Bacterial Phyla
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Bacterial phyla constitute the major lineages of the domain
Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
. While the exact definition of a bacterial
phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...
is debated, a popular definition is that a bacterial phylum is a
monophyletic In biological cladistics for the classification of organisms, monophyly is the condition of a taxonomic grouping being a clade – that is, a grouping of organisms which meets these criteria: # the grouping contains its own most recent co ...
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 image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practi ...
, 89 bacterial phyla are recognized on the 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 (i.e. have no cultured representatives). The rank of phylum has been included in the rules of the International Code of Nomenclature of Prokaryotes, using the ending ''–ota'' for phylum names that must be based on the name of a
genus Genus (; : genera ) is a taxonomic rank above species and below family (taxonomy), family as used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In bino ...
as its nomenclatural type.


List of bacterial phyla

The following is a list of bacterial phyla that have been validly published (not current).


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. The LPSN recognizes four kingdoms of bacteria as validly published: Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati.


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 (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 (PVC group) includes Chlamydiota, Lentisphaerota, candidate phylum " Omnitrophica", Planctomycetota, candidate phylum " Poribacteria", and Verrucomicrobiota.


Bacillati

The kingdom Bacillati, includes Actinomycetota, "Cyanobacteria/Melainabacteria clade", Deinococcota, Chloroflexota,
Bacillota The Bacillota (synonym Firmicutes) are a phylum of bacteria, most of which have Gram-positive cell wall structure. They have round cells, called cocci (singular coccus), or rod-like forms (bacillus). A few Bacillota, such as '' Megasphaera'', ...
, and candidate phylum OP10.


