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Unusual biology across a group comprising more than 15% of domain Bacteria
Open accessAbstract
A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.
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“Trees visualized at https://itol.embl.de/itol.cgiusing Netwick files from Hug et al. (2016) concatenated ribosomal proteins in place of 16S rRNA genes (Fig. 3B) indicate that a large radiation of predominantly uncultured mesophilic taxa, which are comprised of potentially symbiotic organisms with small cells and genomes and are referred to as the bacterial candidate phyla radiation (CPR) and the”
From The Emergence of Life (2019) · cites this paper as Brown et al. 2015
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Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
UniRef: comprehensive and non-redundant UniProt reference clusters
Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., & Wu, C. H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm098 · Cited by 1,613
Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536
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Research works printed but not linked: 56
- Harris, J. K., Kelley, S. T. & Pace, N. R. New perspective on uncultured bacterial phylogenetic division OP11. Appl. Environ. Microbiol. 70, 845–849 (2004). · DOI
- Wrighton, K. C. et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661–1665 (2012). · DOI
- Kantor, R. S. et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. MBio 4, e00708–e00713 (2013). · DOI
- Wrighton, K. C. et al. Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer. ISME J. 8, 1452–1463 (2014). · DOI
- Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). · DOI · Paper page
- Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnol. 31, 533–538 (2013). · DOI
- Luef, B. et al. Diverse, uncultivated ultra-small bacterial cells in groundwater. Nature Commun. 6, 6372 (2015). · DOI
- Burt, A. & Koufopanou, V. Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr. Opin. Genet. Dev. 14, 609–615 (2004). · DOI
- Salman, V., Amann, R., Shub, D. A. & Schulz-Vogt, H. N. Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proc. Natl Acad. Sci. USA 109, 4203–4208 (2012). · DOI
- Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013). · DOI · Paper page
- Evguenieva-Hackenberg, E. Bacterial ribosomal RNA in pieces. Mol. Microbiol. 57, 318–325 (2005). · DOI · Paper page
- Raghavan, R., Hicks, L. D. & Minnick, M. F. Toxic introns and parasitic intein in Coxiella burnetii: legacies of a promiscuous past. J. Bacteriol. 190, 5934–5943 (2008). · DOI
- Baker, B. J., Hugenholtz, P., Dawson, S. C. & Banfield, J. F. Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl. Environ. Microbiol. 69, 5512–5518 (2003). · DOI
- Gong, J., Qing, Y., Guo, X. & Warren, A. ‘Candidatus Sonnebornia yantaiensis’, a member of candidate division OD1, as intracellular bacteria of the ciliated protist Paramecium bursaria (Ciliophora, Oligohymenophorea). Syst. Appl. Microbiol. 37, 35–41 (2014). · DOI
- Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621–1624 (2012). · DOI · Paper page
- Nawrocki, E. P. in Structural RNA Homology Search and Alignment using Covariance Models (ed. Eddy, S. R. et al.) (Washington Univ. in Saint Louis, 2009).
- Baker, B. J. & Dick, G. J. Omic approaches in microbial ecology: charting the unknown. Microbe 8, 353–360 (2013).
