bacterial phyla#Uncultivated Phyla and metagenomics

{{cleanup section|reason=Should be replaced with the lists in doi:10.1099/ijsem.0.006508, which contains all valid publications under the Prokaryotic Code before Dec 2023 plus most of the extra proposals|date=December 2024}}

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

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.https://lpsn.dsmz.de/

{{main|Candidate phyla radiation}}

The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain.{{cite journal|vauthors=Castelle CJ, Banfield JF|date=March 2018|title=Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life|journal=Cell|volume=172|issue=6|pages=1181–1197|doi=10.1016/j.cell.2018.02.016|pmid=29522741|doi-access=free}} It includes two main clades, the Microgenomates and Parcubacteria groups, each containing the eponymous superphyla and a few other phyla.

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.{{Cite journal|last1=Castelle|first1=Cindy J.|last2=Banfield|first2=Jillian F.|date=2018-03-08|title=Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life|journal=Cell|language=en|volume=172|issue=6|pages=1181–1197|doi=10.1016/j.cell.2018.02.016|pmid=29522741|issn=0092-8674|doi-access=free}}

{{main|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".{{cite journal|author=Sekiguchi Y|display-authors=etal|year=2015|title=First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking|journal=PeerJ|volume=3|pages=e740|doi=10.7717/peerj.740|pmc=4312070|pmid=25650158 |doi-access=free }}

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 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.

It has been proposed that some classes of the phylum Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum.{{cite journal|author=Yarza P|s2cid=21895693|display-authors=etal|year=2014|title=Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences|journal=Nature Reviews Microbiology|volume=12|issue=9|pages=635–645|doi=10.1038/nrmicro3330|pmid=25118885|hdl=10261/123763}} For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes.{{cite journal|author=Hug LA|display-authors=et al.|year=2016|title=A new view of the tree of life|journal=Nature Microbiology|volume=Article 16048|issue=5|pages=16048|doi=10.1038/nmicrobiol.2016.48|pmid=27572647|doi-access=free}}

{{main|Planctobacteria}}

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

{{main|Terrabacteria}}

The proposed superphylum, Terrabacteria, includes Actinomycetota, "Cyanobacteria"/"Melainabacteria"-group, Deinococcota, Chloroflexota, Bacillota, and candidate phylum OP10.

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.

{{for|historical classifications of bacteria|Bacterial taxonomy}}{{for|branching order|Branching order of bacterial phyla (Woese, 1987)}}

File:010 small subunit-1FKA.gif of which 16S makes up a part. Proteins are shown in blue and the single RNA strand in tan.{{cite journal|author=Schluenzen F|s2cid=1024446|display-authors=etal|year=2000|title=Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution|journal=Cell|volume=102|issue=5|pages=615–23|doi=10.1016/S0092-8674(00)00084-2|pmid=11007480|doi-access=free}}]]

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) 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.{{cite journal|author=Holland L|date=22 May 1990|title=Carl Woese in forefront of bacterial evolution revolution|url=http://www.the-scientist.com/?articles.view/articleNo/11130/title/Carl-Woese-In-Forefront-Of-Bacterial-Evolution-Revolution/|journal=The Scientist|volume=3|issue=10}}

