Bacterial
phyla Phyla, the plural of ''phylum'', may refer to:
* Phylum, a biological taxon between Kingdom and Class
* by analogy, in linguistics, a large division of possibly related languages, or a major language family which is not subordinate to another
Phy ...
constitute the major lineages of the domain ''
Bacteria
Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
''. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a
monophyletic
In cladistics for a group of organisms, monophyly is the condition of being a clade—that is, a group of taxa composed only of a common ancestor (or more precisely an ancestral population) and all of its lineal descendants. Monophyletic gr ...
lineage of bacteria whose
16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.
It has been estimated that ~1,300 bacterial phyla exist.
As of May 2020,
41 bacterial phyla are formally accepted by the
LPSN
List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...
,
89 bacterial phyla are recognized on th
Silva database dozens more have been proposed,
and hundreds likely remain to be discovered.
As of 2017, approximately 72% of widely recognized bacterial phyla were
candidate phyla
A candidate division, candidate phylum or candidate division-level is a lineage of prokaryotic organisms for which until recently no cultured representatives have been found, but evidence of the existence of the clade has been obtained by 16S rR ...
(i.e. have no cultured representatives).
There are no fixed rules to the nomenclature of bacterial phyla. It was proposed that the suffix "-bacteria" be used for phyla.
List of bacterial phyla
The following is a list of bacterial phyla that have been proposed.
Supergroups
Despite the unclear branching order for most bacterial phyla, several groups of phyla consistently cluster together and are referred to as supergroups or superphyla. In some instances, bacterial clades clearly consistently cluster together but it is unclear what to call the group. For example, the Candidate Phyla Radiation includes the Patescibacteria group which includes Microgenomates group which includes over 11 bacterial phyla.
Candidate phyla radiation (CPR)
The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain.
It includes two main clades, the Microgenomates and Parcubacteria groups, each containing the eponymous superphyla and a few other phyla.
Patescibacteria
The superphylum Patescibacteria was originally proposed to encompass the phyla
Microgenomates (OP11), Parcubacteria (OD1), and
Gracilibacteria (GNO2 / BD1-5).
More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR.
Sphingobacteria
The
Sphingobacteria
The FCB group is a superphylum of bacteria named after the main member phyla Fibrobacterota, Chlorobiota, and Bacteroidota. The members are considered to form a clade due to a number of conserved signature indels.
Cavalier-Smith calls the e ...
(FCB group) includes Bacteroidota, Calditrichota, Chlorobiota, candidate phylum "Cloacimonetes", Fibrobacterota, Gemmatimonadota, Ignavibacteriota, candidate phylum "Latescibacteria", candidate phylum "Marinimicrobia", and candidate phylum "Zixibacteria".
Microgenomates
Microgenomates was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla,
including Curtisbacteria, Daviesbacteria, Levybacteria, Gottesmanbacteria, Woesebacteria, Amesbacteria, Shapirobacteria, Roizmanbacteria, Beckwithbacteria, Collierbacteria, Pacebacteria.
Parcubacteria
Parcubacteria was originally described as a single phylum using fewer than 100 16S rRNA sequences. With a greater diversity of 16S rRNA sequences from uncultured organisms now available, it is estimated it may consist of up to 28 bacterial phyla.
In line with this, over 14 phyla have now been described within the Parcubacteria group,
including Kaiserbacteria, Adlerbacteria, Campbellbacteria, Nomurabacteria, Giovannonibacteria, Wolfebacteria, Jorgensenbacteria, Yanofskybacteria, Azambacteria, Moranbacteria, Uhrbacteria, and Magasanikbacteria.
Proteobacteria
It has been proposed that some classes of the phylum
Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum.
For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.
Planctobacteria
The
Planctobacteria
The PVC superphylum is a superphylum of bacteria named after its three important members, Planctomycetota, Verrucomicrobiota, and Chlamydiota. Cavalier-Smith postulated that the PVC bacteria probably lost or reduced their peptidoglycan cell wal ...
(PVC group) includes
Chlamydiota
The Chlamydiota (synonym Chlamydiae) are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of ...