- Yarza, P. et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Rev. Microbiol. 12, 635–645 (2014). · DOI
- Akanuma, G. et al. Inactivation of ribosomal protein genes in Bacillus subtilis reveals importance of each ribosomal protein for cell proliferation and cell differentiation. J. Bacteriol. 194, 6282–6291 (2012). · DOI
- Lecompte, O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res. 30, 5382–5390 (2002). · DOI
- Lagkouvardos, I., Jehl, M.-A., Rattei, T. & Horn, M. Signature protein of the PVC superphylum. Appl. Environ. Microbiol. 80, 440–445 (2014). · DOI
- Yutin, N., Puigbò, P., Koonin, E. V. & Wolf, Y. I. Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE 7, e36972 (2012). · DOI
- Nowotny, V. & Nierhaus, K. H. Initiator proteins for the assembly of the 50S subunit from Escherichia coli ribosomes. Proc. Natl Acad. Sci. USA 79, 7238–7242 (1982). · DOI
- Atkins, J. F. & Björk, G. R. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol. Mol. Biol. Rev. 73, 178–210 (2009). · DOI
- Schuwirth, B. S. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005). · DOI
- Nevskaya, N. Ribosomal protein L1 recognizes the same specific structural motif in its target sites on the autoregulatory mRNA and 23S rRNA. Nucleic Acids Res. 33, 478–485 (2005). · DOI
- Shajani, Z., Sykes, M. T. & Williamson, J. R. Assembly of bacterial ribosomes. Annu. Rev. Biochem. 80, 501–526 (2011). · DOI
- Luef, B. et al. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME J. 7, 338–350 (2013). · DOI
- Williams, K. H. et al. Acetate availability and its influence on sustainable bioremediation of uranium-contaminated groundwater. Geomicrobiol. J. 28, 519–539 (2011). · DOI
- Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012). · DOI
- Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359 (2012). · DOI · Paper page
- Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). · DOI
- Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010). · DOI
- Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40, D109–D114 (2012). · DOI · Paper page
- Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27 (2000). · DOI · Paper page
- Hug, L. A. et al. Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1, 22 (2013). · DOI
- Castelle, C. J. et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Commun. 4, 2120 (2013). · DOI
- Dick, G. J. et al. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 10, R85 (2009). · DOI
- Raes, J., Korbel, J. O., Lercher, M. J., von Mering, C. & Bork, P. Prediction of effective genome size in metagenomic samples. Genome Biol. 8, R10 (2007). · DOI
- McLean, J. S. et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc. Natl Acad. Sci. USA 110, E2390–E2399 (2013). · DOI
- Podar, M. et al. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73, 3205–3214 (2007). · DOI
- Marcy, Y. et al. Dissecting biological ‘dark matter’ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889–11894 (2007). · DOI
- Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335–1337 (2009). · DOI
- Cannone, J. J. et al. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002). · DOI
- Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41, D226–D232 (2013). · DOI
- Andronescu, M., Condon, A., Hoos, H. H., Mathews, D. H. & Murphy, K. P. Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 23, i19–i28 (2007). · DOI
- Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012). · DOI
- Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014). · DOI · Paper page
- Kelley, L. A. & Sternberg, M. J. E. Protein structure prediction on the Web: a case study using the Phyre server. Nature Protocols 4, 363–371 (2009). · DOI
- Gilbert, J. A. et al. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand. Genomic Sci. 3, 243–248 (2010). · DOI
- Walters, W. A. et al. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics 27, 1159–1161 (2011). · DOI
- Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014). · DOI · Paper page
- Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004). · DOI · Paper page
- Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104–2105 (2005). · DOI · Paper page
- Huson, D. H. & Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067 (2012). · DOI
- Zerbino, D. R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008). · DOI
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Self-citationSabaneyeva, E., Castelli, M., Szokoli, F., Benken, K., Lebedeva, N., Salvetti, A., Schweikert, M., Fokin, S., & Petroni, G. (2018) · European Journal of Protistology · doi:10.1016/j.ejop.2017.12.002 · Cited by 21
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BackgroundWasmund, K., Singleton, C. M., Dueholm, M. S., Wagner, M., & Nielsen, P. H. (2024) · mSystems · doi:10.1128/msystems.00301-24 · Cited by 22
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di Giulio, M. (2019) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2018.10.020 · Cited by 20
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“…understanding microbial communities and their genes (microbiomes), synthetic biology and the adoption of genome sequencing as a routine approach in the clinical and research laboratories (Cameron et al. , 2014; Koser et al. , 2014; Brown et al. , 2015; Luheshi et al. , 2015; Shanahan, 2015).”
BackgroundYe, J., Pérez, P., Zhang, R., Nielsen, S., Huang, D.-F., & Thomas, T. (2017) · Biology and Fertility of Soils · doi:10.1007/s00374-017-1246-5 · Cited by 20
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“, 2013), and (iii) reshaped our understanding of microbial life forms (Brown et al., 2015; Nasir et al., 2015; Wiegand et al., 2020).”
