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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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“Sequences with 85% or greater similarity to Parcubacteria superphylum 16S rRNA genes were extracted and used for phylogenetic reconstruction, along with reference sequences belonging to the Parcubacteria superphylum from previous publications (Wrighton et al., 2012; Kantor et al., 2013; Rinke et al., 2013; Brown et al…”
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“These studies revealed many previously uncharacterized genomes (Brown et al., 2015; Eloe-Fadrosh et al., 2016; Kashtan et al., 2014; Rinke et al., 2013), increasing the total number of sequenced microbial genomes to more than 50,000 (Joint Genome Institute’s Integrated Microbial Genomes database, accessed December 1,…”
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Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts
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“CPR organisms share small genomes and ultrasmall cell sizes (Miyoshi et al. 2005; Brown et al. 2015; Luef et al. 2015).”
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“Although the potential physiology of these candidate phyla MAGs was similar to what has previously been described (Wrighton et al., 2012; Rinke et al., 2013; Brown et al., 2015), the Amazon Microgenomates MAGs retained essential DNA mismatch repair genes (mutS, mutL) that are highly conserved in bacteria likely due to…”
BackgroundResultSulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales
Booker, A. E., Borton, M., Daly, R. A., Welch, S. A., Nicora, C., Hoyt, D. W., Wilson, T., Purvine, S. O., Wolfe, R. A., Sharma, S., et al. (2017) · mSphere · doi:10.1128/mspheredirect.00257-17 · Cited by 93
“Scaffolds were annotated as described previously (3, 36, 37) by predicting open reading frames with MetaProdigal (40).”
Self-citationLau, C. H., van Engelen, K., Gordon, S. B., Renaud, J. B., & Topp, E. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.00989-17 · Cited by 96
“constitute 15% of the bacterial domain and have relatively small genomes that lack numerous biosynthetic pathways (33).”
BackgroundGenome-Based Microbial Taxonomy Coming of AgePreprint
Hugenholtz, P., Skarshewski, A., & Parks, D. H. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018085 · Cited by 70
“…(Di Rienzi et al. 2013; Soo et al. 2014) and a large radiation of candidate bacterial phyla with unusual ribosome structures and biogenesis mechanisms that may actually be more representative of the “average” bacterium than our current preconceptions (Rinke et al. 2013; Brown et al. 2015).”
BackgroundA global atlas of marine antibiotic resistance genes and their expression.
Xu, N., Qiu, D., Zhang, Z.-Y., Wang, Y., Chen, B.-A., Zhang, Q., Wang, T., Hong, W., Zhou, N., Peñuelas, J., et al. (2023) · Water Research · doi:10.1016/j.watres.2023.120488 · Cited by 74
Batinovic, S., Rose, J. J. A., Ratcliffe, J., Seviour, R. J., & Petrovski, S. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00892-1 · Cited by 71
Groundwater cable bacteria conserve energy by sulfur disproportionation
Müller, H., Marozava, S., Probst, A. J., & Meckenstock, R. U. (2019) · The ISME Journal · doi:10.1038/s41396-019-0554-1 · Cited by 95
Getting Momentum: From Biocatalysis to Advanced Synthetic Biology
Badenhorst, C. P. S., & Bornscheuer, U. T. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.01.003 · Cited by 80
Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach
Lambrechts, S., Willems, A., & Tahon, G. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00242 · Cited by 81
“Although the microbial tree of life has greatly expanded over the last decades, from Woese’s 12 phyla to more recent estimates of at least 310 phyla (Brown et al., 2015; Hug et al., 2016; Parks et al., 2017; Zaremba-Niedzwiedzka et al., 2017; Castelle et al., 2018), much is still to be discovered as estimates suggest…”
BackgroundYeoh, Y. K., Sekiguchi, Y., Parks, D., & Hugenholtz, P. (2015) · Molecular biology and evolution · doi:10.1093/molbev/msv281 · Cited by 73
Keren, R., Lawrence, J., Zhuang, W.-Q., Jenkins, D., Banfield, J., Alvarez-Cohen, L., Zhou, L.-J., & Yu, K. (2020) · Microbiome · doi:10.1186/s40168-020-0786-3 · Cited by 72
Self-citationJaffe, A. L., Castelle, C. J., Dupont, C. L., & Banfield, J. F. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy234 · Cited by 84
“The common absence of pathways for synthesis of nucleotides, amino acids, and lipids has led to speculation that they live symbiotic or syntrophic lifestyles (Wrighton et al. 2012; Brown et al. 2015).”
