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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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BackgroundPhysical connections: prokaryotes parasitizing their kin
López‐García, P., & Moreira, D. (2020) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12910 · Cited by 13
“Similarly to the highly diverse DPANN archaea, the Candidate Phyla Radiation (CPR) was recognized a few years ago as a large clade of lineages exhibiting tiny cell size and representing a considerable proportion of bacterial diversity, essentially uncultured (Brown et al., 2015).”
Phenotypic reconstruction of the last universal common ancestor reveals a complex cellPreprint
Baidouri, F. E., Venditti, C., Suzuki, S., Meade, A., & Humphries, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.20.260398 · Cited by 16
Valach, M., Alcazar, J. A. G., Sarrasin, M., Lang, B. F., Gray, M. W., & Burger, G. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa223 · Cited by 12
“Only minor deviations in bacterial ribosomal protein content have been reported (Yutin et al. 2012; Grosjean et al. 2014; Brown et al. 2015).”
BackgroundSolagigasbacteria: Lone genomic giants among the uncultured bacterial phylaPreprint
Becraft, E., Woyke, T., Jarett, J., Ivanova, N., Vitorino, F., Poulton, N., Brown, J. M., Brown, J., Lau, C., Onstott, T., et al. (2017) · bioRxiv · doi:10.1101/176263 · Cited by 11
“…our understanding of the genomic features, evolutionary histories and metabolic capabilities of tens of phylum-level branches of Archaea, Bacteria and Eukarya that lack cultured representatives (Yoon et al., 2011; Rinke et al., 2013; Becraft et al., 2015; Brown et al., 2015; Castelle et al., 2015).”
BackgroundJaffe, A. L., Corel, E., Pathmanathan, J., Lopez, P., & Bapteste, É. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13477 · Cited by 11
“These patterns may indicate that CPR/TM6 have also exchanged genes with other bacteria, and expand upon Brown et al. (2015) proposal of a possible ribosomal protein transfer among members of the CPR.”
BackgroundMethodInfluentialConsPred: a rule-based (re-)annotation framework for prokaryotic genomes
Weinmaier, T., Platzer, A., Frank, J., Hellinger, H.-J., Tischler, P., & Rattei, T. (2016) · Bioinform. · doi:10.1093/bioinformatics/btw393 · Cited by 11
De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioningPreprint
Quince, C., Connelly, S., Raguideau, S., Alneberg, J., Shin, S., Collins, G., & Eren, A. M. (2016) · bioRxiv · doi:10.1101/073825 · Cited by 11
“A situation that is unlikely to change, particularly given the great diversity of unculturable microbes [7].”
BackgroundInfluentialGalal, A., Elhassan, S. I. A., Saleh, A., Ahmed, A. I. S., Abdelrahman, M. M., Kamal, M. M., Khalel, R., & Ziko, L. (2023) · Current Research in Biotechnology · doi:10.1016/j.crbiot.2022.11.004 · Cited by 11
Metagenomics: a powerful lens viewing the microbial world
Tiwari, N., Bansal, M., & Sharma, J. (2021) · Wastewater Treatment Reactors · doi:10.1016/b978-0-12-823991-9.00007-1 · Cited by 11
Biodiversity, the Tree of Life, and Science Communication
Rosindell, J., & Wong, Y. (2018) · Springer eBooks · doi:10.1007/978-3-319-93145-6_3 · Cited by 11
Constructing and Analyzing Metabolic Flux Models of Microbial Communities
Faria, J. P., Khazaei, T., Edirisinghe, J., Weisenhorn, P., Seaver, S. M. D., Conrad, N., Harris, N., DeJongh, M., & Henry, C. (2016) · Springer protocols handbooks/Springer protocols · doi:10.1007/8623_2016_215 · Cited by 11
Carbon source diversity shapes bacterial interspecies interactions
Ono, H., Tsuru, S., & Furusawa, C. (2025) · bioRxiv · doi:10.1093/ismejo/wraf224 · Cited by 10
“Our findings suggest that such culturable bacteria, which are expected to have access to a wider range of carbon sources [71–73], are prone to competitive interactions.”
Hidalgo, K., Centurion, V. B., Lemos, L. N., Soriano, A. U., Valoni, E., Baessa, M. P. M., Richnow, H. H., Vogt, C., & Oliveira, V. M. (2024) · Biodegradation · doi:10.1007/s10532-024-10100-6 · Cited by 13
“This phylum is characterized by small cell and genome sizes (Tian et al. 2020; Hidalgo et al. 2021), carrying only essential genes and lacking a lot of metabolic functions (Hidalgo et al. 2021; Brown et al. 2015).”
