Candidate phyla radiation

Although there are a few exceptions, members of the candidate phyla radiation generally lack several biosynthetic pathways for several amino acids and nucleotides. To date, there has been no genomic evidence that indicates that they are capable of producing the lipids essential for cell envelope formation. Additionally, they tend to lack complete TCA cycles and electron transport chain complexes, including ATP synthase. This lack of several important pathways found in most free-living prokaryotes indicates that the candidate phyla radiation is composed of obligate fermentative symbionts.{{cite journal | vauthors = Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, Wilkins MJ, Wrighton KC, Williams KH, Banfield JF | display-authors = 6 | title = Unusual biology across a group comprising more than 15% of domain Bacteria | journal = Nature | volume = 523 | issue = 7559 | pages = 208–11 | date = July 2015 | pmid = 26083755 | doi = 10.1038/nature14486 | bibcode = 2015Natur.523..208B | osti = 1512215 | s2cid = 4397558 | url = https://escholarship.org/content/qt9ks7v8nv/qt9ks7v8nv.pdf }}

Furthermore, CPR members have unique ribosomal features. While the members of CPR are generally uncultivable, and therefore missed in culture-dependent methods, they are also often missed in culture-independent studies that rely on 16S rRNA sequences. Their rRNA genes appear to encode proteins and have self-splicing introns, features that are rarely seen in bacteria, although they have previously been reported.{{cite journal | vauthors = Belfort M, Reaban ME, Coetzee T, Dalgaard JZ | author-link1=Marlene Belfort|title = Prokaryotic introns and inteins: a panoply of form and function | journal = Journal of Bacteriology | volume = 177 | issue = 14 | pages = 3897–903 | date = July 1995 | pmid = 7608058 | pmc = 177115 | doi = 10.1128/jb.177.14.3897-3903.1995 }} Owing to these introns, members of CPR are not detected in 16S-dependent methods. Additionally, all CPR members are missing the L30 ribosomal protein, a trait that is often seen in symbionts.

Many of its characteristics are similar or analogous to those of ultra-small archaea (DPANN).

File:A Novel Representation Of The Tree Of Life.png

File:MBE TOL.jpg

The Candidate phyla radiation was found to be the most basal-branching lineage in bacteria according to some early phylogenetic analyses of this group based on ribosomal proteins and protein family occurrence profiles. These studies found the following phylogeny between phyla and superphyla. The superphyla are shown in bold.