BackgroundInfluentialJaffe, A. L., Bardot, C., le Jeune, A.-H., Liu, J., Colombet, J., Perrière, F., Billard, H., Castelle, C., Lehours, A., & Banfield, J. (2022) · bioRxiv · doi:10.1186/s40168-022-01416-7 · Cited by 19
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BackgroundWest-Roberts, J., Matheus-Carnevali, P., Schoelmerich, M., Al-Shayeb, B., Thomas, A., Sharrar, A., He, C., Chen, L.-X., Lavy, A., Keren, R., et al. (2021) · bioRxiv · doi:10.1101/2021.08.23.457424 · Cited by 19
Self-citationMaatouk, M., Ibrahim, A., Rolain, J., Merhej, V., & Bittar, F. (2021) · bioRxiv · doi:10.1128/msystems.00898-21 · Cited by 19
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Chen, L.-X., Zhao, Y., McMahon, K., Mori, J. F., Jessen, G., Nelson, T., Warren, L., & Banfield, J. (2019) · mSystems · doi:10.1128/msystems.00410-19 · Cited by 19
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MethodInfluentialSelf-citationCostello, E., Sun, C. L., Carlisle, E., Morowitz, M., Banfield, J., & Relman, D. (2017) · Scientific Reports · doi:10.1038/s41598-017-03821-7 · Cited by 19
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Mallawaarachchi, V., Wickramarachchi, A., Xue, H., Papudeshi, B., Grigson, S., Bouras, G., Prahl, R. E., Kaphle, A., Verich, A., Talamantes-Becerra, B., et al. (2024) · Briefings Bioinform. · doi:10.1093/bib/bbae372 · Cited by 18
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MethodHendrickson, E., Bor, B., Kerns, K. A., Lamont, E., Chang, Y.-J., Liu, J., Cen, L., Schulte, F., Hardt, M., Shi, W., et al. (2022) · Journal of Bacteriology · doi:10.1128/jb.00112-22 · Cited by 18
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BackgroundWienhausen, G., Bruns, S., Sultana, S., Dlugosch, L., Groon, L.-A., Wilkes, H., & Simon, M. (2022) · The ISME Journal · doi:10.1038/s41396-022-01304-w · Cited by 20
“In short, 55 single housekeeping gene copies were searched for in all genomes [39, 40], whereupon we removed all genomes that had fewer than 53 housekeeping genes, applying a stringent selection.”
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Schulz, F., Andréani, J., Francis, R., Boudjemaa, H., Khalil, J. B., Lee, J., Scola, B. L., & Woyke, T. (2020) · mSystems · doi:10.1128/msystems.00048-20 · Cited by 18
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BackgroundDegrune, F., Boeraeve, F., Dufrêne, M., Cornelis, J., Frey, B., & Hartmann, M. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00261 · Cited by 25
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Plominsky, Á. M., Trefault, N., Podell, S. B., Blanton, J. M., la Iglesia, R. D., Allen, E. E., von Dassow, P., & Ulloa, O. (2018) · Environmental Microbiology · doi:10.1111/1462-2920.14109 · Cited by 20
“Gaps due to insertions in 16S rRNA gene sequences were removed (Brown et al., 2015), and their substitution model was calculated with MEGA v6.”
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Phoma, S., Vikram, S., Jansson, J. K., Ansorge, I., Cowan, D. A., de Peer, Y. V., & Makhalanyane, T. P. (2018) · Scientific Reports · doi:10.1038/s41598-018-28939-0 · Cited by 24
Qi, Y., Zou, D.-Y., Hou, J., Zhang, Z.-F., Du, H., Pan, Y.-P., Hua, Z.-S., Zhang, C.-J., & Li, M. (2025) · Environmental Science and Technology · doi:10.1021/acs.est.5c01564 · Cited by 17
RNA control of reverse transcription in a diversity-generating retroelement
Handa, S., Biswas, T., Chakraborty, J., Ghosh, G., Paul, B. G., & Ghosh, P. (2025) · Nature · doi:10.1038/s41586-024-08405-w · Cited by 17
Valentin-Alvarado, L. E., Fakra, S. C., Probst, A. J., Giska, J. R., Jaffe, A. L., Oltrogge, L. M., West-Roberts, J. A., Rowland, J. C., Manga, M., Savage, D. F., et al. (2024) · Microbiome · doi:10.1186/s40168-023-01704-w · Cited by 24
Self-citationMay microbial ecological baseline exist in continental groundwater?