InfluentialThe dynamic history of prokaryotic phyla: discovery, diversity and division
Pallen, M. J. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006508 · Cited by 11
“…[73] Candidatus Adlerbacteria Candidatus Adleribacteriota [65] Candidatus Amesbacteria Candidatus Amesiibacteriota Candidatus Amesibacteriota [65] Candidatus Aminanaerobia Candidatus Aminanaerobiota [155] Candidatus Andersenbacteria Candidatus Anderseniibacteriota Candidatus…”
InfluentialGreco, C., Andersen, D. T., Yallop, M., Barker, G., & Jungblut, A. (2024) · Environmental Microbiology · doi:10.1111/1462-2920.16663 · Cited by 10
Veloso, M. F. C., Waldisperg, A., Arros, P., Berríos-Pastén, C., Acosta, J., Colque, H., Varas, M. A., Allende, M. L., Orellana, L. H., & Marcoleta, A. E. (2023) · Microorganisms · doi:10.3390/microorganisms11112819 · Cited by 9
“Regarding bacteria, we observed a markedly abridged set of functions in Patescibacteria (Figures 5, S3 and S4), in agreement with their reported reduced genome and limited metabolic capabilities due to a probable symbiotic or parasitic lifestyle [55,56].”
Santana-Pereira, A. L. R., Moen, F. S., Severance, B. M., & Liles, M. R. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1114548 · Cited by 10
“, 2022), and utilized the (Brown et al., 2015) proposed nomenclature for phylogenetic affiliations.”
BackgroundMethodInfluentialZheng, J., Liang, J.-L., Jia, P., Feng, S.-W., Lu, J., Luo, Z.-H., Ai, H.-X., Liao, B., Li, J.-T., & Shu, W.-S. (2022) · mSystems · doi:10.1128/msystems.00736-22 · Cited by 10
Microbial assembly and co-occurrence network in an aquifer under press perturbation
Abiriga, D., Jenkins, A., & Klempe, H. (2022) · Annals of Microbiology · doi:10.1186/s13213-022-01698-0 · Cited by 11
“Currently, no cultured representatives of the taxon exist (Brown et al. 2015; Kantor et al. 2013; Wrighton et al. 2012) and little is known about them (Castelle et al.”
BackgroundPerez-Marron, J., Sanders, C., Gómez, E., Escopete, S., Owerkowicz, T., & Orwin, P. (2022) · Comparative biochemistry and physiology. Part A, Molecular & integrative physiology · doi:10.1016/j.cbpa.2022.111319 · Cited by 10
Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome
Kleikamp, H. B. C., Grouzdev, D. S., Schaasberg, P., van Valderen, R., van der Zwaan, R., van de Wijgaart, R., Lin, Y.-M., Abbas, B., Pronk, M., van Loosdrecht, M., et al. (2022) · bioRxiv · doi:10.1101/2022.03.07.483319 · Cited by 10
“However, this approach suffers from the variable 16S gene copy numbers [2040 22] and primer efficiencies across microbes [23, 24].”
BackgroundDegenhardt, J., Merder, J., Heyerhoff, B., Simon, H., Engelen, B., & Waska, H. (2021) · Microorganisms · doi:10.3390/microorganisms9081720 · Cited by 10
“The CPR-group is almost exclusively known from metagenomic studies and is hypothesized to be involved in the degradation of highly recalcitrant OM and partially in nitrate reduction [40,41,76,77].”
BackgroundComplete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle
Baker, J. (2021) · bioRxiv · doi:10.1128/msphere.00530-21 · Cited by 10
Diversity and Molecular Characterization of Marine Halophilic Bacteria from Southeast Coast of India
Narasimman, V., Aavula, T., Venkatesan, M., & Saravanan, R. (2021) · Geomicrobiology Journal · doi:10.1080/01490451.2021.1897711 · Cited by 10
“The identified microbial characteristics of earlier periods and at the phylum level support the Genetic sequences of RNA (Brown et al. 2015; Inagaki et al. 2003).”
BackgroundMéheust, R., Castelle, C. J., Carnevali, P. B. M., Farag, I. F., He, C., Chen, L.-X., Amano, Y., Hug, L. A., & Banfield, J. F. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/765248 · Cited by 5
Self-citationKatayama, T., Nobu, M., Kusada, H., Meng, X.-Y., Yoshioka, H., Kamagata, Y., & Tamaki, H. (2019) · bioRxiv · doi:10.1101/728279 · Cited by 10
Deeg, C. M., Zimmer, M., George, E. E., Husník, F., Keeling, P., & Suttle, C. (2018) · bioRxiv · doi:10.1101/379388 · Cited by 10
“candidate phylum that seem to be distinct from the amoeba-infecting species; however, the interpretation of their genomic complement remains speculative with only amoeba-infecting isolates reported to be in culture [7-9].”
