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.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The bacterial candidate phyla radiation (CPR) and the DPANN archaea diversify near the base of the Bacteria and Archaea respectively.
“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
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 · see citing works
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975 · see citing works
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 · see citing works
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 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603 · see citing works
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works
Self-citationStochastic Community Assembly: Does It Matter in Microbial Ecology?
Zhou, J. Z., & Ning, D. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00002-17 · Cited by 2,773 · see citing works
Shotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works
A new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039 · see citing works
Self-citationRecovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works
“Cyanobacteria (48) Thermotogae (11) Acetothermia (10) Dictyoglomi Coprothermo.”
BackgroundInfluentialRecovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
(2017) · doi:10.1038/s41564-018-0171-1 · Cited by 1,742 · see citing works
Self-citationChklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023) · Nature Methods · doi:10.1038/s41592-023-01940-w · Cited by 1,705 · see citing works
Asgard archaea illuminate the origin of eukaryotic cellular complexity
Zaremba-Niedzwiedzka, K., Caceres, E. F., Saw, J. H., Bäckström, D., Juzokaite, L., Vancaester, E., Seitz, K. W., Anantharaman, K., Starnawski, P., Kjeldsen, K. U., et al. (2017) · Nature · doi:10.1038/nature21031 · Cited by 1,226 · see citing works
Self-citationWhere less may be more: how the rare biosphere pulls ecosystems strings
Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., Küsel, K., Rillig, M. C., Rivett, D. W., Salles, J. F., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2016.174 · Cited by 1,353 · see citing works
“Single-cell genomics (Hedlund et al., 2014) and reconstructed genomes (Brown et al., 2015; Youssef et al., 2015) can provide valuable insights regarding the metabolic capabilities, physiological preferences, genomic architecture and ecological roles of candidate phyla.”
BackgroundInfluentialScaling laws predict global microbial diversity
Locey, K. J., & Lennon, J. T. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521291113 · Cited by 1,184 · see citing works
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
Harrington, L., Burstein, D., Chen, J. S., Páez-Espino, D., Ma, E., Witte, I. P., Cofsky, J. C., Kyrpides, N., Banfield, J., & Doudna, J. (2018) · Science · doi:10.1126/science.aav4294 · Cited by 1,106 · see citing works
Self-citationAnantharaman, K., Brown, C., Hug, L., Sharon, I., Castelle, C., Probst, A., Thomas, B., Singh, A., Wilkins, M., Karaoz, U., et al. (2016) · Nature Communications · doi:10.1038/ncomms13219 · Cited by 1,040 · see citing works
“Thirty of these new phylum-level lineages belong to the recently described Candidate Phyla Radiation (CPR) 17 and two affiliate with the Proteobacteria (Fig.”
BackgroundMethodInfluentialSelf-citationRelic DNA is abundant in soil and obscures estimates of soil microbial diversity
Carini, P., Marsden, P. J., Leff, J., Morgan, E. E., Strickland, M., & Fierer, N. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.242 · Cited by 960 · see citing works
“These 37 methods have advanced our understanding of terrestrial microbiology in a myriad of 38 ways, by: i) revealing that thousands of unique microbial taxa can inhabit a single gram 39 of soil (1-3); ii) uncovering novel soil microbial diversity (4, 5); and iii) identifying putative 40 functions of uncultivated taxa…”
BackgroundAsnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · see citing works
Microbial strain-level population structure and genetic diversity from metagenomes
Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works
A genomic catalog of Earth’s microbiomes
Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N. J., Schulz, F., Wu, D., Páez-Espino, D., Chen, I.-M. A., Huntemann, M., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0718-6 · Cited by 847 · see citing works
Self-citationNew insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D. M., Vangay, P., Garbe, J., Maclean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R. C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 807 · see citing works
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., Golding, S. D., & Tyson, G. W. (2015) · Science · doi:10.1126/science.aac7745 · Cited by 785 · see citing works
The oral microbiome: diversity, biogeography and human health
Baker, J. L., Mark Welch, J. L., Kauffman, K. M., McLean, J. S., & He, X. (2024) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00963-6 · Cited by 661 · see citing works
Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
Castelle, C. J., & Banfield, J. F. (2018) · Cell · doi:10.1016/j.cell.2018.02.016 · Cited by 595 · see citing works
“Although the deep branching order is not well supported, it is possible that the root of the bacterial domain is placed between well-known bacteria (including the commonly known major lineages, such as Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, with well-studied representatives) and the bacteria of…”
InfluentialSelf-citationMicrobial diversity in extreme environments
Shu, W., & Huang, L. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00648-y · Cited by 631 · see citing works
New CRISPR–Cas systems from uncultivated microbes
Burstein, D. E., Harrington, L. B., Strutt, S. C., Probst, A. J., Anantharaman, K., Thomas, B. C., Doudna, J. A., & Banfield, J. F. (2016) · Nature · doi:10.1038/nature21059 · Cited by 574 · see citing works
“These bacteria typically have small cell sizes, very small genomes and a limited biosynthetic capacity 6,30–32 , indicating they are most likely symbionts 6,30–33 .”