BackgroundSelf-citationPhylogenomics of Cas4 family nucleases
Hudaiberdiev, S., Shmakov, S., Wolf, Y., Terns, M., Makarova, K., & Koonin, E. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1081-1 · Cited by 72
“Second, solo-Cas4 is encoded in many genomes of the Candidate Phyla Radiation (CPR), a recently described assemblage of bacteria with small genomes and many unusual features, such as Parcubacteria, Nomurabacteria, Roizmanbacteria and others [34, 35].”
BackgroundA proposal for a standardized bacterial taxonomy based on genome phylogeny
Parks, D., Chuvochina, M., Waite, D., Rinke, C., Skarshewski, A., Chaumeil, P., & Hugenholtz, P. (2018) · bioRxiv · doi:10.1101/256800 · Cited by 70
“Therefore, 16S rRNA gene sequences present in the MAGs were classified against the Greengenes 2013 (McDonald et al., 2012) and SILVA v123.”
BackgroundMethodInfluentialHigh-resolution characterization of the human microbiome
Noecker, C. A., McNally, C. P., Eng, A., & Borenstein, E. (2016) · Translational research · doi:10.1016/j.trsl.2016.07.012 · Cited by 81
“The assembly step can be performed using numerous assemblers that have been optimized for assembling metagenomic reads such as MEGAHIT,32 MetaVelvet-SL,33 Ray Meta,103 or IDBA-UD.104 The binning step often relies on nucleotide composition, exploiting the relationship between phylogenetic relatedness and similarity in…”
MethodGong, J., Qing, Y., Zou, S.-B., Fu, R., Su, L., Zhang, X.-L., & Zhang, Q.-Q. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00498 · Cited by 70
“…rare bacteria-protist association was observed again in the present study (e.g., OD1 and GN02), highlighting that many of these rare bacteria (also known as “microbial dark matter”) are of digestion-resistant and symbiotic nature in the environment (Brown et al., 2015; Nelson and Stegen, 2015).”
BackgroundJin, H., You, L., Zhao, F., Li, S., Ma, T., Kwok, L., Xu, H., & Sun, Z. (2022) · Gut Microbes · doi:10.1080/19490976.2021.2021790 · Cited by 86
“The custom SCG set was constructed by filtering out SGCs that were not conserved across most bacteria (>3000 bacteria species in NCBI database) based on a previously reported list of universal SCGs for bacteria.(54) The method for assessing taxonomically unassigned MAGs was adopted from the study of Stewart et al.”
MethodThe microbial dimension of submarine groundwater discharge: current challenges and future directions
Ruiz‐González, C., Rodellas, V., & García-Orellana, J. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab010 · Cited by 82
State of the Art in the Culture of the Human Microbiota: New Interests and Strategies
Alou, M. T., Naud, S., Khelaifia, S., Bonnet, M., Lagier, J., & Raoult, D. (2020) · Clinical Microbiology Reviews · doi:10.1128/cmr.00129-19 · Cited by 92
“This supergroup covers over 15% of the bacterial domain in the tree of life, consisting of at least 35 phyla (79) that all share the characteristics of being very small organisms with very small genomes lacking basic biosynthetic abilities, such as the capacity to synthesize nucleotides and amino acids (80).”
BackgroundCurrent and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
Douglas, G. M., & Langille, M. G. I. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz184 · Cited by 80
How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity?