BackgroundEcogenomics of Deep-Ocean Microbial Bathytypes
Peoples, L. M., & Bartlett, D. H. (2017) · Springer eBooks · doi:10.1007/978-3-319-51686-8_2 · Cited by 11
“…‘Microgenomates,’ and ‘Parcubacteria,’ members of the “candidate phyla radiation” that show relatively reduced genome size and metabolic potential (Brown et al. 2015), potentially include piezophiles because of their identification at depth within the East Pacific Rise (Hedlund et al.…”
BackgroundBacterial Electron Transfer Chains Primed by Proteomics
Wessels, H. J. C. T., de Almeida, N. M., Kartal, B., & Keltjens, J. T. (2016) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2016.02.006 · Cited by 14
Ye, M., Lv, L.-Y., Chen, W.-X., Gao, W.-F., Chen, Y.-M., & Liu, K. (2026) · Chemical Engineering Journal · doi:10.1016/j.cej.2026.175598 · Cited by 9
A genomic view of Earth’s biomes
Szabó, G., Eloe‐Fadrosh, E. A., Pett‐Ridge, J., & Woyke, T. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00888-1 · Cited by 15
A genomic catalog of Earth’s bacterial and archaeal symbionts
Villada, J. C., Vasquez, Y. M., Szabó, G., Whittaker-Walker, E., Romero, M. F., Qin, S., Varghese, N., Eloe-Fadrosh, E., Kyrpides, N., Stepanauskas, R., et al. (2025) · bioRxiv · doi:10.1101/2025.05.29.656868 · Cited by 9
“For example, the Candidate Phyla Radiation of bacteria (e.g. Patescibacteria) and the DPANN superphylum of archaea (e.g. Nanoarchaeota, Aenigmatarchaeota) consist almost entirely of host-dependent organisms.”
Suzuki, M., Ishii, S., Gonda, K., Kashima, H., Suzuki, S., Uematsu, K., Arai, T., Tachibana, Y., Iwata, T., & Kasuya, K. (2025) · ACS Sustainable Resource Management · doi:10.1021/acssusresmgt.4c00440 · Cited by 10
Amano, Y., Sachdeva, R., Gittins, D. B., Anantharaman, K., Lei, S.-F., Valentin-Alvarado, L., Diamond, S., Beppu, H., Iwatsuki, T., Mochizuki, A., et al. (2024) · Environmental Microbiome · doi:10.1186/s40793-024-00649-3 · Cited by 9
Self-citationCandidate Phyla Radiation bacteria.
Jaffe, A. L., & Banfield, J. (2024) · Current Biology · doi:10.1016/j.cub.2023.12.024 · Cited by 9
Self-citationNovel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters
Dopson, M., Somee, M. R., González, C., Lui, L. M., Turner, S. J., Buck, M., Nilsson, E., Westmeijer, G., Ashoor, K., Nielsen, T., et al. (2024) · ISME Communications · doi:10.1093/ismeco/ycae113 · Cited by 11
“6-F17 previously suggested to lack genes for amino acid or nucleotide biosynthesis [53].”
Yang, Y., Zhou, J., Shi, D.-Y., Yang, Z.-W., Zhou, S.-Q., Yang, D., Chen, T., Li, J.-W., Li, H.-B., & Jin, M. (2023) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2023.132300 · Cited by 9
Cullings, K., Stott, M., Marinkovich, N., DeSimone, J., & Bhardwaj, S. R. (2020) · MicrobiologyOpen · doi:10.1002/mbo3.1062 · Cited by 9
“The CPR comprises more than 15% of all microbial life and contains greater than 70 newly discovered phyla (Brown et al., 2015).”
BackgroundMethodInfluentialHuge and variable diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystemsPreprint
He, C., Keren, R., Whittaker, M. L., Farag, I. F., Doudna, J., Cate, J., & Banfield, J. (2020) · bioRxiv · doi:10.1101/2020.05.14.094862 · Cited by 9
Self-citationCollins, A., Murugkar, P. P., & Dewhirst, F. (2019) · Microbiology Resource Announcements · doi:10.1128/mra.01158-19 · Cited by 9
“A human oral cavity isolate from the candidate phylum Saccharibacteria, TM7x, was the first species to be cultured from the CPR (3, 4).”