BackgroundMethodInfluentialSelf-citationInnovations to culturing the uncultured microbial majority
Lewis, W. H., Tahon, G., Geesink, P., Sousa, D. Z., & Ettema, T. J. G. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-00458-8 · Cited by 618 · see citing works
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
von Meijenfeldt, F. A. B., Arkhipova, K., Cambuy, D. D., Coutinho, F., & Dutilh, B. (2019) · Genome Biology · doi:10.1186/s13059-019-1817-x · Cited by 503 · see citing works
HydDB: A web tool for hydrogenase classification and analysis
Søndergaard, D., Pedersen, C. N. S., & Greening, C. (2016) · Scientific Reports · doi:10.1038/srep34212 · Cited by 514 · see citing works
A review of methods and databases for metagenomic classification and assembly
Breitwieser, F. P., Lu, J., & Salzberg, S. L. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx120 · Cited by 560 · see citing works
“The use of the 16S rRNA gene itself is imperfect as well: for the recently described Candidate Phyla Radiation, which comprises up to 15% of the bacterial domain [26], it was estimated that >50% of the organisms evaded detection with classical 16S amplicon sequencing [27].”
MethodComputational approaches to predict bacteriophage–host relationships
Edwards, R. A., McNair, K. A., Faust, K., Raes, J., & Dutilh, B. E. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv048 · Cited by 453 · see citing works
“…genome space is increasingly sampled by sequencing cultured strains, single cells and assembling metagenomes, we still lack genome sequences for most host strains of naturally occurring phages (Wu et al. 2009; Rinke et al. 2013; Dutilh et al. 2014; Brown et al. 2015; Garza and Dutilh 2015).”
BackgroundBiosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
Castelle, C. J., Brown, C. T., Anantharaman, K., Probst, A. J., Huang, R. H., & Banfield, J. F. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0076-2 · Cited by 454 · see citing works
Self-citationGenome-based microbial ecology of anammox granules in a full-scale wastewater treatment system
Speth, D. R., Zandt, M. H. I. ‘., Guerrero-Cruz, S., Dutilh, B. E., & Jetten, M. S. M. (2016) · Nature Communications · doi:10.1038/ncomms11172 · Cited by 497 · see citing works
Archaea and the origin of eukaryotes
Eme, L., Spang, A., Lombard, J., Stairs, C. W., & Ettema, T. J. G. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.133 · Cited by 549 · see citing works
Diversity, ecology and evolution of Archaea
Baker, B. J., Anda, V. D., Seitz, K. W., Dombrowski, N., Santoro, A. E., & Lloyd, K. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0715-z · Cited by 523 · see citing works
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis
Crits-Christoph, A., Diamond, S., Butterfield, C., Thomas, B., & Banfield, J. (2018) · Nature · doi:10.1038/s41586-018-0207-y · Cited by 409 · see citing works
Self-citationAccurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401 · see citing works
Self-citationExpanded diversity of microbial groups that shape the dissimilatory sulfur cycle
Anantharaman, K., Hausmann, B., Jungbluth, S. P., Kantor, R. S., Lavy, A., Warren, L. A., Rappé, M. S., Pester, M., Loy, A., Thomas, B. C., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0078-0 · Cited by 432 · see citing works
“CPR organisms are common in aquifers where conditions oscillate between oxic and anoxic [24, 26].”