Zhong, S., Zhou, S.-G., Liu, S.-F., Wang, J.-W., Dang, C.-Y., Chen, Q., Hu, J., Yang, S., Deng, C., Li, W., et al. (2023) · Microbiome · doi:10.1186/s40168-023-01572-4 · Cited by 17
“[11] newly defined >35 candidate phyla radiation (CPR), also known as Patescibacteria, by reconstructing 789 draft genomes from groundwater samples.”
Haro-Moreno, J., Cabello-Yeves, P. J., Garcillán-Barcia, M., Zakharenko, A., Zemskaya, T., & Rodríguez-Valera, F. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00473-1 · Cited by 17
“Patescibacteria (formerly the Candidate Phyla Radiation, CPR) is a remarkably diverse set of bacteria discovered by single-cell amplified genomes (SAGs) [1] or metagenome-assembled genomes (MAGs) [2] with only a handful of cultivated representatives all of which seem to be parasites or epibionts of other bacteria or a…”
BackgroundMethodGomez‐Alvarez, V., Siponen, S., Kauppinen, A., Hokajärvi, A.-M., Tiwari, A., Sarekoski, A., Miettinen, I. T., Torvinen, E., & Pitkänen, T. (2022) · Water Research · doi:10.1016/j.watres.2022.119495 · Cited by 25
“, 2018) and groundwater environments (Brown et al., 2015) consists of small size and low-nucleic acid content bacteria of which most lack numerous biosynthetic pathways (Fig.”
BackgroundIt’s a Long Way to the Tap: Microbiome and DNA-Based Omics at the Core of Drinking Water Quality
Bruno, A., Agostinetto, G., Fumagalli, S., Ghisleni, G., & Sandionigi, A. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19137940 · Cited by 17
“Due to their restricted metabolic capacity and unusual biology [10,11,35], it was suggested that Patescibacteria and DPANN are probably in a syntrophic relationship with other microorganisms, relying on them for complete redox transformations.”
BackgroundYu, H., Speth, D., Connon, S., Goudeau, D., Malmstrom, R., Woyke, T., & Orphan, V. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.02109-21 · Cited by 17
“Percoll density separation allowed the purification of anaerobic ammonium-oxidizing bacteria (68), and selective size filtration enabled the description of candidate phyla radiation (or Patescibacteria) (69).”
BackgroundMethanosaeta and “ Candidatus Velamenicoccus archaeovorus”
Kizina, J., Jordan, S. F. A., Martens, G. A., Lonsing, A., Probian, C., Kolovou, A., Santarella‐Mellwig, R., Rhiel, E., Littmann, S., Markert, S., et al. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.02407-21 · Cited by 19
“strain C9 (29), and groundwater-associated bacteria (31).”
BackgroundWatanabe, T., Kubo, K., Kamei, Y., Kojima, H., & Fukui, M. (2022) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2022.126320 · Cited by 17
Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere
Spang, A., Mahendrarajah, T., Offre, P., & Stairs, C. W. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac034 · Cited by 19
Pan, J., Xu, W., Zhou, Z.-C., Shao, Z., Dong, C., Liu, L., Luo, Z.-H., & Li, M. (2022) · Microbiome · doi:10.1186/s40168-021-01202-x · Cited by 17
“Also, the intron inserted in the 16S rRNA genes of CPR may be another barrier for assembling them [45].”
BackgroundSuominen, S., Gomez‐Saez, G. V., Dittmar, T., Damsté, J. S. S., & Villanueva, L. (2021) · Limnology and Oceanography · doi:10.1002/lno.11995 · Cited by 24
“It should be noted that application of these primers may miss some divergent 16S rRNA genes from bacterial groups belonging to the candidate phyla radiation, which are known to be important in anoxic conditions (Brown et al. 2015).”
BackgroundLyons, K. J., Hokajärvi, A.-M., Ikonen, J., Kauppinen, A., Miettinen, I., Pitkänen, T., Rossi, P. M., & Kujala, K. (2021) · Microbiology spectrum · doi:10.1128/spectrum.00179-21 · Cited by 17
Rhizomal Reclassification of Living Organisms
Ibrahim, A., Colson, P., Merhej, V., Zgheib, R., Maatouk, M., Naud, S., Bittar, F., & Raoult, D. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115643 · Cited by 27
“Concerning the other analyzed ancestral genes, in the six constructed trees, the branches representing CPR and archaea were always maintained, Asgard and DPANN members were always grouped with classical archaea, and no other species interfered with clustering.”
