe-oxidising)., some proposed phyla however do not appear in LPSN
as they were insufficiently described or are awaiting approval or it is debated if they may belong to a pre-existing phyla. An example of this is the genus Caldithrix, consisting of C. palaeochoryensis and C.abyssi, which is considered Deferribacteres,, however, it shares only 81% similarity with the other Deferribacteres (Deferribacter
species and relatives) and is considered a separate phylum by Rappé and Giovannoni. Additionally the placement of the genus Geovibrio in the phylum Deferribacteres is debated.
to analyse environmental DNA (metagenomics
), the 16S rRNA of an extremely large number of undiscovered species have been found, showing that there are several whole phyla which have no known cultivable representative and that some phyla lack in culture major subdivisions as is the case for Verrucomicrobia
and Chloroflexi
.
The term Candidatus
is used for proposed species for which the lack of information prevents it to be validated, such as where the only evidence is DNA sequence data, even if the whole genome
has been sequenced. When the species are members of whole phyla it is called a candidate division
and in 2003 there were 26 candidate divisions out of 52.
A candidate division was defined by in 1998 Hugenholtz and Pace
, as a set of 16S ribosomal RNA
sequences with less than 85% similarity.
Three candidate phyla were known before 1998, prior to the 85% threshold definition by Hugenholtz and Pace:
Since then several other cadidate phyla were identified and accepted by Rappé and Giovannoni (2003):)
Since then a candidate phylum called Poribacteria was discovered, living in symbiosis
with sponges and extensively studied. (Note: the divergence of the major bacterial lineages predates sponges)
Other candidate phyla that have been the centre of some studies are TM7
, the genomes of organisms of which have even been sequenced (draft), WS6 and Marine Group A.
Two species of the candidate division OP10, which is now called Armatimonadetes
, where recently cultured: Armatimonas rosea isolated from the rhizoplane of a reed in a lake in Japan and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere
, New Zealand
.
One species, Caldisericum exile, of the candidate division OP5 was cultured, leading to it being named Caldiserica.
Termite Group 1 is now known as Elusimicrobia
, after the ultramicrobacterium Elusimicrobium minutum
was cultured.
The candidate division VadinBE97 is now known as Lentisphaerae
after Lentisphaera araneosa and Victivallis vadensis were cultured.
Despite these lineages not being officially recognised, due to the ever increasing number of sequences belonging to non-existent phyla, ARB-Silva list 57 phyla, not only the 27 phyla with validly accepted species, but also 30 Candidate divisions (BD1-5, BHI80-139, BRC1, CK-1C4-19, EM19, GAL08, GOUTA4, Hyd24-12, JL-ETNP-Z39, Kazan-3B-28, LD1-PA38, MVP-21, NPL-UPA2, OC31, OD1, OP3, OP9, OP10, OP11, RF3, RsaHF231, SM2F11, SR1, TA06, TM6, TM7, WCHB1-60, WS3 and WS6), while Ribosomal Database Project 10, list 29 phyla and 7 candidate divisions (OP10, OP11, OD1, BRC1, SR1, WS3, TM7)
The FCB group includes Chlorobi, Bacteroidetes, Fibrobacteres, Gemmatimonadates, Caldithrix and Marine group A.
The PVC group includes Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia, Poribacteria and OP3.
(antibiotic production), Propionibacterium acnes
(odorous skin commensal) and Propionibacterium freudenreichii
(holes in Emmental)
and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies may be one of the most deep branching phyla.
(diderms, weakly Gram negative) is a phylum of the PVC superphylum. It is composed of only 6 genera of obbligate intracellular pathogens with a complex life cycle. Species include Chlamydia trachomatis
(chlamydia infection).
as opposed to phycobilisomes of cyanobacteria (another photosynthetic group).
,diverse phylum including thermophiles and halorespirers, known colloquially as Green non-sulfur bacteria.
, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phyla
, formerly candidate division Termite Group 1
, Low-G+C Gram positive species most often spore-forming, in two/three classes: the class Bacilli
such as the Bacillus
spp. (e.g. B. anthracis, a pathogen, and B. subtilis, biotechnologically useful), lactic acid bacteria
(e.g. Lactobacillus casei
in yoghurt, Oenococcus oeni
in malolactic fermentation
, Streptococcus pyogenes
, pathogen), the class Clostridia
of mostly anaerobic sulphite-reducing saprophytic species, includes the genus Clostridium
(e.g. the pathogens C. dificile, C. tetani
, C. botulinum
and the biotech C. acetobutylicum
)
, member of the FBC superphylum.
, formerly clade VadinBE97, member of the PVC superphylum.
, contains most of the "commonly known" species, such as Escherichia coli
or Pseudomonas aeruginosa
, which causes Lyme disease
, formerly/debatedly of the phylum Firmicutes
(sister clades). Despite their monoderm Gram positive relatives, they lack peptidoglycan and instead possess mycolic acid
. Notable genus: Mycoplasma
.
Caldimicrobium, Thermodesulfatator and Thermodesulfobacterium). The members of the phylum are thermophilic sulphate-reducers.
and are hyperthermophilic obligate anaerobic fermenters.