BackgroundInfluentialSelf-citationHigh proportions of bacteria and archaea across most biomes remain uncultured
Steen, A. D., Crits‐Christoph, A., Carini, P., DeAngelis, K. M., Fierer, N., Lloyd, K. G., & Thrash, J. C. (2019) · The ISME Journal · doi:10.1038/s41396-019-0484-y · Cited by 454 · see citing works
“Because the length of the 16S rRNA genes can vary considerably [12], gaps are important markers of evolutionary distance [6].”
BackgroundMeasurement of bacterial replication rates in microbial communities
Brown, C., Olm, M., Thomas, B., & Banfield, J. (2016) · Nature Biotechnology · doi:10.1038/nbt.3704 · Cited by 388 · see citing works
Self-citationThe growing tree of Archaea: new perspectives on their diversity, evolution and ecology
Adam, P. S., Borrel, G., Brochier‐Armanet, C., & Gribaldo, S. (2017) · The ISME Journal · doi:10.1038/ismej.2017.122 · Cited by 394 · see citing works
“Nevertheless, by applying a sophisticated approach to uncover the ancient phylogenetic signal in proteins shared between Archaea and Bacteria, we have recently challenged this root.”
BackgroundInfluentialTian, R., Ning, D., He, Z., Zhang, P., Spencer, S. J., Gao, S.-H., Shi, W., Wu, L., Zhang, Y., Yang, Y., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00825-w · Cited by 377 · see citing works
“In addition to the bacterial cell size study of Brown et al. [7], Luef et al. also proved the ultra-small cell size of Microgenomates (OP11), Parcubacteria (OD1), and Katanobacteria (WWE3) from groundwater using cryogenic transmission election microscope [8].”
BackgroundMethodResultInfluentialCoral-associated bacteria demonstrate phylosymbiosis and cophylogeny
Pollock, F. J., McMinds, R., Smith, S. J., Bourne, D. G., Willis, B. L., Medina, M., Thurber, R. L. V., & Zaneveld, J. (2018) · Nature Communications · doi:10.1038/s41467-018-07275-x · Cited by 379 · see citing works
Microbial diversity in European alpine permafrost and active layers
Frey, B., Rime, T., Phillips, M., Stierli, B., Hajdas, I., Widmer, F., & Hartmann, M. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw018 · Cited by 354 · see citing works
“2013) and other related candidate phyla of the recently proposed CPR supergroup (Brown et al. 2015) are characterized by small genomes (approximately 1MB) with lower GC contents (30–50%) and reduced metabolic capabilities that likely have prevented their cultivation so far (Kantor et al 2013; Rinke et al.”
BackgroundEvolutionary Genomics of Defense Systems in Archaea and Bacteria
Koonin, E. V., Makarova, K. S., & Wolf, Y. I. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090816-093830 · Cited by 335 · see citing works
“Compared to our previous similar census (109), the distributions have shifted to the left owing to the discovery of numerous genomes with few identifiable defense systems, the socalled candidate phyla radiation (CPR) of bacteria, and novel phyla of archaea with small genomes (17, 62).”
BackgroundTargeted isolation and cultivation of uncultivated bacteria by reverse genomics
Cross, K. L., Campbell, J. H., Balachandran, M., Campbell, A. G., Cooper, C. J., Griffen, A. L., Heaton, M., Joshi, S. S., Klingeman, D. M., Leys, E. J., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0260-6 · Cited by 370 · see citing works
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J. G., Belda‐Ferre, P., Al‐Ghalith, G. A., Kopylova, E., McDonald, D. T., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13443-4 · Cited by 338 · see citing works
Ecology of the Oral Microbiome: Beyond Bacteria
Baker, J. L., Bor, B., Agnello, M., Shi, W., & He, X. (2017) · Trends in Microbiology · doi:10.1016/j.tim.2016.12.012 · Cited by 364 · see citing works
“Like other CPR members, TM7x has an ultra-small cell size (200–300 nm) and a reduced genome lacking essential pathways (~700 genes) [32, 33].”