Rodriguez‐R, L. M., Castro, J. C., Kyrpides, N. C., Cole, J. R., Tiedje, J. M., & Konstantinidis, K. T. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.00014-18 · Cited by 75
Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review.
Cárdenas, J. P., Quatrini, R., & Holmes, D. (2016) · Research in Microbiology · doi:10.1016/j.resmic.2016.06.007 · Cited by 69
Rodriguez-R., L., Tsementzi, D., Luo, C., & Konstantinidis, K. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15112 · Cited by 68
Expanding magnetic organelle biogenesis in the domain Bacteria
Lin, W., Zhang, W.-S., Paterson, G., Zhu, Q.-Y., Zhao, X., Knight, R., Bazylinski, D., Roberts, A., & Pan, Y.-X. (2020) · Microbiome · doi:10.1186/s40168-020-00931-9 · Cited by 68
A Bioinformatics Guide to Plant Microbiome Analysis
Lucaciu, C. R., Pelikan, C., Gerner, S. M., Zioutis, C., Köstlbacher, S., Marx, H., Herbold, C. W., Schmidt, H., & Rattei, T. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01313 · Cited by 93
Size Matters: Ultra-small and Filterable Microorganisms in the Environment
Nakai, R. (2020) · Microbes and Environments · doi:10.1264/jsme2.me20025 · Cited by 86
“Metagenomics was then used to reconstruct the genomes of filterable members in the aquifer system, representing >35 candidate phyla named CPR (Brown et al., 2015).”
BackgroundMethodSuominen, S., Dombrowski, N., Damsté, J. S. S., & Villanueva, L. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14902 · Cited by 73
Nixon, S., Daly, R., Borton, M., Solden, L., Welch, S., Cole, D., Mouser, P., Wilkins, M., & Wrighton, K. (2019) · Msphere · doi:10.1128/msphere.00613-19 · Cited by 67
“For each metagenome, we obtained the genome-resolved bins using a combination of phylogenetic signal, coverage, and GC content (34, 67, 68; http://github.com/ TheWrightonLab/metagenome_analyses).”
Self-citationTsao, H.-F., Scheikl, U., Herbold, C., Indra, A., Walochnik, J., & Horn, M. (2019) · Water Research · doi:10.1016/j.watres.2019.04.028 · Cited by 67
Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants
Hu, H., Kristensen, J. M., Herbold, C. W., Pjevac, P., Kitzinger, K., Hausmann, B., Dueholm, M. S., Nielsen, P. H., & Wagner, M. (2024) · Microbiome · doi:10.1186/s40168-024-01769-1 · Cited by 75
“…and structural peculiarities of patescibacterial ribosomes include the absence of ribosomal protein L30 (rpL30) in all known genomes, and the absence of rpL9 and rpL1 in several groups, including the classes Microgenomatia and Saccharimonadia (also known as Saccharibacteria / TM7) [10].”
BackgroundInfluentialMicrobial paracetamol degradation involves a high diversity of novel amidase enzyme candidates
Rios-Miguel, A. B., Smith, G., Cremers, G., van Alen, T. V., Jetten, M., den Camp, H. O., & Welte, C. (2022) · bioRxiv · doi:10.1016/j.wroa.2022.100152 · Cited by 66
Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene
Fukuda, K., Ogawa, M., Taniguchi, H., & Saito, M. (2016) · Journal of UOEH · doi:10.7888/juoeh.38.223 · Cited by 95
Enhancing metaproteomics—The value of models and defined environmental microbial systems
Herbst, F., Lünsmann, V., Kjeldal, H., Jehmlich, N., Tholey, A., von Bergen�, M., Nielsen, J. L., Hettich, R. L., Seifert, J., & Nielsen, P. H. (2015) · PROTEOMICS · doi:10.1002/pmic.201500305 · Cited by 75
“This helps to assess the importance of microbial groups or to identify present phyla that might have been missed by other approaches [4].”