Cryptic superphyla

Several candidate phyla ( Microgenomates, Omnitrophica, Parcubacteria, and Saccharibacteria) and several accepted phyla ( Elusimicrobiota, Caldisericota, 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 term ''division'' was used, but now that bacterial nomenclature (with the exception of
cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
) 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 16S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S ...
(SSU) sequences, listed below. * Purple Bacteria and their relatives (later renamed Proteobacteria) ** alpha subdivision ( purple non-sulfur bacteria, rhizobacteria, '' Agrobacterium'', '' Rickettsiae'', '' Nitrobacter'') ** beta subdivision ('' Rhodocyclus'', (some) ''
Thiobacillus ''Thiobacillus'' is a genus of Gram-negative Betaproteobacteria. ''Thiobacillus thioparus'' is the type species of the genus, and the type strain thereof is the StarkeyT strain, isolated by Robert Starkey in the 1930s from a field at Rutgers U ...
'', '' Alcaligenes'', '' Spirillum'', '' Nitrosovibrio'') ** gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, ''
Legionella ''Legionella'' is a genus of gram-negative bacteria, gram-negative bacteria that can be seen using a silver stain or grown in a special media that contains cysteine, an amino acid. It is known to cause legionellosis (all illnesses caused by ''Legi ...
'', (some) '' Beggiatoa'') ** delta subdivision (Sulfur and sulfate reducers ('' Desulfovibrio''), Myxobacteria, '' Bdellovibrio'') *
Gram-positive In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. The Gram stain is ...
Eubacteria ** High-G+C species (later renamed Actinobacteria) ('' Actinomyces'', '' Streptomyces'', ''
Arthrobacter ''Arthrobacter'' (from the Greek, "jointed small stick”) is a genus of bacterium, bacteria that is commonly found in soil. All species in this genus are Gram-positive obligate aerobes that are bacterial shape, rods during exponential growth and ...
'', '' Micrococcus'', '' Bifidobacterium'') ** Low-G+C species (later renamed Firmicutes) ('' Clostridium'', '' Peptococcus'', ''
Bacillus ''Bacillus'', from Latin "bacillus", meaning "little staff, wand", is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum ''Bacillota'', with 266 named species. The term is also used to describe the shape (rod) of other so-sh ...
'', '' Mycoplasma'') ** Photosynthetic species ('' Heliobacteria'') ** Species with Gram-negative walls ('' Megasphaera'', '' Sporomusa'') *
Cyanobacteria Cyanobacteria ( ) are a group of autotrophic gram-negative bacteria that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" () refers to their bluish green (cyan) color, which forms the basis of cyanobacteri ...
and chloroplasts ('' Aphanocapsa'', '' Oscillatoria'', '' Nostoc'', '' Synechococcus'', '' Gloeobacter'', ''
Prochloron ''Prochloron'' (from the Greek ''pro'' (before) and the Greek ''chloros'' (green) ) is a genus of unicellular oxygenic photosynthetic prokaryotes commonly found as an extracellular symbiont on coral reefs, particularly in didemnid ascidians (sea ...
'') * Spirochetes and relatives ** Spirochetes ('' Spirochaeta'', '' Treponema'', '' Borrelia'') ** Leptospiras ('' Leptospira'', '' Leptonema'') * Green sulfur bacteria ('' Chlorobium'', '' Chloroherpeton'') * Bacteroides, Flavobacteria and relatives (later renamed Bacteroidetes ** Bacteroides ('' Bacteroides'', '' Fusobacterium'') ** 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 cause ...
'', '' Cytophaga'', '' Saprospira'', '' Flexibacter'') * Planctomyces and relatives (later renamed Planctomycetes) ** Planctomyces group ('' Planctomyces'', '' Pasteuria'' 'sic'' ** Thermophiles ('' Isocystis pallida'') * Chlamydiae ('' Chlamydia psittaci'', ''
Chlamydia trachomatis ''Chlamydia trachomatis'' () is a Gram-negative, Anaerobic organism, anaerobic bacterium responsible for Chlamydia infection, chlamydia and trachoma. ''C. trachomatis'' exists in two forms, an extracellular infectious elementary body (EB) and an ...
'') *Radioresistant micrococci and relatives (later renamed Deinococcus–Thermus or Thermi) ** Deinococcus group ('' Deinococcus radiodurans'') ** Thermophiles (''
Thermus aquaticus ''Thermus aquaticus'' is a species of bacteria that can tolerate high temperatures, one of several thermophile, thermophilic bacteria that belong to the ''Deinococcota'' phylum. It is the source of the heat-resistant enzyme Taq polymerase, ''Taq' ...
'') *Green non-sulfur bacteria and relatives (later renamed Chloroflexi) ** Chloroflexus group ('' Chloroflexus'', '' Herpetosiphon'') ** Thermomicrobium group ('' Thermomicrobium roseum'') * Thermotogae ('' Thermotoga maritima'') Traditionally,
phylogeny A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or Taxon, taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, M ...
was inferred and
taxonomy image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme o ...
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 Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
and
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
sequences, for example their
ribosomal DNA The ribosomal DNA (rDNA) consists of a group of ribosomal RNA encoding genes and related regulatory elements, and is widespread in similar configuration in all domains of life. The ribosomal DNA encodes the non-coding ribosomal RNA, integral struc ...
. 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, have myocytes and are able to move, can reproduce sexually, and grow from a ...
and
plants Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars f ...
, hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese, is ''
Pseudomonas ''Pseudomonas'' is a genus of Gram-negative bacteria belonging to the family Pseudomonadaceae in the class Gammaproteobacteria. The 348 members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a ...
'' 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 Metagenomics is the study of all genetics, genetic material from all organisms in a particular environment, providing insights into their composition, diversity, and functional potential. Metagenomics has allowed researchers to profile the mic ...
and single-cell genomics.


See also

* Bacterial taxonomy#Phyla endings *
International Code of Nomenclature of Bacteria The International Code of Nomenclature of Prokaryotes (ICNP) or Prokaryotic Code, formerly the International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC), governs the scientific names for Bacteria and Archaea.P. H. A. Sneath ...
* Branching order of bacterial phyla (Woese, 1987) * Branching order of bacterial phyla (Gupta, 2001) * Branching order of bacterial phyla (Cavalier-Smith, 2002) * Branching order of bacterial phyla (Rappe and Giovanoni, 2003) * Branching order of bacterial phyla (Battistuzzi et al.,2004) * Branching order of bacterial phyla (Ciccarelli et al., 2006) * Branching order of bacterial phyla after ARB Silva Living Tree * Branching order of bacterial phyla (Genome Taxonomy Database, 2018) *
List of Bacteria genera This article lists the genera of the bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, ...
*
List of bacterial orders This article lists the orders of the Bacteria. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16 ...
* List of sequenced bacterial genomes


Footnotes


References

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