Candidate phyla radiation

Candidate phyla radiation
Drawing of a CPR bacterium from a "GWB1" sample.
Scientific classification
Domain: Bacteria
Kingdom: incertae sedis
Informal group: Bacteria candidate phyla
Informal group:
Phyla[1][2]
Synonyms

Superphylum:

  • "Patescibacteria" Rinke et al. 2013

Phylum:

  • "Patescibacteria" Parks et al. 2018
  • "Patescibacteriota" Dutkiewicz et al. 2025

The candidate phyla radiation (also referred to as CPR group) is a large evolutionary radiation of bacterial lineages whose members are mostly uncultivated and only known from metagenomics and single cell sequencing. They have been described as nanobacteria (not to be confused with non-living nanoparticles of the same name) or ultra-small bacteria due to their reduced size (nanometric) compared to other bacteria.

Originally (circa 2016), it has been suggested that CPR represents over 15% of all bacterial diversity and may consist of more than 70 different phyla.[3] However, the Genome Taxonomy Database (2018) based on relative evolutionary divergence found that CPR represents a single phylum,[4] with earlier figures inflated by the rapid evolution of ribosomal proteins.[5] CPR lineages are generally characterized as having small genomes and lacking several biosynthetic pathways and ribosomal proteins. This has led to the speculation that they are likely obligate symbionts.[6][7]

Earlier work proposed a superphylum called Patescibacteria which encompassed several phyla later attributed to the CPR group.[8] Therefore, Patescibacteria and CPR are often used as synonyms.[9] The former name is not necessarily obsolete: for example, the GTDB uses the similar name Patescibacteriota because they consider the CPR group a phylum.[4]

  1. ^ Cite error: The named reference NCBI was invoked but never defined (see the help page).
  2. ^ Cite error: The named reference LPSN was invoked but never defined (see the help page).
  3. ^ Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ (September 2017). "Members of the candidate phyla radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities". Microbiome. 5 (1) 112. doi:10.1186/s40168-017-0331-1. PMC 5581439. PMID 28865481.
  4. ^ a b Parks, Donovan; Chuvochina, Maria; Waite, David; Rinke, Christian; Skarshewski, Adam; Chaumeil, Pierre-Alain; Hugenholtz, Philip (27 August 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
  5. ^ Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria; Chaumeil, Pierre-Alain; Woodcroft, Ben J.; Evans, Paul N.; Hugenholtz, Philip; Tyson, Gene W. (November 2017). "Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life". Nature Microbiology. 2 (11): 1533–1542. doi:10.1038/s41564-017-0012-7. PMID 28894102.
  6. ^ Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. (April 2016). "A new view of the tree of life". Nature Microbiology. 1 (5) 16048. doi:10.1038/nmicrobiol.2016.48. PMID 27572647.
  7. ^ Castelle CJ, Banfield JF (March 2018). "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell. 172 (6): 1181–1197. doi:10.1016/j.cell.2018.02.016. PMID 29522741.
  8. ^ Rinke C; et al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–7. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. hdl:10453/27467. PMID 23851394.
  9. ^ Beam, Jacob P.; Becraft, Eric D.; Brown, Julia M.; Schulz, Frederik; Jarett, Jessica K.; Bezuidt, Oliver; Poulton, Nicole J.; Clark, Kayla; Dunfield, Peter F.; Ravin, Nikolai V.; Spear, John R.; Hedlund, Brian P.; Kormas, Konstantinos A.; Sievert, Stefan M.; Elshahed, Mostafa S.; Barton, Hazel A.; Stott, Matthew B.; Eisen, Jonathan A.; Moser, Duane P.; Onstott, Tullis C.; Woyke, Tanja; Stepanauskas, Ramunas (2020). "Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN". Frontiers in Microbiology. 11: 1848. doi:10.3389/fmicb.2020.01848. PMC 7507113. PMID 33013724.
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