,
Lentisphaerota
Lentisphaerota is a phylum of bacteria closely related to Chlamydiota and Verrucomicrobiota.
It includes two monotypic orders Lentisphaerales and Victivallales. Phylum members can be aerobic or anaerobic and fall under two distinct phenotyp ...
, candidate phylum "
Omnitrophica",
Planctomycetota, candidate phylum "
Poribacteria
Poribacteria are a candidate phylum of bacteria originally discovered in the microbiome of marine sponges (''Porifera''). Poribacteria are Gram-negative primarily aerobic mixotrophs with the ability for oxidative phosphorylation, glycolysis, ...
", and
Verrucomicrobiota.
Terrabacteria
The proposed superphylum,
Terrabacteria,
includes
Actinomycetota, "
Cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
"/"
Melainabacteria"-
group,
Deinococcota,
Chloroflexota
The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for p ...
,
Bacillota, and candidate phylum OP10.
Cryptic superphyla
Several candidate phyla (
Microgenomates, Omnitrophica, Parcubacteria, and
Saccharibacteria) and several accepted phyla (
Elusimicrobiota,
Caldisericota
''Caldisericum exile'' is a species of bacteria sufficiently distinct from other bacteria to be placed in its own family, order, class and phylum
In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below ...
, and
Armatimonadota) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining a bacterial phylum are lacking or due to a lack of sequence diversity in databases when the phylum was first established.
For example, it is suggested that candidate phylum Parcubacteria is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimicrobia is actually a superphylum that encompasses 7 subordinate phyla.
Historical perspective
Given the rich history of the field of bacterial taxonomy and the rapidity of changes therein in modern times, it is often useful to have a historical perspective on how the field has progressed in order to understand references to antiquated definitions or concepts.
When bacterial nomenclature was controlled under the
Botanical Code
The ''International Code of Nomenclature for algae, fungi, and plants'' (ICN) is the set of rules and recommendations dealing with the formal botanical names that are given to plants, fungi and a few other groups of organisms, all those "trad ...
, the term ''division'' was used, but now that bacterial nomenclature (with the exception of
cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
) is controlled under the
Bacteriological Code, the term ''phylum'' is preferred.
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, listed below.
*
Purple Bacteria
Purple bacteria or purple photosynthetic bacteria are Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', together with variou ...
and their relatives (later renamed
Proteobacteria)
**
alpha subdivision (
purple non-sulfur bacteria
Purple bacteria or purple photosynthetic bacteria are Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', together with variou ...
,
rhizobacteria, ''
Agrobacterium
''Agrobacterium'' 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. ''Agrobacterium ...
'', ''
Rickettsiae
''Rickettsia'' is a genus of nonmotile, gram-negative, nonspore-forming, highly pleomorphic bacteria that may occur in the forms of cocci (0.1 μm in diameter), bacilli (1–4 μm long), or threads (up to about 10 μm long). The term "ricket ...
'', ''
Nitrobacter'')
**
beta subdivision (''
Rhodocyclus'', (some) ''
Thiobacillus'', ''
Alcaligenes'', ''
Spirillum
''Spirillum'' is a genus of Gram-negative bacteria in the family '' Spirillaceae'' of the '' Nitrosomonadales'' of the '' Betaproteobacteria''.Garrity, George M.; Brenner, Don J.; Krieg, Noel R.; Staley, James T. (eds.) (2005). Bergey's Manual ...
'', ''
Nitrosovibrio'')
**
gamma subdivision (enterics,
fluorescent pseudomonads,
purple sulfur bacteria, ''
Legionella'', (some) ''
Beggiatoa
''Beggiatoa'' is a genus of '' Gammaproteobacteria'' belonging the order ''Thiotrichales,'' in the '' Pseudomonadota'' phylum. This genus was one of the first bacteria discovered by Ukrainian botanist Sergei Winogradsky. During his research in ...
'')
**
delta subdivision (Sulfur and sulfate reducers (''
Desulfovibrio''),
Myxobacteria, ''
Bdellovibrio
''Bdellovibrio'' is a genus of Gram-negative, obligate aerobic bacteria. One of the more notable characteristics of this genus is that members can prey upon other Gram-negative bacteria and feed on the biopolymers, e.g. proteins and nucleic ac ...