{{Clade

|style= font-size:100%; line-height:100%

|label1=Bacteria

|1={{clade

|1=The other bacteria

|label2=CPR

|2={{Clade

|1=Wirthbacteria

|2={{Clade

|1={{Clade

|1=Dojkabacteria

|2={{Clade

|1=Katanobacteria

|2=Microgenomates

}}

}}

|2={{Clade

|1={{Clade

|1=Berkelbacteria

|2=Saccharibacteria

}}

|2={{Clade

|1={{Clade

|1=Peregrinibacteria

|2={{Clade

|1=Absconditabacteria

|2=Gracilibacteria

}}

}}

|2=Parcubacteria

}}

}}

}}

}}

}}

}}

However, several recent studies have suggested that the CPR belongs to Terrabacteria and is more closely related to Chloroflexota.{{cite journal | vauthors = Coleman GA , Davín AA , Mahendrarajah TA, Szánthó LL , Spang A , Hugenholtz P , Szöllősi GJ, Williams TA | title = A rooted phylogeny resolves early bacterial evolution | journal = Science | year = 2021 | volume = 372 | issue = 6542 | doi = 10.1126/science.abe0511 | pmid = 33958449| s2cid = 233872903 | url = https://research-information.bris.ac.uk/en/publications/51e9e402-36b7-47a6-91de-32b8cf7320d2 | hdl = 1983/51e9e402-36b7-47a6-91de-32b8cf7320d2 | hdl-access = free }}{{cite journal | vauthors = Martinez-Gutierrez CA, Aylward FO | title = Phylogenetic signal, congruence, and uncertainty across bacteria and archaea | journal = Molecular Biology and Evolution | year = 2021 | volume = 38 | issue = 12 | pages = 5514–5527 | doi = 10.1093/molbev/msab254 | pmid = 34436605| pmc = 8662615 }}{{cite journal | vauthors = Taib N , Megrian D , Witwinowski J , Adam P , Poppleton D , Borrel G , Beloin C , Gribaldo S | title = Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition | journal = Nature Ecology and Evolution | year = 2020 | volume = 4 | issue = 12 | pages = 1661–1672 | doi = 10.1038/s41559-020-01299-7 | pmid = 33077930| s2cid = 224810982 | url = https://hal-pasteur.archives-ouvertes.fr/pasteur-03207762/file/Taibetal2020.pdf }} The evolutionary relationships that are typically supported by these studies are as follows.

{{Clade

|style= font-size:100%; line-height:100%

|label1=Bacteria

|1={{clade

|1=Gracilicutes

|label2=Terrabacteria

|2={{clade

|1=DST

|2={{clade

|1=Cyanobacteria/Melainabacteria

|2={{Clade

|1={{Clade

|1=Bacillota and Mycoplasmatota

|2=Actinomycetota

}}

|2={{Clade

|1={{Clade

|1=Armatimonadota

|2=Eremiobacteraeota

}}

|2={{Clade

|1=CPR

|2={{Clade

|1=Dormibacteraeota

|2=Chloroflexota

}}

}}

}}

}}

}}

}}

}}

}}

Because many CPR members are uncultivable, they cannot be formally put into the bacterial taxonomy, but a number of provisional, or Candidatus, names have been generally agreed on.{{cite web |author=A.C. Parte |url=https://lpsn.dsmz.de/phylum/Minisyncoccota |title=Minisyncoccota |access-date=2025-02-28 |publisher=List of Prokaryotic names with Standing in Nomenclature (LPSN) |display-authors=et al.}}{{cite web |author = Sayers| url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1783273&lvl=2&lin=f&keep=1&srchmode=1&unlock |title=Patescibacteria group |publisher=National Center for Biotechnology Information (NCBI) taxonomy database |access-date=2021-03-20}} As of 2017, two superphyla are generally recognized under CPR, Parcubacteria and Microgenomates. The Phyla under CPR include:

{{cladogram|title=Phylogeny of Minisyncoccota Nakajima et al. 2025{{cite web |title=GTDB release 09-RS220 |url=https://gtdb.ecogenomic.org/about#4%7C |website=Genome Taxonomy Database|access-date=10 May 2024}}{{cite web |title=bac120_r220.sp_labels |url=https://data.gtdb.ecogenomic.org/releases/release220/220.0/auxillary_files/bac120_r220.sp_labels.tree |website=Genome Taxonomy Database|access-date=10 May 2024}}{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=Genome Taxonomy Database|access-date=10 May 2024}}|

{{clade|style=font-size:90%;line-height:90%;width:400px

|1={{Clade

|1="Wirthbacteria" (CG2-30-54-11)

|2={{Clade

|1={{Clade

|label1="Microgenomates"

|sublabel1=cluster

|1={{Clade

|1="Dojkabacteria"

|2={{Clade

|1="Katanobacteria" (WWE3)

|2="Microgenomatia"

}}

}}

}}

|2={{Clade

|1={{Clade

|label1="Saccharibacteria"

|sublabel1=cluster

|1={{Clade

|1="Berkelbacteria" (UBA1384)

|2={{Clade

|1="Kazanbacteria" (Kazan)

|2={{Clade

|1="Howlettbacteria" (CPR2) {{Failed verification|date=February 2024}}

|2="Saccharimonadia"