For example, in studies using 16S and few other sequences Thermotogae and Aquificae appear as the most basal phyla, whereas in several phylogenomic studies, Firmicutes are the most basal.
Phylum
In biology, a phylum The term was coined by Georges Cuvier from Greek φῦλον phylon, "race, stock," related to φυλή phyle, "tribe, clan." is a taxonomic rank below kingdom and above class. "Phylum" is equivalent to the botanical term division....
or divisions) of the domain 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 bacterial strain has to be assigned to a species (binary nomenclature), which is a lower level of a hierarchy of ranks. Currently, the most accepted mega-classification system is under the three-domain system
Three-domain system
The three-domain system is a biological classification introduced by Carl Woese in 1977 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria and Archaebacteria...
, which is based on molecular phylogeny
Molecular phylogeny
Molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree...
. In this system bacteria are members of the domain Bacteria and "phylum" is the rank below domain as the rank "kindgom" is disused at present in bacterial taxonomy
Bacterial taxonomy
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 , which in turn is a lower level of a hierarchy of ranks .In the currently accepted classification...
.
In this classification scheme Bacteria is (unofficially) subdivided into over 29 phyla with representatives cultured in a lab. Many major clades of bacteria that exist but cannot currently be cultured are known solely via etagenomics] and are called candidate phyla. If these are included the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 52 as of 2003.
Regarding the precise phylogeny at the base of the clade Bacteria, some scientists believe there may be a branching order, whereas other scientists, such as Norman Pace, believe the various Bacterial phyla represent a large hard polytomy
Polytomy
A polytomy , meaning many temporal based branches, is a section of a phylogeny in which the evolutionary relationships can not be fully resolved to dichotomies. In a phylogenetic tree, a polytomy is represented as a node which has more than two immediate descending branches...
(a simultaneous multiple speciation event).
Molecular phylogenetics
Traditionally, phylogeny were inferred and taxonomy established based on studies of morphology. Recently molecular phylogenetics has been used to allow better elucidation of the evolutionary relationship of the species by analysing their DNA/protein sequences, for example their ribosomal DNARibosomal DNA
Ribosomal DNA codes for ribosomal RNA. The ribosome is an intracellular macromolecule that produces proteins or polypeptide chains. The ribosome itself consists of a composite of proteins and RNA. As shown in the figure, rDNA consists of a tandem repeat of a unit segment, an operon, composed of...
. The lack of easily accessible morphological features, such as those present in animals and plants, hampered early efforts of classification and resulted in erroneous, distored and confusion classification, an examples of which, noted Carl Woese, is 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...
whose etymology ironically matched its taxonomy, namely "false unit".
Initial sub-division
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, divided Eubacteria into 11 divisions based on 16S ribosomal RNA
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
(SSU) sequences:
- Purple BacteriaPurple bacteriaPurple bacteria or purple photosynthetic bacteria are proteobacteria that are phototrophic, that is capable of producing energy through photosynthesis...
and their relatives- alpha subdivisionAlphaproteobacteriaAlphaproteobacteria is a class of Proteobacteria. Like all Proteobacteria, they are Gram-negative.-Characteristics:The Alphaproteobacteria comprise most phototrophic genera, but also several genera metabolising C1-compounds , symbionts of plants and animals, and a group of pathogens, the...
(purple non-sulfur bacteria, rhizobacteriaRhizobacteriaRhizobacteria are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties...
, AgrobacteriumAgrobacteriumAgrobacterium is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. Agrobacterium tumefaciens is the most commonly studied species in this genus...
, Rickettsiae, NitrobacterNitrobacterNitrobacter is genus of mostly rod-shaped, gram-negative, and chemoautotrophic bacteria.Nitrobacter plays an important role in the nitrogen cycle by oxidizing nitrite into nitrate in soil...
) - beta subdivisionBetaproteobacteriaBetaproteobacteria is a class of Proteobacteria. Betaproteobacteria are, like all Proteobacteria, gram-negative.The Betaproteobacteria consist of several groups of aerobic or facultative bacteria which are often highly versatile in their degradation capacities, but also contain chemolithotrophic...
(Rhodocyclus, (some) Thiobacillus, AlcaligenesAlcaligenesAlcaligenes is a genus of Gram-negative, aerobic, rod-shaped bacteria. The species are motile with one or more peritrichous flagella.Alcaligenes species have been used for the industrial production of non-standard amino acids; A. eutrophus also produces the biopolymer polyhydroxybutyrate .-External...
, 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:...
, Nitrosovibrio) - gamma subdivisionGammaproteobacteriaGammaproteobacteria 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...
(enterics, fluorescent pseudomonadsPseudomonadaceaeThe Pseudomonadaceae is a family of bacteria that includes the genera Azomonas, Azomonotrichon, Azorhizophilus, Azotobacter, Cellvibrio, Mesophilobacter, Pseudomonas , Rhizobacter, Rugamonas, and Serpens...