BackgroundMetagenome-assembled genomes uncover a global brackish microbiome
Hugerth, L. W., Larsson, J., Alneberg, J., Lindh, M. V., Legrand, C., Pinhassi, J., & Andersson, A. F. (2015) · Genome biology · doi:10.1186/s13059-015-0834-7 · Cited by 243
“More recently, coverage variation across multiple samples has been used, allowing binning down to species and sometimes strain level [24, 29, 32–35].”
Microbial ecology of the deep terrestrial subsurface
Beaver, R. C., & Neufeld, J. D. (2024) · The ISME Journal · doi:10.1093/ismejo/wrae091 · Cited by 82
“…reported for many deep subsurface environments, likely due to their recent discovery, it may well be that they are difficult to detect using traditional sampling methods due to their small size (i.e. passing through sample filters), unusual ribosome structure, and missing ribosomal proteins [139].”
BackgroundA genome catalogue of lake bacterial diversity and its drivers at continental scale
Garner, R. E., Kraemer, S. A., Onana, V. E., Fradette, M., Varin, M.-P., Huot, Y., & Walsh, D. A. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01435-6 · Cited by 76
“Metagenomes were co-assembled in MEGAHIT (v.1.2.7) using k -mer lengths of 27, 37, 47, 57, 67, 77 and 87 and a minimum k -mer multiplicity filter of two 79 .”
BackgroundMethodInfluentialA scoutRNA Is Required for Some Type V CRISPR-Cas Systems
Harrington, L. B., Ma, E., Chen, J. S., Witte, I. P., Gertz, D., Páez-Espino, D., Al-Shayeb, B., Kyrpides, N. C., Burstein, D., Banfield, J. F., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.022 · Cited by 76
“We next examined environmental metatranscriptomic data (Brown et al., 2015) to determine whether this RNA is also produced in native uncultured hosts of Cas12d.”
BackgroundSelf-citationSmith, H. J., Zelaya, A. J., León, K. B. D., Chakraborty, R., Elias, D. A., Hazen, T. C., Arkin, A. P., Cunningham, A. B., & Fields, M. W. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy191 · Cited by 84
The Modern Synthesis in the Light of Microbial Genomics
Booth, A., Mariscal, C., & Doolittle, W. F. (2016) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095456 · Cited by 83
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
Chiriac, M., Bulzu, P.-A., Andrei, A., Okazaki, Y., Nakano, S., Haber, M., Kavagutti, V., Layoun, P., Ghai, R., & Salcher, M. (2021) · Microbiome · doi:10.1186/s40168-022-01274-3 · Cited by 64
“Patescibacteria, also known as Candidate Phyla Radiation (CPR) is a bacterial phylum [1] with peculiar ribosomal structures [2], reduced metabolic capacities, and small genome and cell sizes [3].”
BackgroundMicrobial dark matter filling the niche in hypersaline microbial mats
Wong, H. L., MacLeod, F. I., White, R. A., III, Visscher, P. T., & Burns, B. P. (2020) · Microbiome · doi:10.1186/s40168-020-00910-0 · Cited by 70
“It is estimated that at least 80% of environmental genomic content 61 could be considered as ‘genomic dark matter’ [5, 9-11], with the majority found in subsurface 62 environments [4, 12-15].”
BackgroundWu, L., Gingery, M., Abebe, M., Arambula, D. G., Czornyj, E., Handa, S., Khan, H. A., Liu, M., Pohlschröder, M., Shaw, K. L., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1150 · Cited by 94
Kell, D. B., Potgieter, M., & Pretorius, E. (2015) · F1000Research · doi:10.12688/f1000research.6709.2 · Cited by 59
An estimate of the deepest branches of the tree of life from ancient vertically-evolving genesPreprint
Moody, E. R. R., Mahendrarajah, T., Dombrowski, N., Clark, J., Petitjean, C., Offre, P., Szöllősi, G. J., Spang, A., & Williams, T. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.19.427276 · Cited by 5
“Our analysis placed the Candidate Phyla Radiation (CPR) (Brown et al., 2015) as a sister lineage to Chloroflexi (Chloroflexota) rather than as a deep-branching bacterial superphylum.”