BackgroundTwenty years of bacterial genome sequencing
Loman, N. J., & Pallen, M. J. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3565 · Cited by 346 · see citing works
GUNC: detection of chimerism and contamination in prokaryotic genomes
Orakov, A. N., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T., & Bork, P. (2021) · Genome biology · doi:10.1186/s13059-021-02393-0 · Cited by 307 · see citing works
A rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285 · see citing works
“Recent phylogenomic analyses of expanded sets of diverse bacteria have placed the root between one of the recently identified groups, the Candidate Phyla Radiation [CPR, also knownasPatescibacteria (15, 16)] and all other Bacteria (11, 16, 17).”
BackgroundGrad-seq guides the discovery of ProQ as a major small RNA-binding protein
Smirnov, A., Förstner, K., Holmqvist, E., Otto, A., Günster, R. A., Becher, D., Reinhardt, R., & Vogel, J. (2016) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1609981113 · Cited by 280
“Conclusions The Grad-seq approach provides an experimental and analytical framework to rapidly visualize the major RNA collectives of an organism of interest, which will be particularly useful in drafting initial functional RNA landscapes for many understudied microbes with unexplored RNA biology (41, 42).”
MethodMalla, M. A., Dubey, A., Kumar, A., Yadav, S., Hashem, A., & Allah, E. F. A. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02868 · Cited by 350 · see citing works
“Some of the novel findings enabled by metagenomics involve the identification of endosymbiotic bacterial phyla (46), nitrification processes (47, 48), human disease pathogens associated with epidemics (49), bacteria (50), and viruses (51) associated with inflammatory bowel diseases, and the identification of commensal…”
BackgroundMethanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions
Angle, J., Morin, T., Solden, L., Narrowe, A. B., Smith, G., Borton, M., Rey-Sánchez, C., Daly, R., Mirfenderesgi, G., Hoyt, D., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01753-4 · Cited by 272 · see citing works
Self-citationYutin, N., Makarova, K., Gussow, A. B., Krupovic, M., Segall, A., Edwards, R., & Koonin, E. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0053-y · Cited by 270 · see citing works
“Among the other sequences included in the family, several are assigned to other bacteria, in particular, Chlamydia trachomatis, as well as several members of the recently identified candidate phyla radiation (CPR) 16 .”
Structure of the bacterial ribosome at 2 Å resolution
Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263 · see citing works
“, 2009) and fully described in (Brown et al., 2015).”
Self-citationProbst, A. J., Ladd, B., Jarett, J. K., Geller‐McGrath, D., Sieber, C. M. K., Emerson, J., Anantharaman, K., Thomas, B. C., Malmstrom, R. R., Stieglmeier, M., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-017-0098-y · Cited by 258 · see citing works
Self-citationPresent and Future of Culturing Bacteria
Overmann, J., Abt, B., & Sikorski, J. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090816-093449 · Cited by 283 · see citing works
The bright side of microbial dark matter: lessons learned from the uncultivated majority.
Solden, L., Lloyd, K., & Wrighton, K. (2016) · Current Opinion in Microbiology · doi:10.1016/j.mib.2016.04.020 · Cited by 253 · see citing works
Self-citationGarber, A. I., Nealson, K. H., Okamoto, A., McAllister, S. M., Chan, C. S., Barco, R. A., & Merino, N. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00037 · Cited by 430 · see citing works
“While we present results for only a select set of 17 candidate taxa ( Supplementary Data Sheets S8, S9 ), all publicly-available genomes from the CPR and other candidate strains were analyzed ( Supplementary Data Sheets S10, S11 ).”
BackgroundMethodInfluentialBoers, S. A., Jansen, R., & Hays, J. P. (2019) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-019-03520-3 · Cited by 281 · see citing works
Machine learning for microbiologists
Asnicar, F., Thomas, A. M., Passerini, A., Waldron, L., & Segata, N. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00984-1 · Cited by 269 · see citing works
“…was applied on Jaccard distances calculated using the protein content of 3,598 genomes collected by Méheust et al. 121 from four published data sets 122–125 The genomes were sorted using agglomerative hierarchical clustering applied on Jaccard pairwise distances and calculated using the protein…”
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems
Burstein, D. E., Sun, C. L., Brown, C. T., Sharon, I., Anantharaman, K., Probst, A. J., Thomas, B. C., & Banfield, J. F. (2016) · Nature Communications · doi:10.1038/ncomms10613 · Cited by 235 · see citing works
“Notably, organisms from CPR, TM6 and Chlamydiae have very small genomes ( B 1 Mbp) and they are inferred to be obligate symbionts 11,25–29 .”