, purple sulfur bacteriaPurple sulfur bacteriaThe purple sulfur bacteria are a group of Proteobacteria capable of photosynthesis, collectively referred to as purple bacteria. They are anaerobic or microaerophilic, and are often found in hot springs or stagnant water. Unlike plants, algae, and cyanobacteria, they do not use water as their...
, LegionellaLegionellaLegionella is a pathogenic Gram negative bacterium, including species that cause legionellosis or Legionnaires' disease, most notably L. pneumophila. It may be readily visualized with a silver stain....
, (some) BeggiatoaBeggiatoaBeggiatoa is a genus of bacteria in the order Thiotrichales. They are named after the Italian medic and botanist F.S. Beggiato. The organisms live in sulfur-rich environments...
) - delta subdivisionDeltaproteobacteriaDeltaproteobacteria is a class of Proteobacteria. All species of this group are, like all Proteobacteria, gram-negative.The Deltaproteobacteria comprise a branch of predominantly aerobic genera, the fruiting-body-forming Myxobacteria which release myxospores in unfavorable environments, and a...
(Sulfur and sulfate reducers (DesulfovibrioDesulfovibrioDesulfovibrio is a genus of Gram negative sulfate-reducing bacteria. Some species of Desulfovibrio are capable of transduction. Desulfovibrio species are commonly found in aquatic environments with high levels of organic material, as well as in water-logged soils, and form major community members...
), MyxobacteriaMyxobacteriaThe myxobacteria are a group of bacteria that predominantly live in the soil. The myxobacteria have very large genomes, relative to other bacteria, e.g. 9-10 million nucleotides. Sorangium cellulosum has the largest known bacterial genome, at 13.0 million nucleotides...
, BdellovibrioBdellovibrioBdellovibrio is a genus of Gram-negative, obligate aerobic bacteria.One of the more notable characteristics of this genus is that members parasitize other Gram-negative bacteria by entering into their periplasmic space and feeding on the biopolymers, e.g. proteins and nucleic acids, of their hosts...
)
- alpha subdivision
- Gram-positiveGram-positiveGram-positive bacteria are those that are stained dark blue or violet by Gram staining. This is in contrast to Gram-negative bacteria, which cannot retain the crystal violet stain, instead taking up the counterstain and appearing red or pink...
Eubacteria- High-G+C speciesGC-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...
- 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....
(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...
, StreptomycesStreptomycesStreptomyces is the largest genus of Actinobacteria and the type genus of the family Streptomycetaceae. Over 500 species of Streptomyces bacteria have been described. As with the other Actinobacteria, streptomycetes are gram-positive, and have genomes with high guanine and cytosine content...
, ArthrobacterArthrobacterArthrobacter is a genus of bacteria that is commonly found in soil. All species in this genus are Gram-positive obligate aerobes that are rods during exponential growth and cocci in their stationary phase....
, MicrococcusMicrococcusMicrococcus is a genus of bacteria in the Micrococcaceae family. Micrococcus occurs in a wide range of environments, including water, dust, and soil. Micrococci have Gram-positive spherical cells ranging from about 0.5 to 3 micrometers in diameter and are typically appear in tetrads...
, BifidobacteriumBifidobacteriumBifidobacterium is a genus of Gram-positive, non-motile, often branched anaerobic bacteria. They are ubiquitous, endosymbiotic inhabitants of the gastrointestinal tract, vagina and mouth of mammals and other animals. Bifidobacteria are one of the major genera of bacteria that make up the colon...
) - Low-G+C species - 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...
(ClostridiumClostridiumClostridium 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...
, Peptococcus, 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...
, MycoplasmaMycoplasmaMycoplasma refers to a genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many common antibiotics such as penicillin or other beta-lactam antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans,...
) - Photosynthetic species (Heliobacterium)
- Species with gram-negative walls (Megasphaera, SporomusaSporomusaSporomusa is a genus of Firmicutes bacteria classified within the class Negativicutes.-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...
)
- High-G+C species
- Cyanobacteria and chloroplasts (Aphanocapsa, OscillatoriaOscillatoriaOscillatoria is a genus of filamentous cyanobacterium which is named for the oscillation in its movement. Filaments in the colonies can slide back and forth against each other until the whole mass is reoriented to its light source. It is commonly found in watering-troughs waters, and is mainly...
, NostocNostocNostoc 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...
, SynechococcusSynechococcusSynechococcus is a unicellular cyanobacterium that is very widespread in the marine environment. Its size varies from 0.8 µm to 1.5 µm...
, Gleoebacter, ProchloronProchloronProchloron is a unicellular oxygenic photosynthetic prokaryote commonly found as symbionts in coral reefs, particularly in didemnid ascidians...
) - Spirochetes and relatives
- Spirochetes (Spirochaeta, TreponemaTreponemaTreponema 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....
, BorreliaBorreliaBorrelia is a genus of bacteria of the spirochete phylum. It causes borreliosis, a zoonotic, vector-borne disease transmitted primarily by ticks and some by lice, depending on the species...
) - Leptospiras (LeptospiraLeptospiraLeptospira is a genus of spirochaete bacteria, including a small number of pathogenic and saprophytic species...