MethodResultInfluentialScientific novelty beyond the experiment
Hallsworth, J. E., Udaondo, Z., Pedrós‐Alió, C., Höfer, J., Benison, K. C., Lloyd, K. G., Cordero, R. J. B., de Campos, C. B. L., Yakimov, M. M., & Amils, R. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14222 · Cited by 62
Wang, C.-Z., Mantilla-Calderon, D., Xiong, Y.-H., Alkahtani, M., Bashawri, Y. M., Qarni, H. A., & Hong, P. (2022) · Environmental Science and Technology · doi:10.1021/acs.est.2c01834 · Cited by 62
Mori, J. F., Chen, L.-X., Jessen, G., Rudderham, S. B., McBeth, J., Lindsay, M., Slater, G., Banfield, J., & Warren, L. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02435 · Cited by 62
Self-citationOverholt, W. A., Hölzer, M., Geesink, P., Diezel, C., Marz, M., & Küsel, K. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15186 · Cited by 72
“Again we focused on the Patescibacteria, since this group had the largest differences in the number of recovered MAGs, contains almost no cultivated representatives, and they are often highly abundant in groundwater systems (Brown et al., 2015; Pedron et al., 2019).”
BackgroundInfluentialExtreme halophilic archaea derive from two distinct methanogen Class II lineages.
Aouad, M., Taib, N., Oudart, A., Lecocq, M., Gouy, M., & Brochier-Armanet, C. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.04.011 · Cited by 61
“This is for instance the case of the Candidate Phyla Radiation bacteria (Brown et al., 2015) or the DPANN super-phylum in Archaea (Rinke et al., 2013).”
TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses
Faure, G., Saito, M., Wilkinson, M. E., Quinones‐Olvera, N., Xu, P., Flam-Shepherd, D., Kim, S. S., Reddy, N. R., Zhu, S., Evgeniou, L., et al. (2025) · Science · doi:10.1126/science.adv9789 · Cited by 74
Fujii, N., Kuroda, K., Narihiro, T., Aoi, Y., Ozaki, N., Ohashi, A., & Kindaichi, T. (2022) · Microbes and Environments · doi:10.1264/jsme2.me22012 · Cited by 80
“The HHAS7 bin was classified as Nomurabacteria and was related to genomes from groundwater samples (Brown et al., 2015).”
BackgroundChen, C., Wang, X., & Wang, J.-L. (2019) · Chemosphere · doi:10.1016/j.chemosphere.2019.07.028 · Cited by 60
Vigneron, A., Lovejoy, C., Cruaud, P., Kalenitchenko, D., Culley, A. I., & Vincent, W. F. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01656 · Cited by 82
“Genomic bin reconstruction highlighted that most of the enzymatic potential of these lineages differed from other bacterial lineages since only few genes were identified, as previously reported (Brown et al., 2015).”
BackgroundTahon, G., Tytgat, B., Lebbe, L., Carlier, A. L., & Willems, A. (2018) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2018.01.009 · Cited by 72
Kleikamp, H. B. C., Grouzdev, D. S., Schaasberg, P., van Valderen, R. D., van der Zwaan, R., van de Wijgaart, R., Lin, Y., Abbas, B. A., Pronk, M., van Loosdrecht, M. C. M., et al. (2023) · Water Research · doi:10.1016/j.watres.2023.120700 · Cited by 79
Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'.