BackgroundResultInfluentialMueller, R. C., Peach, J. T., Skorupa, D. J., Copié, V., Bothner, B., & Peyton, B. (2020) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaa246 · Cited by 17
Lewis, W. H., & Ettema, T. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0300-2 · Cited by 17
Honnay, O., Helsen, K., & Geel, M. V. (2017) · Biological Conservation · doi:10.1016/j.biocon.2017.06.017 · Cited by 17
Higher recall in metagenomic sequence classification exploiting overlapping reads
Girotto, S., Comin, M., & Pizzi, C. (2016) · BMC Genomics · doi:10.1186/s12864-017-4273-6 · Cited by 17
“Furthermore, not all taxa can be captured by traditional 16S sequencing, because of its divergent gene sequences [4].”
BackgroundLloyd, K. (2015) · Science · doi:10.1126/science.aad4066 · Cited by 17
Dorador, C., Molina, V., Hengst, M., Eissler, Y., Cornejo, M., Fernández, C., & Pérez, V. (2020) · Springer eBooks · doi:10.1007/978-3-030-36192-1_9 · Cited by 15
Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments
Tong, X., Luo, D., Leung, M. H. Y., Lee, J. Y. Y., Shen, Z., Jiang, W., Mason, C. E., & Lee, P. K. H. (2024) · Microbiome · doi:10.1186/s40168-024-01926-6 · Cited by 18
“1.2) [68] was used to assess the quality of the rMAGs, utilizing a default universal set of 104 bacterial marker genes to evaluate the non-Patescibac-teria rMAGs, whereas a custom set of 43 single-copy genes [69] was utilized to assess the two Patescibacteria rMAGs.”
MethodInfluentialAnthropogenic impacts on the terrestrial subsurface biosphere
Amundson, K. K., Borton, M., & Wilkins, M. J. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-024-01110-5 · Cited by 14
Self-citationChimeric origins and dynamic evolution of central carbon metabolism in eukaryotes
Santana‐Molina, C., Williams, T. A., Snel, B., & Spang, A. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02648-0 · Cited by 18
Inter-comparison of marine microbiome sampling protocols
Pascoal, F., Tomasino, M. P., Piredda, R., Quero, G. M., Torgo, L., Poulain, J., Galand, P. E., Fuhrman, J. A., Mitchell, A., Tinta, T., et al. (2023) · ISME Communications · doi:10.1038/s43705-023-00278-w · Cited by 20
Peters, E. E., Cahn, J., Lotti, A., Gavriilidou, A., Steffens, U. A. E., Loureiro, C., Schorn, M., Cárdenas, P., Vickneswaran, N., Crews, P., et al. (2023) · ISME Communications · doi:10.1038/s43705-023-00259-z · Cited by 16
Chen, X., Molenda, O., Brown, C., Toth, C. R. A., Guo, S., Luo, F., Howe, J. Y., Nesbø, C., He, C., Montabana, E., et al. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.00025-23 · Cited by 16
“logenetically diverse and ubiquitous but are especially abundant in lakes, sediment, and groundwater (2, 3).”
BackgroundMethodInfluentialSelf-citationKuroda, K., Kubota, K., Kagemasa, S., Nakai, R., Hirakata, Y., Yamamoto, K., Nobu, M., & Narihiro, T. (2022) · Microbes and Environments · doi:10.1264/jsme2.me22063 · Cited by 16
“…Candidatus Patescibacteria, 32-520/UBA5633, Methanospirillum, cross-domain symbiosis The Candidatus Patescibacteria/Candidate Phyla Radia‐ tion (CPR) superphylum is a major bacterial phylogenetic group that includes various uncultivated lineages (Brown et al., 2015; Parks et al., 2018).”
BackgroundInfluentialKumar, S., Paul, D., Bhushan, B., Wakchaure, G., Meena, K., & Shouche, Y. (2020) · Critical reviews in microbiology · doi:10.1080/1040841x.2020.1819770 · Cited by 16
“15% of all bacterial diversity (Brown et al. 2015).”