, LeptonemaLeptonemaLeptonema is a genus of flowering plant belonging to the family Phyllanthaceae....
)
- Spirochetes (Spirochaeta, Treponema
- Green sulfur bacteriaGreen sulfur bacteriaThe green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum....
(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+...
, Chloroherpeton) - 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...
, FlavobacteriaFlavobacteriaThe class Flavobacteria is composed of a single order of environmental bacteria. Flavobacteria are a group of commensal bacteria and opportunistic pathogens. Flavobacterium psychrophilum causes the septicemic diseases rainbow trout fry syndrome and bacterial cold water disease...
and relatives- Bacteroides (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...
, 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...
) - Flavobacterium group (FlavobacteriumFlavobacteriumFlavobacterium is a genus of Gram-negative, non-motile and motile, rod-shaped bacteria that consists of ten recognized species, as well as three newly proposed species . Flavobacteria are found in soil and fresh water in a variety of environments...
, CytophagaCytophagaCytophaga is a genus of Gram-negative, gliding, rod-shaped bacteria.-Species:The following are some species in Cytophaga:* Cytophaga columnaris — the cause of columnaris disease in salmonid fish, as associated with increased water temperature; it is characterized by white necrotic plaques...
, Saprospira, FlexibacterFlexibacterFlexibacter is a genus of bacteria consisting of some seventeen strains , known for their yellow hue.Etymology: L. part. adj. flexus , bent, winding; N.L. masc. n. bacter, rod; N.L. masc. n. Flexibacter, intended to mean flexible rod....
)
- Bacteroides (Bacteroides
- PlanctomycesPlanctomycetesPlanctomycetes 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...
and relatives- Planctomyces group (Planctomyces, Pasteuria)
- Thermophiles (Isocystis pallida)
- 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....
(Chlamydia psittaci, Chlamydia trachomatisChlamydia trachomatisChlamydia trachomatis, an obligate intracellular human pathogen, is one of three bacterial species in the genus Chlamydia. C. trachomatis is a Gram-negative bacteria, therefore its cell wall components retain the counter-stain safranin and appear pink under a light microscope.The inclusion bodies...
) - Radioresistant micrococci and relatives
- Deinococcus group (Deinococcus radioduransDeinococcus radioduransDeinococcus radiodurans is an extremophilic bacterium, one of the most radioresistant organisms known. It can survive cold, dehydration, vacuum, and acid, and is therefore known as a polyextremophile and has been listed as the world's toughest bacterium in The Guinness Book Of World Records.-Name...
) - Thermophiles (Thermus aquaticusThermus aquaticusThermus aquaticus is a species of bacterium that can tolerate high temperatures, one of several thermophilic bacteria that belong to the Deinococcus-Thermus group...
)
- Deinococcus group (Deinococcus radiodurans
- Green non-sulfur bacteria and relatives
- Chloroflexus group (Chloroflexus, HerpetosiphonHerpetosiphonHerpetosiphon is a genus of bacteria in the family Herpetosiphonaceae....
) - Thermomicrobium group (Thermomicrobium roseum)
- Chloroflexus group (Chloroflexus, Herpetosiphon
- ThermotogaeThermotogaeThermotogae is a phylum of the domain "Bacteria". This phylum comprises merely the class "Thermotogae", with the order "Thermotogales" and the family "Thermotogaceae"....
The "purple bacteria and relatives" were renamed Proteobacteria
Proteobacteria
The 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....
.
The low and high CG content gram positive subdivisions were renamed Actinobacteria
Actinobacteria
Actinobacteria 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....
and Firmicutes
Firmicutes
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...
divisions, making the number of phyla 12.
Until recently, it was believed than only Firmicutes and Actinobacteria were Gram-positive. The candidate phylum TM7 may be Gram positive. 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....
however possess a single bilayer, but stain negative (with some exceptions).
"Green non-sulfur bacteria and relatives" was renamed 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....
.
"Radioresistant micrococci and relatives" are commonly referred to as 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...
clade,, although it has been prosed to call the clade Xenobacteria or Hadobacteria (latter is illegitimate).
New cultured phyla
New species have been cultured since 1987, when Woese's review paper was published, that are sufficiently different to warrant a new phylum, mostly thermophiles and often also chemolithoautotrophs, such as AquificaeAquificae
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...
, which oxidises hydrogen gas. Other non-thermophiles, such as Acidobacteria
Acidobacteria
Acidobacteria are a newly devised phylum of Bacteria, whose members are physiologically diverse and ubiquitous, especially in soils, but are under-represented in culture....
, a ubiquitous phyla with divergent physiologies, have been found, some of which are chemolithotrophs, such as Nitrospira (nitrile-oxidising) or Leptospirillum (Fe-oxidising)., some proposed phyla however do not appear in LPSN
LPSN
List 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...
as they were insufficiently described or are awaiting approval or it is debated if they may belong to a pre-existing phyla. An example of this is the genus Caldithrix, consisting of C. palaeochoryensis and C.abyssi, which is considered Deferribacteres,, however, it shares only 81% similarity with the other Deferribacteres (Deferribacter
Deferribacter
Deferribacter 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...
species and relatives) and is considered a separate phylum by Rappé and Giovannoni. Additionally the placement of the genus Geovibrio in the phylum Deferribacteres is debated.