Yakimov, M., Merkel, A., Gaisin, V., Pilhofer, M., Messina, E., Hallsworth, J., Klyukina, A., Tikhonova, E., & Gorlenko, V. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15823 · Cited by 59
Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis
Schwartz, M. H., Wang, H., Pan, J. N., Clark, W. C., Cui, S., Eckwahl, M. J., Pan, D. W., Parisien, M., Owens, S. M., Cheng, B. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07675-z · Cited by 59
Whaley-Martin, K. J., Chen, L.-X., Nelson, T. C., Gordon, J., Kantor, R. S., Twible, L. E., Marshall, S., McGarry, S., Rossi, L., Bessette, B., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37426-8 · Cited by 59
Self-citationType IV pili trigger episymbiotic association of Saccharibacteria with its bacterial host
Xie, B., Wang, J., Nie, Y., Tian, J., Wang, Z., Chen, D., Hu, B., Wu, X., & Du, W. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215990119 · Cited by 60
“Specifically, TM7 is a ubiquitous CPR group widely discovered in soils, sediments, wastewater, mammals, and humans (the gastrointestinal tract and oral cavity) (1, 3, 24, 25).”
BackgroundInfluentialAncient origin and constrained evolution of the division and cell wall gene cluster in Bacteria
Megrian, D., Taïb, N., Jaffe, A. L., Banfield, J. F., & Gribaldo, S. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01257-y · Cited by 60
Self-citationTian, J., Utter, D. R., Cen, L., Dong, P., Shi, W., Bor, B., Qin, M., McLean, J. S., & He, X. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114909119 · Cited by 62
“Long considered microbial “dark matter,” the CPR is a group of phylogenetically related yet genomically diverse bacteria whose evolution, lifestyle, and ecological role remain largely elusive due to their recalcitrance to cultivation (1, 2, 4).”
BackgroundNicolas, A., Jaffe, A. L., Nuccio, E., Taga, M., Firestone, M., & Banfield, J. (2021) · mSystems · doi:10.1128/msystems.01205-20 · Cited by 58
“Genome-resolved metagenomic analyses circumvent the limitations of isolation-based methods that fail for organisms unable to grow alone and for bacteria that evade detection by primers used in 16S rRNA gene surveys (11); yet, there are few reports of CPR metagenome-assembled genomes (MAGs) from soil (12–15) almost cer…”
BackgroundSelf-citationMurugkar, P. P., Collins, A., Chen, T.-T., & Dewhirst, F. (2020) · Journal of Oral Microbiology · doi:10.1080/20002297.2020.1814666 · Cited by 58
“It was noted by several authors that organisms with similar small genome size and limited synthetic capability are usually obligate symbionts or parasites of other organisms [18,20,24].”
BackgroundThe rise of diversity in metabolic platforms across the Candidate Phyla Radiation
Jaffe, A. L., Castelle, C., Carnevali, P. B. M., Gribaldo, S., & Banfield, J. (2019) · bioRxiv · doi:10.1186/s12915-020-00804-5 · Cited by 58
“We next computed contamination and completeness for all genomes using a set of 43 marker genes sensitive to described lineage-specific losses in the CPR (Anantharaman et al., 2016; Brown et al., 2015) using the custom workflow in checkm (Parks et al.”
BackgroundMethodResultInfluentialSelf-citationEndosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes
Zachar, I., & Boza, G. (2020) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-020-03462-6 · Cited by 64
Genomic and metagenomic insights into the microbial community of a thermal spring
Pedron, R., Esposito, A., Bianconi, I., Pasolli, E., Tett, A., Asnicar, F., Cristofolini, M., Segata, N., & Jousson, O. (2019) · Microbiome · doi:10.1186/s40168-019-0625-6 · Cited by 64
“Although this aspect deserves further investigation, it is consistent with the fact that groundwater microorganisms (defined as “unusual” from Brown et al. 2015) genome structure lacks primary biosynthetic pathways, contain introns and miss specific ribosomal proteins [12].”
BackgroundMethodResultInfluentialSaha, R. P., Samanta, S., Patra, S., Sarkar, D., Saha, A., & Singh, M. K. (2017) · BioMetals · doi:10.1007/s10534-017-0020-3 · Cited by 57
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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