InfluentialSelf-citationCryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes
Roux, S., Krupovic, M., Daly, R., Borges, A. L., Nayfach, S., Schulz, F., Sharrar, A., Carnevali, P. B. M., Cheng, J.-F., Ivanova, N., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0510-x · Cited by 241 · see citing works
Self-citationVollmers, J., Wiegand, S., & Kaster, A.-K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169662 · Cited by 240 · see citing works
Gifted microbes for genome mining and natural product discovery
Baltz, R. (2017) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-016-1815-x · Cited by 239 · see citing works
Palomo, A., Fowler, J., Gülay, A., Rasmussen, S., Sicheritz‐Pontén, T., & Smets, B. F. (2016) · The ISME Journal · doi:10.1038/ismej.2016.63 · Cited by 233 · see citing works
“, 2015) and the expansion of the tree of life (Brown et al., 2015).”
BackgroundDoolittle, W. F., & Brunet, T. D. P. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005912 · Cited by 45 · see citing works
“Several recent metagenomic surveys have uncovered heterogeneous populations of previously unknown small-genomed bacteria or archaea that may be metabolically dependent on each other in this way [31,32].”
BackgroundShelton, A. N., Seth, E. C., Mok, K. C., Han, A. W., Jackson, S., Haft, D., & Taga, M. (2018) · The ISME Journal · doi:10.1038/s41396-018-0304-9 · Cited by 235 · see citing works
Genomes OnLine database (GOLD) v.7: updates and new features
Mukherjee, S., Stamatis, D., Bertsch, J., Ovchinnikova, G., Katta, H. Y., Mojica, A., Chen, I.-M. A., Kyrpides, N. C., & Reddy, T. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky977 · Cited by 230 · see citing works
“This can be largely attributed to the increasing interest in sequencing of metagenome samples as well as several recent large-scale projects to identify novel MAGs from environmental samples (22,23).”
BackgroundMicrobial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales
Daly, R., Borton, M., Wilkins, M., Hoyt, D., Kountz, D. J., Wolfe, R. A., Welch, S., Marcus, D., Trexler, R., MacRae, J., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.146 · Cited by 228 · see citing works
Self-citationRecovering complete and draft population genomes from metagenome datasets
Sangwan, N., Xia, F., & Gilbert, J. A. (2016) · Microbiome · doi:10.1186/s40168-016-0154-5 · Cited by 255 · see citing works
“This method can be extrapolated to uncultured, unknown genomes without a close reference sequence [65, 66].”
BackgroundMethodInsights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages
Liu, X., Li, M., Castelle, C., Probst, A., Zhou, Z.-C., Pan, J., Liu, Y., Banfield, J., & Gu, J.-D. (2018) · Microbiome · doi:10.1186/s40168-018-0488-2 · Cited by 227 · see citing works
“[15, 27], sediment [28, 29], and freshwater [16].”
Self-citationBrooks, B., Olm, M. R., Firek, B. A., Baker, R., Thomas, B. C., Morowitz, M. J., & Banfield, J. F. (2017) · Nature Communications · doi:10.1038/s41467-017-02018-w · Cited by 226 · see citing works
Self-citationMarine mammals harbor unique microbiotas shaped by and yet distinct from the sea
Bik, E. M., Costello, E. K., Switzer, A. D., Callahan, B. J., Holmes, S., Wells, R. S., Carlin, K. P., Jensen, E. D., Venn-Watson, S. K., & Relman, D. A. (2016) · Nature Communications · doi:10.1038/ncomms10516 · Cited by 280 · see citing works
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation
Liu, S.-J., Moon, C., Zheng, N., Huws, S., Zhao, S.-G., & Wang, J.-Q. (2022) · Microbiome · doi:10.1186/s40168-022-01272-5 · Cited by 223 · see citing works
“used this method to culture Saccharibacteria (TM7), a phylum belonging to the bacterial candidate phyla radiation [109], from human saliva samples, which represented three different species-level lineages of Saccharibacteria.”