Uncultivated and metagenomics
With the advent of methodsNucleic acid methods
Nucleic acid methods are the techniques used to study nucleic acids .Purification*Phenol-chloroform extraction*minicolumn purification*RNA extractionQuantification*Abundance in weight: spectroscopic quantification...
to analyse environmental DNA (metagenomics
Metagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...
), the 16S rRNA of an extremely large number of undiscovered species have been found, showing that there are several whole phyla which have no known cultivable representative and that some phyla lack in culture major subdivisions as is the case for Verrucomicrobia
Verrucomicrobia
Verrucomicrobia 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...
and 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....
.
The term Candidatus
Candidatus
Candidatus is in scientific classification 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. An example would be "Candidatus Phytoplasma allocasuarinae"...
is used for proposed species for which the lack of information prevents it to be validated, such as where the only evidence is DNA sequence data, even if the whole genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
has been sequenced. When the species are members of whole phyla it is called a candidate division
Candidate division
A candidate division, candidate phylum or candidate division-level is a lineage of Prokaryotic organisms for which no cultured representatives have been found, but evidence of the existence of the clade has been obtained by 16S rRNA metagenomic analysis of environmental samples...
and in 2003 there were 26 candidate divisions out of 52.
A candidate division was defined by in 1998 Hugenholtz and Pace
Norman R. Pace
Norman Richard Pace, Jr. is an American biochemist, and is Distinguished Professor of Molecular, Cellular and Developmental Biology at the University of Colorado. He is principal investigator at the Pace lab....
, as a set of 16S ribosomal RNA
16S ribosomal RNA
16S ribosomal RNA is a component of the 30S subunit of prokaryotic ribosomes. It is approximately 1.5kb in length...
sequences with less than 85% similarity.
Three candidate phyla were known before 1998, prior to the 85% threshold definition by Hugenholtz and Pace:
- OS-K group (from Octopus spring)
- Marine Group A (from Pacific ocean)
- Termite Group 1 (from TermiteTermiteTermites are a group of eusocial insects that, until recently, were classified at the taxonomic rank of order Isoptera , but are now accepted as the epifamily Termitoidae, of the cockroach order Blattodea...
gut, now 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...
)
Since then several other cadidate phyla were identified and accepted by Rappé and Giovannoni (2003):)
- OP1, OP3, OP5 (now Caldiserica), OP8, OP9, OP10 (now ArmatimonadetesArmatimonadetesPreviously known as candidate phylum OP10 and was comprised solely of environmental 16S rRNA gene clone sequences, however recently three strains were formally described two of which are in press at the International Journal of Systematic and Evolutionary Microbiology, thus nearing validation as...
), OP11 (obsidian pool, yellowstone national parkYellowstone National ParkYellowstone National Park, established by the U.S. Congress and signed into law by President Ulysses S. Grant on March 1, 1872, is a national park located primarily in the U.S. state of Wyoming, although it also extends into Montana and Idaho...
) - WS2, WS3, WS5, WS6 (Wurtsmith contaminated aquifer)
- SC3 and SC4 (from arid soil)
- vadinBE97 (now 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...
) - NC10 (from flooded caves)
- BRC1 (from bulk soil and rice roots)
- ABY1 (from sediment)
- Guyamas1 (from hydrothermal)
- NKB19 (from activated sludge)
- SBR1093 (from activated sludge)
- TM6 and TM7Candidate division TM7The candidate division TM7, is a major lineage of Bacteria, the existence of which is known solely through environmental 16S rRNA sequences as to date no species has been grown in the lab, a requirement for taxonomy, making it a candidate phylum....
(Torf, Mittlere Schicht)
Since then a candidate phylum called Poribacteria was discovered, living in symbiosis
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
with sponges and extensively studied. (Note: the divergence of the major bacterial lineages predates sponges)
Other candidate phyla that have been the centre of some studies are TM7
Candidate division TM7
The candidate division TM7, is a major lineage of Bacteria, the existence of which is known solely through environmental 16S rRNA sequences as to date no species has been grown in the lab, a requirement for taxonomy, making it a candidate phylum....
, the genomes of organisms of which have even been sequenced (draft), WS6 and Marine Group A.
Two species of the candidate division OP10, which is now called Armatimonadetes
Armatimonadetes
Previously known as candidate phylum OP10 and was comprised solely of environmental 16S rRNA gene clone sequences, however recently three strains were formally described two of which are in press at the International Journal of Systematic and Evolutionary Microbiology, thus nearing validation as...
, where recently cultured: Armatimonas rosea isolated from the rhizoplane of a reed in a lake in Japan and Chthonomonas calidirosea from an isolate from geothermally heated soil at Hell's Gate, Tikitere
Tikitere
Tikitere, also known as "Hell's Gate", is Rotorua's most active geothermal area on State Highway 30, between Lake Rotorua and Lake Rotoiti in the Bay of Plenty, New Zealand...