}}

}}

}}

}}

|2={{Clade

|label1="Gracilibacteria"

|sublabel1=cluster

|1={{Clade

|1="Absconditabacteria" (JAEDAM01)

|2="Gracilibacteria"

}}

|label2="Parcubacteria"

|sublabel2=cluster

|2={{Clade

|1="Doudnabacteria"

|2={{Clade

|1="Andersenbacteria"

|2={{Clade

|1={{Clade

|1="Torokbacteria" (GCA-2792135)

|2="Patescibacteriia" (ABY1)

}}

|2=Minisyncoccia

}}

}}

}}

}}

}}

}}

}}

}}

}}

{{cladogram|title=Phylogeny of Microgenomatia|

{{clade|style=font-size:90%;line-height:90%;width:400px

|1={{Clade

|1={{Clade

|1="Woykebacterales" (CG2-30-54-11)

|2={{Clade

|1="Curtissbacterales"

|2="Daviesbacterales"

}}

}}

|2={{Clade

|1={{Clade

|1="Roizmanbacterales" (UBA1406)

|2={{Clade

|1="Gottesmanbacterales" (UBA10105)

|2="Levybacterales"

}}

}}

|2={{Clade

|1={{Clade

|label1=GWA2-44-7

|1={{Clade

|1="Amesbacteraceae"

|2={{Clade

|1="Blackburnbacteraceae" (UBA10165)

|2="Woesebacteraceae" (UBA8517)

}}

}}

}}

|2={{Clade

|1="Shapirobacterales" (UBA12405)

|2={{Clade

|label1="Chazhemtobacteriales"

|1={{Clade

|1="Beckwithbacteraceae" (CG1-02-47-37)

|2={{Clade

|1={{Clade

|1="Collierbacteraceae" (UBA12108)

|2="Chazhemtonibacteraceae"

}}

|2={{Clade

|1="Chisholmbacteraceae"

|2={{Clade

|1="Cerribacteraceae" (UBA12028)

|2="Pacebacteraceae" (PJMF01)

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

{{cladogram|title=Phylogeny of Gracilibacteria|

{{clade|style=font-size:90%;line-height:90%;width:400px

|1={{Clade

|label1="Absconditabacteria"

|1={{Clade

|1="Ca. Altimarinus" {BD1-5: UBA6164}

|2= "Absconditicoccaceae" {"Absconditabacterales"}

}}

|label2="Gracilibacteria"

|2={{Clade

|1="Abawacabacteriales" (RBG-16-42-10)

|2={{Clade

|1="Peregrinibacterales" (UBA1369)

|2={{Clade

|1="Fallacibacteriales" (UBA4473)

|2="Peribacterales"

}}

}}

}}

}}

}}

}}

{{cladogram|title=Phylogeny of "Patescibacteriia"|

{{clade|style=font-size:90%;line-height:90%;width:400px

|1={{Clade

|1="Kerfeldbacterales" (SBBC01)

|2={{Clade

|1={{Clade

|1="Jacksonbacterales" (UBA9629)

|2={{Clade

|1="Komeilibacterales" (UBA1558)

|2="Kuenenbacterales" (UBA2196)

}}

}}

|2={{Clade

|1={{Clade

|1="Veblenbacterales"

|2={{Clade

|1="Magasanikbacterales"

|2="Uhrbacterales" (SG8-24)

}}

}}

|2={{Clade

|1="Buchananbacterales"

|2={{Clade

|1="Falkowbacterales" (BM507)

|2="Moisslbacterales" (UBA2591)

}}

}}

}}

}}

}}

}}

}}

{{cladogram|title=Phylogeny of Minisyncoccia|

{{clade|style=font-size:90%;line-height:90%;width:400px

|1={{Clade

|1="Moranbacterales"

|2={{Clade

|1={{Clade

|label1=UBA6257

|1={{Clade

|1="Brennerbacteraceae"

|2={{Clade

|1="Jorgensenbacteraceae" (GWB1-50-10)

|2={{Clade

|1="Wolfebacteraceae" (UBA9933)

|2={{Clade

|1="Colwellbacteraceae" (UBA9933)

|2={{Clade

|1="Harrisonbacteraceae" (WO2-44-18)

|2="Liptonbacteraceae" (2-01-FULL-56-20)