Bacterial Origin and Reductive Evolution of the CPR Group
Bokhari, R. H., Amirjan, N., Jeong, H., Kim, K. M., Caetano‐Anollés, G., & Nasir, A. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa024 · Cited by 21
Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland
Miettinen, H., Bomberg, M., & Vikman, M. (2018) · Géosciences · doi:10.3390/geosciences8110399 · Cited by 16
“Patescibacteria also have small genomes [59,60], and Parcubacteria, a patescibacterial class, are found to lack biosynthetic capabilities, but to have potential attachment and adhesion proteins, which suggests ectosymbiotic or parasitic behaviour [61].”
BackgroundSarhan, M. S., Patz, S., Hamza, M. A., Youssef, H. H., Mourad, E. F., Fayez, M., Murphy, B., Ruppel, S., & Hegazi, N. A. (2018) · Microbes and Environments · doi:10.1264/jsme2.me18023 · Cited by 22
“The recent development of metagenomics led to a series of studies that performed functional analyses on entirely uncultured bacterial groups (5, 40, 46, 53, 60, 63).”
BackgroundGajigan, A. P., Yñiguez, A. T., Villanoy, C., Diego‐McGlone, M. L. S., Jacinto, G. S., & Conaco, C. (2018) · PeerJ · doi:10.7717/peerj.4781 · Cited by 22
“In addition, taxa under the candidate phyla radiation (CPR) will evade detection using this V4 primer set (Brown et al., 2015).”
MethodPeura, S., Buck, M., Aalto, S. L., Morales, S., Nykänen, H., & Eiler, A. (2018) · mBio · doi:10.1128/mbio.00916-18 · Cited by 16
“The limitations of the approach are that (i) in the deeper layers a high proportion of the community was composed of members of candidate phyla that are known to lack some of the single-copy genes (21) and (ii) some of the single-copy genes might not be recognized in our screening.”
C21orf57 is a human homologue of bacterial YbeY proteins
Ghosal, A., Kohrer, C., Babu, V. M., Yamanaka, K., Davies, B., Jacob, A., Ferullo, D. J., Gruber, C., Vercruysse, M., & Walker, G. (2017) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2017.01.149 · Cited by 16
“Even the small genomes of the unusual bacteria in the recently recognized Candidate Phyla Radiation (CPR) [8], which lack multiple biosynthetic pathways”
InfluentialCoutinho, F., Dutilh, B., Thompson, C., & Thompson, F. (2016) · Archives of Microbiology · doi:10.1007/s00203-016-1256-y · Cited by 16
“2016) and uncultured microorganisms, from which complete genomes can now be obtained without the need for cultivation (Iverson et al. 2012; Hugerth et al. 2015; Brown et al. 2015).”
BackgroundLopez, P., Halary, S., & Bapteste, E. P. (2015) · Biology Direct · doi:10.1186/s13062-015-0092-3 · Cited by 20
“Do divergent lineages of environmental genes point to divergent, deep-branching lineages of organismal hosts? There are good reasons to assume the present analysis, as many studies before [9], has revealed molecular cues of novel major life divisions in the environment.”
BackgroundResultInfluentialIsobe, N., Tanaka, K., Ishii, S., Shimane, Y., Okada, S., Daicho, K., Sakuma, W., Uetani, K., Yoshimura, T., Kimoto, K., et al. (2025) · Science Advances · doi:10.1126/sciadv.ads2426 · Cited by 15
“The gene encoding ribosomal protein S3 (rpsC, K02981), which is a key marker single-copy housekeeping gene for the phylogeny of microorganisms ( 77 ), was used for metagenome-based population analysis, as described previously ( 78 ).”
Iniesta, M., Vasconcelos, V., Sanz, M., & Herrera, D. (2024) · Antibiotics · doi:10.3390/antibiotics13060571 · Cited by 20
“In general, the genera of the class Bacilli decreased, and the class Clostridia and Negativicutes increased in both the sub-and the supragingival biofilms.”