, New Zealand
New Zealand
New Zealand is an island country in the south-western Pacific Ocean comprising two main landmasses and numerous smaller islands. The country is situated some east of Australia across the Tasman Sea, and roughly south of the Pacific island nations of New Caledonia, Fiji, and Tonga...
.
One species, Caldisericum exile, of the candidate division OP5 was cultured, leading to it being named Caldiserica.
Termite Group 1 is now known as Elusimicrobia
Elusimicrobia
The 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...
, after the ultramicrobacterium Elusimicrobium minutum
Elusimicrobium minutum
Elusimicrobium minutum is an ultramicrobacterium and first accepted member to be cultured of a major bacterial lineage previously known only as candidate phylum Termite Gut 1 , which has accordingly been renamed phylum Elusimicrobia....
was cultured.
The candidate division VadinBE97 is now known as Lentisphaerae
Lentisphaerae
Lentisphaerae 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...
after Lentisphaera araneosa and Victivallis vadensis were cultured.
Despite these lineages not being officially recognised, due to the ever increasing number of sequences belonging to non-existent phyla, ARB-Silva list 57 phyla, not only the 27 phyla with validly accepted species, but also 30 Candidate divisions (BD1-5, BHI80-139, BRC1, CK-1C4-19, EM19, GAL08, GOUTA4, Hyd24-12, JL-ETNP-Z39, Kazan-3B-28, LD1-PA38, MVP-21, NPL-UPA2, OC31, OD1, OP3, OP9, OP10, OP11, RF3, RsaHF231, SM2F11, SR1, TA06, TM6, TM7, WCHB1-60, WS3 and WS6), while Ribosomal Database Project 10, list 29 phyla and 7 candidate divisions (OP10, OP11, OD1, BRC1, SR1, WS3, TM7)
Superphyla
Despite the unclear branching order for most phyla, two groups of phyla have clear clustering and are referred to as superphyla: the FCB group and the PVC group.The FCB group includes Chlorobi, Bacteroidetes, Fibrobacteres, Gemmatimonadates, Caldithrix and Marine group A.
The PVC group includes Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia, Poribacteria and OP3.
Overview of phyla
Currently there are 29 phyla accepted by LPSN. There are no fixed rules to the nomenclature of bacterial phyla, it was proposed that the suffix "-bacteria" be used for phyla,, but generally 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 (Actinobacteria instead is from Actinomyces).Acidobacteria
The Acidobacteria (diderm Gram negative) is most abundant bacterial phylum in many soils, but its members are mostly uncultured. Additionally, they phenotypically diverse and include not only acidophiles, but also many non-acidophiles. Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions and can tolerate well fluctuations in soil hydration.Actinobacteria
The Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which notable secondary metabolite producers. There are only two phyla of monoderm Gram positive bacteria, the other being the Firmicutes; the actinobacteria generally have higher GC content so are sometimes called "high-CG Gram positive bacteria". Notable genera/species include StreptomycesStreptomyces
Streptomyces is the largest genus of Actinobacteria and the type genus of the family Streptomycetaceae. Over 500 species of Streptomyces bacteria have been described. As with the other Actinobacteria, streptomycetes are gram-positive, and have genomes with high guanine and cytosine content...
(antibiotic production), Propionibacterium acnes
Propionibacterium acnes
Propionibacterium acnes is a relatively slow growing, typically aerotolerant anaerobic gram positive bacterium that is linked to the skin condition acne; it can also cause chronic blepharitis and endophthalmitis, the latter particularly following intraocular surgery...
(odorous skin commensal) and Propionibacterium freudenreichii
Propionibacterium freudenreichii
Propionibacterium freudenreichii is a Gram-positive, nonmotile bacterium that plays an important role in the creation of Emmental cheese, and to some extent, leerdammer. Its concentration in Swiss-type cheeses is higher than in any other cheese. Propionibacteria are commonly found in milk and dairy...
(holes in Emmental)
Aquificae
The Aquificae (diderm Gram negative) contains only 14 genera (including AquifexAquifex
Aquifex is a genus of bacteria, one of the few in the phylum Aquificae. The two species generally classified in Aquifex are A. pyrophilus and A. aeolicus. Both are highly thermophilic, growing best in water temperature of 85 °C to 95 °C...
and Hydrogenobacter). The species are hyperthermophiles and chemolithotrophs (sulphur). According to some studies may be one of the most deep branching phyla.
Bacteroidetes
The Bacteroidetes (diderm Gram negative) is a member of the FBC superphylum. Some species are opportunistic pathogens, while other are the most common human gut commensal. Gained notority in the non-scientific comunity with the urban myth as a bacterial weight loss powder.Caldiserica
This phylum was formerly known as candidate division OP5, Caldisericum exile is the sole representative.Chlamydiae
The ChlamydiaeChlamydiae
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....
(diderms, weakly Gram negative) is a phylum of the PVC superphylum. It is composed of only 6 genera of obbligate intracellular pathogens with a complex life cycle. Species include Chlamydia trachomatis
Chlamydia trachomatis
Chlamydia trachomatis, an obligate intracellular human pathogen, is one of three bacterial species in the genus Chlamydia. C. trachomatis is a Gram-negative bacteria, therefore its cell wall components retain the counter-stain safranin and appear pink under a light microscope.The inclusion bodies...