• Purple Bacteria and their relatives (later renamed Proteobacteria{{cite journal|author=Stackebrandt|display-authors=etal|year=1988|title=Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives"|journal=Int. J. Syst. Bacteriol.|volume=38|issue=3|pages=321–325|doi=10.1099/00207713-38-3-321|doi-access=free}})
• alpha subdivision (purple non-sulfur bacteria, rhizobacteria, Agrobacterium, Rickettsiae, Nitrobacter)
• beta subdivision (Rhodocyclus, (some) Thiobacillus, Alcaligenes, Spirillum, Nitrosovibrio)
• gamma subdivision (enterics, fluorescent pseudomonads, purple sulfur bacteria, Legionella, (some) Beggiatoa)
• delta subdivision (Sulfur and sulfate reducers (Desulfovibrio), Myxobacteria, Bdellovibrio)
• Gram-positive Eubacteria{{#tag:ref | Until recently, it was believed than only Bacillota and Actinomycetota were Gram-positive. However, the candidate phylum TM7 may also be Gram positive.{{Cite journal | last1 = Hugenholtz | first1 = P. | last2 = Tyson | first2 = G. W. | last3 = Webb | first3 = R. I. | last4 = Wagner | first4 = A. M. | last5 = Blackall | first5 = L. L. | title = Investigation of Candidate Division TM7, a Recently Recognized Major Lineage of the Domain Bacteria with No Known Pure-Culture Representatives | journal = Applied and Environmental Microbiology | volume = 67 | issue = 1 | pages = 411–9 | year = 2001 | pmid = 11133473 | pmc = 92593 | doi = 10.1128/AEM.67.1.411-419.2001| bibcode = 2001ApEnM..67..411H }} Chloroflexi however possess a single bilayer, but stain negative (with some exceptions{{Cite journal | last1 = Yabe | first1 = S. | last2 = Aiba | first2 = Y. | last3 = Sakai | first3 = Y. | last4 = Hazaka | first4 = M. | last5 = Yokota | first5 = A. | doi = 10.1099/ijs.0.024877-0 | title = Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 61 | issue = 4 | pages = 903–910 | year = 2010 | pmid = 20495028| doi-access = free }}).{{Cite journal | last1 = Sutcliffe | first1 = I. C. | title = Cell envelope architecture in the Chloroflexi: A shifting frontline in a phylogenetic turf war | doi = 10.1111/j.1462-2920.2010.02339.x | journal = Environmental Microbiology | volume = 13 | issue = 2 | pages = 279–282 | year = 2011 | pmid = 20860732 | bibcode = 2011EnvMi..13..279S }} | group = Note | name = GramPos }}
• High-G+C species (later renamed Actinobacteria{{Cite journal|last1=Stackebrandt|first1=E.|last2=Rainey|first2=F. A.|last3=Ward-Rainey|first3=N. L.|year=1997|title=Proposal for a New Hierarchic Classification System, Actinobacteria classis nov|journal=International Journal of Systematic Bacteriology|volume=47|issue=2|pages=479–491|doi=10.1099/00207713-47-2-479|doi-access=free}}) (Actinomyces, Streptomyces, Arthrobacter, Micrococcus, Bifidobacterium)
• Low-G+C species (later renamed Firmicutes) (Clostridium, Peptococcus, Bacillus, Mycoplasma)
• Photosynthetic species (Heliobacteria)
• Species with Gram-negative walls (Megasphaera, Sporomusa)
• Cyanobacteria and chloroplasts (Aphanocapsa, Oscillatoria, Nostoc, Synechococcus, Gloeobacter, Prochloron)
• 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, Cytophaga, Saprospira, Flexibacter)
• Planctomyces and relatives (later renamed Planctomycetes)
• Planctomyces group (Planctomyces, Pasteuria [sic]{{#tag:ref | Pasteuria is now assigned to phylum Bacillota, not to phylum Planctomycetota. | group = Note | name = Pasteuria }})
• Thermophiles (Isocystis pallida)
• Chlamydiae (Chlamydia psittaci, Chlamydia trachomatis)
• Radioresistant micrococci and relatives (later renamed Deinococcus–Thermus{{Cite web|title=List of Prokaryotic names with Standing in Nomenclature: classification of Deinococcus–Thermus|url=http://www.bacterio.cict.fr/classifphyla.html#DeinococcusThermus|author=J.P. Euzéby|url-status=dead|archive-url=https://web.archive.org/web/20130127030659/http://www.bacterio.cict.fr/classifphyla.html|archive-date=27 January 2013|access-date=30 December 2010}} or Thermi){{#tag:ref | It has been proposed to call the clade XenobacteriaBergey's Manual of Systematic Bacteriology 1st Ed. or Hadobacteria{{Cite journal | last1 = Cavalier-Smith | first1 = T | title = The neomuran origin of Archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 52 | issue = Pt 1 | pages = 7–76 | year = 2002 | pmid = 11837318 | doi=10.1099/00207713-52-1-7| doi-access = free }} (the latter is considered an illegitimate name{{Cite web | url = http://www.bacterio.cict.fr/h/hadobacteria.html | title = List of Prokaryotic names with Standing in Nomenclature—Class Hadobacteria | work = LPSN | access-date = 30 December 2010 | archive-url = https://web.archive.org/web/20120419180430/http://www.bacterio.cict.fr/h/hadobacteria.html | archive-date = 19 April 2012 | url-status = dead}} {{cite journal | last1 = Euzéby | first1 = J.P. | year = 1997 | title = List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet | journal = Int J Syst Bacteriol | volume = 47 | issue = 2 | pages = 590–2 | pmid = 9103655 | doi = 10.1099/00207713-47-2-590 | issn = 0020-7713 | url = http://ijs.sgmjournals.org/cgi/reprint/47/2/590 | doi-access = free }}). | group = Note | name = Thermi }}
• Deinococcus group (Deinococcus radiodurans)
• Thermophiles (Thermus aquaticus)
• Green non-sulfur bacteria and relatives (later renamed Chloroflexi{{cite book|author1=Boone DR|url=https://archive.org/details/bergeysmanualofs00boon/page/721|title=The Archaea and the Deeply Branching and Phototrophic Bacteria|author2=Castenholz RW|date=18 May 2001|publisher=Springer|isbn=978-0-387-98771-2|editor=Garrity GM|edition=2nd|series=Bergey's Manual of Systematic Bacteriology|volume=1|location=New York|pages=[https://archive.org/details/bergeysmanualofs00boon/page/721 721]|id=British Library no. GBA561951|orig-year=1984 (Williams & Wilkins)|url-access=registration}})
• Chloroflexus group (Chloroflexus, Herpetosiphon)
• Thermomicrobium group (Thermomicrobium roseum)
• Thermotogae (Thermotoga maritima)

Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. The advent of molecular phylogenetics has allowed for improved elucidation of the evolutionary relationship of species by analyzing their DNA and protein sequences, for example their ribosomal DNA.{{cite journal|vauthors=Olsen GJ, Woese CR, Overbeek R|year=1994|title=The winds of (evolutionary) change: breathing new life into microbiology|url= |journal=Journal of Bacteriology|volume=176|issue=1|pages=1–6|doi=10.2172/205047|pmc=205007|pmid=8282683}} The lack of easily accessible morphological features, such as those present in animals 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.

• Bacterial taxonomy#Phyla endings
• International Code of Nomenclature of Bacteria
• 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
• List of bacterial orders
• List of sequenced bacterial genomes

{{reflist | group = Note | refs =

}}

{{reflist|3|refs=

{{cite journal|last1=Battistuzzi|first1=F. U.|last2=Hedges|first2=S. B.|title=A Major Clade of Prokaryotes with Ancient Adaptations to Life on Land|journal=Molecular Biology and Evolution|date=6 November 2008|volume=26|issue=2|pages=335–343|doi=10.1093/molbev/msn247|pmid=18988685|doi-access=}}

{{cite journal | vauthors = Battistuzzi FU, Feijao A, Hedges SB | title = A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land | journal = BMC Evolutionary Biology | volume = 4 | pages = 44 | date = November 2004 | pmid = 15535883 | pmc = 533871 | doi = 10.1186/1471-2148-4-44 | doi-access = free }}

{{Cite journal | last1 = Woese | first1 = CR | title = Bacterial evolution | journal = Microbiological Reviews | volume = 51 | issue = 2 | pages = 221–71 | year = 1987 | doi = 10.1128/MMBR.51.2.221-271.1987 | pmid = 2439888 | pmc = 373105}}

{{cite journal | author = Robert E. Danczak, M. D. Johnston, C. Kenah, M. Slattery, K. C. Wrighton, M. J. Wilkins | title = Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities | journal = Microbiome | volume = 5 | issue = 1 | pages = 112 | date = Sep 2017 | pmid = 28865481 | pmc = 5581439 | doi = 10.1186/s40168-017-0331-1 | doi-access = free }}

Cindy J. Castelle, Christopher T. Brown, Brian C. Thomas, Kenneth H. Williams, Jillian F. Banfield: [https://www.nature.com/articles/srep40101 Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation]. In: Sci Rep 7, 40101; Jan 9, 2017; doi:10.1038/srep40101

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