BackgroundA systematic exploration of bacterial form I rubisco maximal carboxylation rates
de Pins, B., Greenspoon, L., Bar-On, Y., Shamshoum, M., Ben-Nissan, R., Milshtein, E., Davidi, D., Sharon, I., Mueller-Cajar, O., Noor, E., et al. (2024) · EMBO Journal · doi:10.1038/s44318-024-00119-z · Cited by 15
“…method described in Davidi et al, 2020; (ii) in-house assemblies of the 244 samples from the Tara Oceans expedition (Sunagawa et al, 2015); (iii) assemblies and rubisco sequences published by Wrighton et al, 2012; Brown et al, 2015; Anantharaman et al, 2016; Tabita et al, 2008b; Banda et al, 2020.”
Self-citationGenomic insights into versatile lifestyle of three new bacterial candidate phyla
Zhang, X.-X., Liu, Z., Xu, W., Pan, J., Huang, Y., Cai, M.-W., Luo, Z.-H., & Li, M. (2022) · Science China Life Sciences · doi:10.1007/s11427-021-2037-x · Cited by 15
“…author (email: limeng848@szu.edu.cn) field thanks to important advances and rapid development in the sequencing technology and bioinformatics (Brown et al., 2015; Grossart et al., 2020; Gutleben et al., 2018; Kumar Awasthi et al., 2020; Momper et al., 2017; Urich et al., 2014; Zhang et…”
BackgroundTsurumaki, M., Saito, M., Tomita, M., & Kanai, A. (2022) · RNA · doi:10.1261/rna.079103.122 · Cited by 18
“However, the lifestyles of most CPR bacteria have not been clarified, except for Saccharibacteria, which attaches to a bacterium of the genus Actinomyces (He et al. 2015), and a member of the Parcubacteria, “ Candidatus Sonnebornia yantaiensis, ” which lives in the cytoplasm of Paramecium bursaria (Gong et al. 2014).”
InfluentialKajitani, R., Noguchi, H., Gotoh, Y., Ogura, Y., Yoshimura, D., Okuno, M., Toyoda, A., Kuwahara, T., Hayashi, T., & Itoh, T. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab831 · Cited by 13
“For example, metagenomic data have been used to characterize the genomic information of the candidate phyla radiation (CPR), which is estimated to represent 15% of unidentified species in the bacterial domain (6), the Asgard superphylum (7,8), and phages in the human gut (9,10).”
MethodOverlooked Diversity of Ultramicrobacterial Minorities at the Air-Sea Interface
Rahlff, J., Giebel, H., Stolle, C., Wurl, O., Probst, A., & Herlemann, D. (2020) · Atmosphere · doi:10.3390/atmos11111214 · Cited by 15
“addition to the filtration bias, universal 16S RNA primer and protocols d not cover the complete bacterial diversity and up to 20% of environmental bacterial sequenc s re missi g [2,55].”
BackgroundPereira‐Santana, A., Gamboa-Tuz, S. D., Zhao, T., Schranz, M. E., Vinuesa, P., Bayona, A., Rodríguez‐Zapata, L. C., & Castaño, E. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008318 · Cited by 19
“Similarly, no FIB sequences were detected in any of the 212 bacterial genomes analyzed (182 well described bacteria [WDB] [36] and 30 species from the candidate phyla radiation [CPR] group [36, 37]; S2 Table), consistent with previous reports [2, 3].”
Watts, M., Spurr, L. P., Cao, K., Wick, R., Banfield, J., & Moreau, J. (2019) · Water Research · doi:10.1016/j.watres.2019.02.058 · Cited by 15
Self-citationSelection of a Microbial Community in the Course of Formation of Acid Mine Drainage
Kadnikov, V., Gruzdev, E. V., Ivasenko, D., Beletsky, A., Mardanov, A., Danilova, E. V., Karnachuk, O., & Ravin, N. (2019) · Microbiology · doi:10.1134/s0026261719030056 · Cited by 15
Collins-Fairclough, A., Co, R., Ellis, M., & Hug, L. (2018) · Msphere · doi:10.1128/msphere.00346-18 · Cited by 15
“There is evidence for novel microbially diverse populations within the dump environment— one MAG was taxonomically assigned to the Candidate Phylum Radiation candidate phylum CPR2, a radiation currently represented by four environmentally derived genomes, including the MAG from this study (20) (Fig.”