BackgroundMurugkar, P. P., Collins, A., & Dewhirst, F. (2019) · Microbiology Resource Announcements · doi:10.1128/mra.01159-19 · Cited by 9
“Oral isolate TM7x (3, 4) was the first CPR bacterium cultured.”
BackgroundSulfur-Oxidizing Bacteria Dominate in the Water from a Flooded Coal Mine Shaft in Kuzbass
Kadnikov, V., Mardanov, A., Beletsky, A., Antsiferov, D. V., Kovalyova, A. A., Karnachuk, O., & Ravin, N. (2019) · Microbiology · doi:10.1134/s0026261719010107 · Cited by 9
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Farrell, F. F., Soyer, O. S., & Quince, C. (2018) · bioRxiv · doi:10.1101/307157 · Cited by 9
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
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Metagenomics: Applications of functional and structural approaches and meta-omics
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Jonas, L., Lee, Y., Bachvaroff, T. R., Hill, R. T., & Li, Y. (2025) · mBio · doi:10.1128/mbio.01231-25 · Cited by 8
“Reduced genome sizes lead to another hallmark feature of Patescibacteria, limited metabolic capabilities (13, 76, 78).”
He, Y., Zhuo, S., Li, M., Pan, J., Jiang, Y., Hu, Y., Sanford, R. A., Lin, Q., Sun, W., Wei, N., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02077-y · Cited by 8
Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater
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“One of the most important traits was the presence of introns, which set CPR apartfromothernon-CPRbacteria 2 .”
InfluentialSudarshan, A., Dai, Z., Gabrielli, M., Oosthuizen-Vosloo, S., Konstantinidis, K., & Pinto, A. (2024) · bioRxiv · doi:10.1021/acs.est.4c05086 · Cited by 8
“63 Further, Patescibacteria have highly reduced genomes and lack of several ribosomal proteins commonly found in bacteria 64 and thus genome-centric studies often discard genome bins from this phylum due to lower estimates of genome completeness using CheckM.”
Barak, H., Fuchs, N., Liddor-Naim, M., Nir, I., Sivan, A., & Kushmaro, A. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1247119 · Cited by 12
“Moreover, they often have unusual ribosome compositions that contain self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria (Brown et al., 2015).”
BackgroundHay, M. C., Mitchell, A. C., Soares, A., Debbonaire, A. R., Mogrovejo, D., Els, N., & Edwards, A. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001131 · Cited by 8
“To screen bins for Candidate Phyla Radiation (CPR), which often contain reduced genomes [59], anvi- script- gen- CPR-classifier was run on the Campbell taxonomy [60].”
MethodMaatouk, M., Ibrahim, A., Pinault, L., Armstrong, N., Azza, S., Rolain, J., Bittar, F., & Raoult, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105446 · Cited by 8
“This ribonuclease activity has been described with multi-motifs and can be used for the formation of different proteins with several functions, depending on the splicing site of their RNAs having intron sequences, such as the case of some CPR genomes [3,15,45].”
BackgroundDanczak, R., Sengupta, A., Fansler, S., Chu, R. K., Garayburu-Caruso, V., Renteria, L., Toyoda, J. G., Wells, J. R., & Stegen, J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.803420 · Cited by 8
What Do the DPANN Archaea and the CPR Bacteria Tell Us about the Last Universal Common Ancestors?
Lineweaver, C. H. (2020) · Wiley eBooks · doi:10.1002/9781119593096.ch17 · Cited by 8
Colombet, J., Billard, H., Viguès, B., Balor, S., Boulé, C., Geay, L., Benzerara, K., Menguy, N., Ilango, G., Fuster, M., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02376 · Cited by 8
“ultramicro-prokaryotes (Duda et al., 2012; Brown et al., 2015; Hug et al., 2016; Ortiz-Alvarez and Casamayor, 2016; Wurch et al., 2016; Castelle et al., 2018; Ghuneim et al., 2018), and biomimetic mineralo-organic particles (BMOPs) (Wu et al.”
BackgroundBiogeography, Ecology, and Evolution of Deep Life
Magnabosco, C., Biddle, J. F., Cockell, C. S., Jungbluth, S. P., & Twing, K. I. (2019) · Cambridge University Press eBooks · doi:10.1017/9781108677950.017 · Cited by 9
“” The prevalence of “ Hadesarchaea ” and other candidate phyla (155) within subsurface environments is rapidly expanding our understanding of microbial diversity and changing the way we view the tree of life (156).”
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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