}}

}}

}}

}}

}}

}}

|2={{Clade

|1={{Clade

|1={{Clade

|1="Spechtbacterales"

|2="Terrybacterales"

}}

|2={{Clade

|1="Parcunitrobacterales" (GWA2-38-13b)

|2={{Clade

|1="Portnoybacterales"

|2={{Clade

|label1="Paceibacterales"

|sublabel1=?Minisyncoccales

|1={{Clade

|1="Wildermuthbacteraceae" (UBA10102)

|2={{Clade

|1="Gribaldobacteraceae" (CG1-02-41-26)

|2={{Clade

|1="Paceibacteraceae" ("Parcubacteria")

|2={{Clade

|1="Nealsonbacteraceae" (PWPS01)

|2="Staskawiczbacteraceae"

}}

}}

}}

}}

}}

}}

}}

}}

|2={{Clade

|1="Azambacterales" (UBA10092)

|2={{Clade

|1="Yanofskybacterales" (2-02-FULL-40-12)

|2={{Clade

|1="Sungbacterales"

|2={{Clade

|1="Ryanbacterales"

|2={{Clade

|1="Giovannonibacterales" (UBA11713)

|2={{Clade

|1="Niyogibacterales" (HO2-45-28)

|2={{Clade

|1="Tagabacterales"

|2={{Clade

|label1=UBA9983

|1={{Clade

|1="Vogelbacteraceae" (XYD1-FULL-46-19)

|2={{Clade

|1="Yonathbacteraceae" (UBA1539)

|2={{Clade

|1="Nomurabacteraceae" (UBA9973)

|2={{Clade

|1={{Clade

|1="Adlerbacteraceae" (SBAW01)

|2="Kaiserbacteraceae" (UBA2163)

}}

|2={{Clade

|1="Campbellbacteraceae" (UBA12079)

|2={{Clade

|1="Taylorbacteraceae" (PALSA-1337)

|2="Zambryskibacteraceae"