InfluentialSelf-citationMethodological Strategies in Microbiome Research and their Explanatory Implications
O’Malley, M. A., & Skillings, D. (2018) · Perspectives on Science · doi:10.1162/posc_a_00274 · Cited by 22
“coveries of putative bacterial phyla (e.g., Yarza et al. 2014; Brown et al. 2015).”
BackgroundJewell, T. N., Karaoz, U., Bill, M., Chakraborty, R., Brodie, E. L., Williams, K., & Beller, H. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00040 · Cited by 15
Self-citationSchoelmerich, M. C., Ly, L., West-Roberts, J., Shi, L.-D., Shen, C., Malvankar, N. S., Taib, N., Gribaldo, S., Woodcroft, B. J., Schadt, C. W., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49548-8 · Cited by 14
Self-citationLee, S., Hazard, C., & Nicol, G. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae205 · Cited by 14
“Genome bins were dominated by representatives of the super phylum Patescibacteria (synonymous with Parcubacteria using NCBI classification) of the Candidate Phyla Radiation [97] and consistent with the recovery of ultrasmall bacteria in soil viromes [80].”
Tallada, S., Hall, G., Barich, D., Morgan-Kiss, R., & Slonczewski, J. (2022) · bioRxiv · doi:10.1017/s0954102022000360 · Cited by 14
Inter‐domain horizontal gene transfer of nickel‐binding superoxide dismutase
Sutherland, K. M., Ward, L. M., Colombero, C.-R., & Johnston, D. T. (2021) · Geobiology · doi:10.1111/gbi.12448 · Cited by 16
Fiskal, A., Anthamatten, E., Deng, L.-H., Han, X.-G., Lagostina, L., Michel, A., Zhu, R., Dubois, N., Schubert, C., Bernasconi, S., et al. (2020) · Biogeosciences · doi:10.5194/bg-2020-318-supplement · Cited by 14
“Similarly unclear is the host relationship with ZOTU199, which belongs to the candidate phylum Parcubacteria of the Candidate Phyla Radiation (Brown et al., 2015).”
BackgroundFukushi, M., Mino, S., Tanaka, H., Nakagawa, S., Takai, K., & Sawabe, T. (2020) · iScience · doi:10.1016/j.isci.2020.101462 · Cited by 18
Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes
Bray, M. S., Wu, J., Padilla, C., Stewart, F., Fowle, D., Henny, C., Simister, R., Thompson, K., Crowe, S., & Glass, J. (2019) · bioRxiv · doi:10.1101/668343 · Cited by 14
Youssef, N. H., Farag, I., Hahn, C. R., Jarett, J. K., Becraft, E. D., Eloe‐Fadrosh, E. A., Lightfoot, J. D., Bourgeois, A., Cole, T., Ferrante, S., et al. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.00110-19 · Cited by 19
Metadata
- Authors
- Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F.
- Affiliations
- University of California, Berkeley (US)
- The Ohio State University (US)
- Lawrence Berkeley National Laboratory (US)
- Corresponding author
- Banfield, Jillian F.
- ORCID
- Venue
- Nature
- Published
- 2015-06-15
- Volume
- 523
- Issue
- 7559
- Pages
- 208-211
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1528357204
- Cited by
- 1,216
- References
- 63
- Citations by year
- 2026: 56 · 2025: 100 · 2024: 95 · 2023: 125 · 2022: 108 · 2021: 120 · 2020: 144 · 2019: 121 · 2018: 116 · 2017: 104 · 2016: 101 · 2015: 26
- FWCI
- 50.17
- Type
- journal article
- Language
- en
- Open access
- green
- www.osti.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Energy (DESC0004918, DE AC02 05CH11231)
- Joint Genome Institute
- Office of Science
- Biological and Environmental Research
- Pacific Northwest National Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Candidate Phyla Radiation, uncultured bacteria, bacterial evolution, ribosome composition, ribosome biogenesis, self-splicing introns, small genomes, groundwater bacteria, metagenome-assembled genomes, symbionts
- MeSH terms
- Bacteria, Environmental Microbiology, Introns, Phylogeny, Ribosomal Proteins, RNA, Ribosomal, 16S, Genome, Bacterial
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