(chlamydia infection).
Chlorobi
Chlorobi is a member of the FBC superphylum. It contains only 7 genera of obligately anaerobic photoautotrophic bacteria, known colloquially as Green sulfur bacteria. The reaction centre for photosynthesis in Chlorobi and Chloroflexi (another photosynthetic group) is formed by a structures called the chlorosomeChlorosome
A Chlorosome is a photosynthetic antenna complex found in green sulfur bacteria and some green filamentous anoxygenic phototrophs . They differ from other antenna complexes by their large size and lack of protein matrix supporting the photosynthetic pigments...
as opposed to phycobilisomes of cyanobacteria (another photosynthetic group).
Chloroflexi
ChloroflexiChloroflexi
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....
,diverse phylum including thermophiles and halorespirers, known colloquially as Green non-sulfur bacteria.
Chrysiogenetes
Chrysiogenetes, only 3 genera (Chrysiogenes arsenatis, Desulfurispira natronophila, Desulfurispirillum alkaliphilum)Cyanobacteria
Cyanobacteria, major photosynthetic clade believed to have caused Earth's oxygen atmosphere, also known as the blue-green algaeDeinococcus-Thermus
Deinococcus-ThermusDeinococcus-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...
, Deinococcus radiodurans and Thermus aquaticus are "commonly known" species of this phyla
Elusimicrobia
ElusimicrobiaElusimicrobia
The 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...
, formerly candidate division Termite Group 1
Firmicutes
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...
, Low-G+C Gram positive species most often spore-forming, in two/three classes: the class 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:...
such as the Bacillus
Bacillus
Bacillus 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...
spp. (e.g. B. anthracis, a pathogen, and B. subtilis, biotechnologically useful), lactic acid bacteria
Lactic acid bacteria
The lactic acid bacteria comprise a clade of Gram-positive, low-GC, acid-tolerant, generally non-sporulating, non-respiring rod or cocci that are associated by their common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and lactic products, produce...
(e.g. Lactobacillus casei
Lactobacillus casei
Lactobacillus casei is a species of genus Lactobacillus found in the human intestine and mouth. As a lactic acid producer, it has been found to assist in the propagation of desirable bacteria. This particular species of Lactobacillus is documented to have a wide pH and temperature range, and...
in yoghurt, Oenococcus oeni
Oenococcus oeni
Oenococcus oeni is a Gram-positive bacteria species in the genus of Oenococcus. It used to be the only species in the genus . In 2006, the species Oenococcus kitaharae was identified...
in malolactic fermentation
Malolactic fermentation
Malolactic fermentation is a process in winemaking where tart-tasting malic acid, naturally present in grape must, is converted to softer-tasting lactic acid. Malolactic fermentation tends to create a rounder, fuller mouthfeel. It has been said that malic acid tastes of green apples...
, Streptococcus pyogenes
Streptococcus pyogenes
Streptococcus pyogenes is a spherical, Gram-positive bacterium that is the cause of group A streptococcal infections. S. pyogenes displays streptococcal group A antigen on its cell wall. S...
, pathogen), the class Clostridia
Clostridia
The Clostridia are a class of Firmicutes, including Clostridium and other similar genera. They are distinguished from the Bacilli by lacking aerobic respiration. They are obligate anaerobes and oxygen is toxic to them. Species of the genus Clostridium are all Gram-positive and have the ability to...
of mostly anaerobic sulphite-reducing saprophytic species, includes the genus 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...
(e.g. the pathogens C. dificile, C. tetani
Clostridium tetani
Clostridium tetani is a rod-shaped, anaerobic bacterium of the genus Clostridium. Like other Clostridium species, it is Gram-positive, and its appearance on a gram stain resembles tennis rackets or drumsticks. C. tetani is found as spores in soil or in the gastrointestinal tract of animals. C...
, C. botulinum
Clostridium botulinum
Clostridium botulinum is a Gram-positive, rod-shaped bacterium that produces several toxins. The best known are its neurotoxins, subdivided in types A-G, that cause the flaccid muscular paralysis seen in botulism. It is also the main paralytic agent in botox. C. botulinum is an anaerobic...
and the biotech C. acetobutylicum
Clostridium acetobutylicum
Clostridium acetobutylicum, ATCC 824, is included in the genus Clostridium, is a commercially valuable bacterium sometimes called the "Weizmann Organism", after Jewish-Russian born Chaim Weizmann, then senior lecturer at the University of Manchester, England, used them in 1916 as a bio-chemical...
)
Gemmatimonadetes
GemmatimonadetesGemmatimonadetes
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...
, member of the FBC superphylum.
Lentisphaerae
LentisphaeraeLentisphaerae
Lentisphaerae 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...
, formerly clade VadinBE97, member of the PVC superphylum.
Proteobacteria
ProteobacteriaProteobacteria
The 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....