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

{{Expand list|date=April 2020}}

• ?"Elulimicrobiota" Rodriguez-R et al. 2020
• Clade "Patescibacteria" Rinke et al. 2013 non Parks et al. 2018
• "Wirthbacteria" Hug et al. 2016
• Microgenomates Cluster
• "Dojkabacteria" Wrighton et al. 2016 (WS6)
• "Katanobacteria" Hug et al. 2016b (WWE3)
• Superphylum Microgenomates
• ?"Microgenomates" Rinke et al. 2013
• "Woykebacteria" Anantharaman et al. 2016 (RIF34)
• "Curtissbacteria" Brown et al. 2015
• "Daviesbacteria" Brown et al. 2015
• "Roizmanbacteria" Brown et al. 2015
• "Gottesmanbacteria" Brown et al. 2015
• "Levybacteria" Brown et al. 2015
• "Shapirobacteria" Brown et al. 2015
• Clade GWA2-44-7
• ?"Genascibacteria" He et al. 2021
• "Amesbacteraceaeia" Brown et al. 2015
• "Blackburnbacteria" Anantharaman et al. 2016 (RIF35)
• "Woesebacteria" Brown et al. 2015 (DUSEL-2, DUSEL-4)
• Clade "Chazhemtobacteriales" Pallen, Rodriguez-R & Alikhan 2022 [UBA1400]
• "Beckwithbacteria" Brown et al. 2015
• "Collierbacteria" Brown et al. 2015 (MFAQ01)
• "Chazhemtonibacteraceae" corrig. Kadnikov et al. 2020
• "Chisholmbacteria" Anantharaman et al. 2016 (RIF36)
• "Cerribacteria" Kroeger et al. 2018
• "Pacebacteria" Brown et al. 2015 (PJMF01)
• Saccharibacteria Cluster
• "Berkelbacteria" Wrighton et al. 2014 (ACD58)
• "Kazanbacteria" Jaffe et al. 2020 (Kazan)
• "Howlettbacteria" Probst et al. 2018 (CPR2){{Failed verification|date=February 2024}}
• "Saccharibacteria" Albertsen et al. 2013 (TM7)
• Gracilibacteria Cluster
• Clade "Absconditabacteria"
• "Absconditabacteria" Hug et al. 2016b (SR1)
• "Ca. Altimarinus" Rinke et al. 2013 {BD1-5: UBA6164} (GN02)
• Superphylum "Gracilibacteria"
• "Abawacabacteria" Anantharaman et al. 2016 (RIF46)
• "Peregrinibacteria" Brown et al. 2015 (PER)
• "Fallacibacteriota" Dudek et al. 2017 ["Fertabacteria" (sic)] (DOLZORAL124_38_8)
• "Peribacteria" Anantharaman et al. 2016
• Parcubacteria Cluster
• ?"Baikalibacteria" Haro-Moreno et al. 2023
• "Doudnabacteria" Anantharaman et al. 2016 (SM2F11)
• "Andersenbacteria" Anantharaman et al. 2016 (RIF9)
• "Torokbacteria" Probst et al. 2018
• Superphylum "Patescibacteria" (ABY1)
• ?"Brownbacteria" Danczak et al. 2017
• "Kerfeldbacteria" Anantharaman et al. 2016 (RIF4)
• "Jacksonbacteria" Anantharaman et al. 2016 (RIF38)
• "Komeilibacteria" Anantharaman et al. 2016 (RIF6)
• "Kuenenbacteria" Brown et al. 2015
• "Veblenbacteria" Anantharaman et al. 2016 (RIF39)
• "Magasanikbacteria" Brown et al. 2015
• "Uhrbacteria" Brown et al. 2015 (SG8-24)
• "Buchananbacteria" Anantharaman et al. 2016 (RIF37)
• "Patescibacteria" (sic) Parks et al. 2018 non Rinke et al. 2013
• "Falkowbacteria" Brown et al. 2015
• "Moisslbacteria" Probst et al. 2018
• Superphylum Parcubacteria
• ?"Montesolbacteria " He et al. 2021
• "Moranbacteria" Brown et al. 2015 (OD1-i)
• Clade UBA6257
• "Brennerbacteria" Anantharaman et al. 2016 (RIF18)
• "Jorgensenbacteria" Brown et al. 2015
• "Wolfebacteria" Brown et al. 2015
• "Colwellbacteria" Anantharaman et al. 2016 (RIF41)
• "Harrisonbacteria" Anantharaman et al. 2016 (RIF43)
• "Liptonbacteria" Anantharaman et al. 2016 (RIF42)
• "Spechtbacteria" Anantharaman et al. 2016 (RIF19)
• "Terrybacteria" Anantharaman et al. 2016 (RIF13)
• "Parcunitrobacteria" Castelle et al. 2017 (GWA2-38-13b)
• "Portnoybacteria" Anantharaman et al. 2016 (RIF22)
• Clade "Paceibacteria"
• ?Minisyncoccota Nakajima et al. 2025
• "Wildermuthbacteria" Anantharaman et al. 2016 (RIF21)
• "Gribaldobacteria" Probst et al. 2018
• "Paceibacteria" (sic) Brown et al. 2015
• "Nealsonbacteria" Anantharaman et al. 2016 (RIF40)
• "Staskawiczbacteria" Anantharaman et al. 2016 (RIF20)
• "Azambacteria" Brown et al. 2015
• "Yanofskybacteria" Brown et al. 2015
• "Sungbacteria" Anantharaman et al. 2016 (RIF17)
• "Ryanbacteria" Anantharaman et al. 2016 (RIF10)
• "Giovannonibacteria" Brown et al. 2015
• "Niyogibacteria" Anantharaman et al. 2016 (RIF11)
• "Tagabacteria" Anantharaman et al. 2016 (RIF12)
• Clade UBA9973
• ?"Hugbacteria" Danczak et al. 2017
• ?"Llyodbacteria" Anantharaman et al. 2016 (RIF45)
• "Vogelbacteria" Anantharaman et al. 2016 (RIF14)
• "Yonathbacteria" Anantharaman et al. 2016 (RIF44)
• "Nomurabacteria" Brown et al. 2015
• "Adlerbacteria" Brown et al. 2015
• "Kaiserbacteria" Brown et al. 2015
• "Campbellbacteria" Brown et al. 2015
• "Taylorbacteria" Anantharaman et al. 2016 (RIF16)
• "Zambryskibacteria" Anantharaman et al. 2016 (RIF15)