'')
*
Gram-positive Eubacteria
**
High-G+C species (later renamed Actinobacteria
) (''
Actinomyces'', ''
Streptomyces
''Streptomyces'' is the largest genus of Actinomycetota and the type genus of the family Streptomycetaceae. Over 500 species of ''Streptomyces'' bacteria have been described. As with the other Actinomycetota, streptomycetes are gram-positiv ...
'', ''
Arthrobacter
''Arthrobacter'' (from the Greek, "jointed small stick”) 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 statio ...
'', ''
Micrococcus
''Micrococcus'' (mi’ krō kŏk’ Əs) 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 ...
'', ''
Bifidobacterium'')
**
Low-G+C species (later renamed
Firmicutes) (''
Clostridium
''Clostridium'' is a genus of anaerobic, Gram-positive bacteria. Species of ''Clostridium'' inhabit soils and the intestinal tract of animals, including humans. This genus includes several significant human pathogens, including the causative a ...
'', ''
Peptococcus'', ''
Bacillus'', ''
Mycoplasma
''Mycoplasma'' is a genus of bacteria that, like the other members of the class '' Mollicutes'', lack a cell wall around their cell membranes. Peptidoglycan ( murein) is absent. This characteristic makes them naturally resistant to antibioti ...
'')
** Photosynthetic species (''
Heliobacteria'')
** Species with Gram-negative walls (''
Megasphaera'', ''
Sporomusa
''Sporomusa'' is a genus of Bacillota bacteria classified within the class Negativicutes.
Further examination of members of this clade suggest that this group are actually members of the ''Clostridia''.Yutin N, Galperin MY (2013) A genomic upd ...
'')
*
Cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, bl ...
and chloroplasts (''
Aphanocapsa
''Aphanocapsa'' is a genus of cyanobacteria belonging to the family Merismopediaceae
The Merismopediaceae are a family of cyanobacteria
Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energ ...
'', ''
Oscillatoria'', ''
Nostoc
''Nostoc'', also known as star jelly, troll’s butter, spit of moon, fallen star, witch's butter (not to be confused with the fungi commonly known as witches' butter), and witch’s jelly, is the most common genus of cyanobacteria found in var ...
'', ''
Synechococcus'', ''
Gloeobacter
''Gloeobacter'' is a genus of cyanobacteria. It is the sister group to all other cyanobacteria. ''Gloeobacter'' is unique among cyanobacteria in not having thylakoids, which are characteristic for all other cyanobacteria and chloroplasts. Ins ...
'', ''
Prochloron'')
*
Spirochetes and relatives
** Spirochetes (''
Spirochaeta
''Spirochaeta'' is a genus of bacteria classified within the phylum Spirochaetota.See the List of Prokaryotic names with Standing in Nomenclature. Data extracted from See the NCBIbr>webpage on SpirochaetesData extracted from
Phylogeny
Taxono ...
'', ''
Treponema'', ''
Borrelia'')
** Leptospiras (''
Leptospira'', ''
Leptonema'')
*
Green sulfur bacteria (''
Chlorobium'', ''
Chloroherpeton'')
*
Bacteroides
''Bacteroides'' is a genus of Gram-negative, obligate anaerobic bacteria. ''Bacteroides'' species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unus ...
,
Flavobacteria and relatives (later renamed
Bacteroidetes
** Bacteroides (''
Bacteroides
''Bacteroides'' is a genus of Gram-negative, obligate anaerobic bacteria. ''Bacteroides'' species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unus ...
'', ''
Fusobacterium
''Fusobacterium'' is a genus of anaerobic, Gram-negative, non-sporeforming bacteria belonging to Gracilicutes. Individual cells are slender, rod-shaped bacilli with pointed ends.
Strains of ''Fusobacterium'' cause several human diseases, includin ...
'')
** Flavobacterium group (''
Flavobacterium
''Flavobacterium'' is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Flavobacteria are found in soil and fresh water in a variety of environments. Several species are known to caus ...