, contains most of the "commonly known" species, such as 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...
or Pseudomonas aeruginosa
Pseudomonas aeruginosa
Pseudomonas aeruginosa is a common bacterium that can cause disease in animals, including humans. It is found in soil, water, skin flora, and most man-made environments throughout the world. It thrives not only in normal atmospheres, but also in hypoxic atmospheres, and has, thus, colonized many...
Spirochaetes
Spirochaetes, notable for compartmentalisation and species include 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....
, which causes Lyme disease
Synergistetes
The Synergistetesis a phylum whose members are diderm Gram negative, rod-shaped obligate anaerobes, some of which human commanals.Tenericutes
The Tenericutes includes the class MollicutesMollicutes
The Mollicutes are a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis , and cutis . They are parasites of various animals and plants, living on or in the host's cells. Individuals are very small, typically only 0.2–0.3 μm in size...
, formerly/debatedly of the phylum Firmicutes
Firmicutes
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...
(sister clades). Despite their monoderm Gram positive relatives, they lack peptidoglycan and instead possess mycolic acid
Mycolic acid
Mycolic acids are long fatty acids found in the cell walls of the mycolata taxon, a group of bacteria that includes Mycobacterium tuberculosis, the causative agent of the disease tuberculosis. They form the major component of the cell wall of mycolata species...
. Notable genus: Mycoplasma
Mycoplasma
Mycoplasma refers to a genus of bacteria that lack a cell wall. Without a cell wall, they are unaffected by many common antibiotics such as penicillin or other beta-lactam antibiotics that target cell wall synthesis. They can be parasitic or saprotrophic. Several species are pathogenic in humans,...
.
Thermodesulfobacteria
The Thermodesulfobacteria is a phylum composed of only three genera in the same family (Thermodesulfobacteriaceae:Caldimicrobium, Thermodesulfatator and Thermodesulfobacterium). The members of the phylum are thermophilic sulphate-reducers.
Thermotogae
The Thermotogae is a phylum of whose members possess an unusual outer membrane called the togaToga
The toga, a distinctive garment of Ancient Rome, was a cloth of perhaps 20 ft in length which was wrapped around the body and was generally worn over a tunic. The toga was made of wool, and the tunic under it often was made of linen. After the 2nd century BC, the toga was a garment worn...
and are hyperthermophilic obligate anaerobic fermenters.
Verrucomicrobia
Verrucomicrobia is a phylum of the PVC superphylum. Like the Planctomycetes species, its members possess a compartmentalised cell plan with a condensed nucleoid and the ribosomes pirellulosome (enclosed by the intracytoplasmic membrane) and paryphoplasm compartment between the intracytoplasmic membrane and cytoplasmic membrane.Branching order
The branching order of the phyla of bacteria is unclear. Different studies arrive at different results due to different datasets and methods.For example, in studies using 16S and few other sequences Thermotogae and Aquificae appear as the most basal phyla, whereas in several phylogenomic studies, Firmicutes are the most basal.
- Branching order of bacterial phyla (Woese, 1987)Branching order of bacterial phyla (Woese, 1987)There are several models of the Branching order of bacterial phyla, one of these was proposed in 1987 paper by Carl Woese.The branching order proposed by Carl Woese was based on molecular phylogeny, which was considered revolutionary as all preceding models were based on discussions of morphology....
- Branching order of bacterial phyla (Rappe and Giovanoni, 2004)
- Branching order of bacterial phyla after ARB Silva Living Tree
- Branching order of bacterial phyla (Ciccarelli et al., 2006)Branching order of bacterial phyla (Ciccarelli et al., 2006)There are several models of the Branching order of bacterial phyla, one of these was proposed in 2006 by Ciccarelli et al. for their iTOL project.This tree is based on a concatenated set of conserved protein and not 16S rRNA There are several models of the Branching order of bacterial phyla, one of...
- Branching order of bacterial phyla (Battistuzzi et al.,2004)Branching order of bacterial phyla (Battistuzzi et al.,2004)There are several models of the Branching order of bacterial phyla, one of these was proposed in 2004 by Battistuzzi and Hedges,, note the coinage of the taxa Terrabacteria and Hydrobacteria.-See also:* Branching order of bacterial phyla...
- Branching order of bacterial phyla (Gupta, 2001)Branching order of bacterial phyla (Gupta, 2001)There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved...
- Branching order of bacterial phyla (Cavalier-Smith, 2002)Branching order of bacterial phyla (Cavalier-Smith, 2002)There are several models of the Branching order of bacterial phyla, one of these was proposed in 2002 and 2004 by Thomas Cavalier-Smith. In this frame of work, the branching order of the major lineage of bacteria are determined based on some morphological characters, such as cell wall structure,...
See also
- Bacterial taxonomy#Phyla endings
- List of bacterial orders
- List of Bacteria genera
- List of sequenced bacterial genomes
- International Code of Nomenclature of BacteriaInternational Code of Nomenclature of BacteriaThe International Code of Nomenclature of Bacteria or Bacteriological Code governs the scientific names for bacteria, including Archaea. It denotes the rules for naming taxa of bacteria, according to their relative rank...