The current phylogeny is based on ribosomal proteins (Hug et al., 2016). Other approaches, including protein family existence and 16S ribosomal RNA, produce similar results at lower resolutions.{{cite journal |last1=Méheust |first1=Raphaël |last2=Burstein |first2=David |last3=Castelle |first3=Cindy J. |last4=Banfield |first4=Jillian F. |title=The distinction of CPR bacteria from other bacteria based on protein family content |journal=Nature Communications |date=13 September 2019 |volume=10 |issue=1 |page=4173 |doi=10.1038/s41467-019-12171-z|pmid=31519891 |pmc=6744442 |bibcode=2019NatCo..10.4173M |doi-access=free }}

• List of bacteria genera
• List of bacterial orders
• {{section link|Bacterial phyla|Uncultivated phyla and metagenomics}} for some of the phyla in CPR.

{{Reflist}}

• [https://www.theatlantic.com/science/archive/2016/04/the-tree-of-life-just-got-a-lot-weirder/477729/ Most of the Tree of Life is a Complete Mystery]. We know certain branches exist, but we have never seen the organisms that perch there. by Ed Yong, April 12, 2016, atlantic.com.
• [https://scitechdaily.com/ultra-small-parasitic-bacteria-found-in-groundwater-dogs-cats-and-you/ Ultra-Small, Parasitic Bacteria Found in Groundwater, Dogs, Cats — And You]; on: SciTechDaily; July 21, 2020; source: Forsyth Institute
• {{cite journal |biorxiv=10.1101/258137|doi=10.1016/j.celrep.2020.107939|title=Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts|year=2020|last1=McLean|first1=Jeffrey S.|last2=Bor|first2=Batbileg|last3=Kerns|first3=Kristopher A.|last4=Liu|first4=Quanhui|last5=To|first5=Thao T.|last6=Solden|first6=Lindsey|last7=Hendrickson|first7=Erik L.|last8=Wrighton|first8=Kelly|last9=Shi|first9=Wenyuan|last10=He|first10=Xuesong|journal=Cell Reports|volume=32|issue=3|page=107939|pmid=32698001|pmc=7427843}}
• {{cite journal |last1=Bokhari |first1=RH |last2=Amirjan |first2=N |last3=Jeong |first3=H |last4=Kim |first4=KM |last5=Caetano-Anollés |first5=G |last6=Nasir |first6=A |title=Bacterial Origin and Reductive Evolution of the CPR Group |journal=Genome Biology and Evolution |date=1 March 2020 |volume=12 |issue=3 |pages=103–121 |doi=10.1093/gbe/evaa024 |pmid=32031619|pmc=7093835 |doi-access=free }}

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{{Bacteria classification}}

{{Taxonbar|from=Q27110262}}

Category:Bacteriology

Category:Candidatus taxa

Category:Bacteria phyla