'', ''
Cytophaga
''Cytophaga'' is a genus of Gram-negative, gliding, rod-shaped bacteria. This bacterium is commonly found in soil, rapidly digests crystalline cellulose ''C. hutchinsonii'' is able to use its gliding motility to move quickly over surfaces. ...
'', ''
Saprospira'', ''
Flexibacter'')
*
Planctomyces and relatives (later renamed
Planctomycetes)
** Planctomyces group (''
Planctomyces'', ''
Pasteuria
''Pasteuria'' is a genus of mycelial and endospore-forming, nonmotile gram-positive bacteria that are obligate parasites of some nematodes and crustaceans. The genus of ''Pasteuria'' was previously classified within the family Alicyclobacillace ...
''
'sic''
** Thermophiles (''
Isocystis pallida'')
*
Chlamydiae (''
Chlamydia psittaci'', ''
Chlamydia trachomatis'')
*Radioresistant micrococci and relatives (later renamed
Deinococcus–Thermus
''Deinococcota'' (synonym, ''Deinococcus-Thermus'') is a phylum of bacteria with a single class, ''Deinococci'', that are highly resistant to environmental hazards, also known as extremophiles.
These bacteria have thick cell walls that give th ...
or
Thermi)
** Deinococcus group (''
Deinococcus radiodurans'')
** Thermophiles (''
Thermus aquaticus'')
*Green non-sulfur bacteria and relatives (later renamed
Chloroflexi)
** Chloroflexus group (''
Chloroflexus'', ''
Herpetosiphon
''Herpetosiphon'' is a genus of bacteria in the family '' Herpetosiphonaceae''.
Phylogeny
References
{{Taxonbar, from=Q16965551
Phototrophic bacteria
Bacteria genera
Chloroflexota ...
'')
** Thermomicrobium group (''
Thermomicrobium roseum'')
*
Thermotogae (''
Thermotoga maritima'')
Traditionally,
phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological s ...
was inferred and
taxonomy
Taxonomy is the practice and science of categorization or classification.
A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...
established based on studies of morphology. The advent of
molecular phylogenetics
Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to ...
has allowed for improved elucidation of the evolutionary relationship of species by analyzing their
DNA and
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
sequences, for example their
ribosomal DNA
Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. These sequences regulate transcription initiation and amplification, and contain both transcribed and non-transcribed spacer segments.
In the human genome there are 5 chro ...
.
The lack of easily accessible morphological features, such as those present in
animals
Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage in ...
and
plants, hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted
Carl Woese, is ''
Pseudomonas'' whose etymology ironically matched its taxonomy, namely "false unit".
Many bacterial taxa were re-classified or re-defined using molecular phylogenetics.
The advent of molecular sequencing technologies has allowed for the recovery of genomes directly from environmental samples (i.e. bypassing culturing), leading to rapid expansion of our knowledge of the diversity of bacterial phyla. These techniques are genome-resolved
metagenomics and
single-cell genomics.
See also
*
Bacterial taxonomy#Phyla endings
*
International Code of Nomenclature of Bacteria
*
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 p ...
*
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 ex ...
*
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 mor ...
*
Branching order of bacterial phyla (Rappe and Giovanoni, 2003)
There are several models of the Branching order of bacterial phyla, the most cited of these was proposed in 1987 paper by Carl Woese. This cladogram was later expanded by Rappé and Giovanoni in 2003 to include newly discovered phyla. Clear nam ...
*
Branching order of bacterial phyla (Battistuzzi et al.,2004)
*
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 (cf. Branchi ...
*
Branching order of bacterial phyla after ARB Silva Living Tree
The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species ...
*
*
List of Bacteria genera
*
List of bacterial orders
*
List of sequenced bacterial genomes
This list of sequenced eubacterial genomes contains most of the eubacteria known to have publicly available complete genome sequences. Most of these sequences have been placed in the International Nucleotide Sequence Database Collaboration, a publi ...
Footnotes
References
{{DEFAULTSORT:Bacterial Phyla