MethodThe nature of the last universal common ancestor and its impact on the early Earth system
Moody, E. R. R., Álvarez-Carretero, S., Mahendrarajah, T., Clark, J., Betts, H. C., Dombrowski, N., Szánthó, L. L., Boyle, R. A., Daines, S. J., Chen, X., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02461-1 · Cited by 256 · see citing works
“3), and a combination of both the DPANN and CPR constraints (topology 2); these were tested against the ML topo logy, both using the normal 20 amino acid alignments and also with Susko–Roger recoding 88 .”
InfluentialTransitory microbial habitat in the hyperarid Atacama Desert
Schulze-Makuch, D., Wagner, D., Kounaves, S., Mangelsdorf, K., Devine, K. G., de Vera, J. D., Schmitt-Kopplin, P., Grossart, H., Parro, V., Kaupenjohann, M., et al. (2018) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1714341115 · Cited by 222 · see citing works
“No rain can fall from the Martian atmosphere today (35), but liquid water can be present near the Martian surface in the form of nightly snow storms/ice microbursts (36), fog (37), near-surface groundwater (38), and possibly also from mineral dehydration reactions (39).”
BackgroundMethodIt’s the song, not the singer: an exploration of holobiosis and evolutionary theory
Doolittle, W., & Booth, A. (2017) · Biology & Philosophy · doi:10.1007/s10539-016-9542-2 · Cited by 222 · see citing works
“Shared metabolisms are part of the fabric of Nature (Falkowski et al. 2008): very recent metagenomic sequencing surveys have uncovered communities made up of multiple bacterial or archaeal cellular lineages whose genomes lack one or another gene necessary for independent growth (Brown et al. 2015).”
BackgroundShaiber, A., Willis, A. D., Delmont, T. O., Roux, S., Chen, L.-X., Schmid, A. C., Yousef, M., Watson, A. R., Lolans, K., Esen, Ö. C., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02195-w · Cited by 227 · see citing works
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Eme, L., Tamarit, D., Caceres, E., Stairs, C. W., Anda, V. D., Schön, M. E., Seitz, K. W., Dombrowski, N., Lewis, W. H., Homa, F., et al. (2023) · Nature · doi:10.1038/s41586-023-06186-2 · Cited by 236 · see citing works
“The ggKbase genome bins were individually curated to fix local assembly errors using ra2.py 59 .”
Self-citationMetagenomics uncovers gaps in amplicon-based detection of microbial diversity
Eloe-Fadrosh, E., Ivanova, N., Woyke, T., & Kyrpides, N. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2015.32 · Cited by 216 · see citing works
PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes
Zeng, J., Tu, Q., Yu, X.-L., Qian, L., Wang, C., Shu, L.-F., Liu, F., Liu, S.-W., Huang, Z.-J., He, J.-G., et al. (2022) · Microbiome · doi:10.1186/s40168-022-01292-1 · Cited by 215 · see citing works
“Also, it has been reported that about 20% of bacteria would be undetectable using currently available primers due to well-recognized biases [20].”
BackgroundHerrmann, M., Wegner, C., Taubert, M., Geesink, P., Lehmann, K., Yan, L.-J., Lehmann, R., Totsche, K., & Küsel, K. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01407 · Cited by 210
“Patescibacteria depend on the uptake of nucleotides and amino acids from co-localized organisms (Brown et al., 2015).”
BackgroundInfluentialStarr, E. P., Nuccio, E., Pett-Ridge, J., Banfield, J., & Firestone, M. (2019) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1908291116 · Cited by 209 · see citing works
“com/christophertbrown/ fix_assembly_errors) (90).”
Self-citationReference standards for next-generation sequencing
Hardwick, S. A., Deveson, I. W., & Mercer, T. R. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.44 · Cited by 223 · see citing works
Resilience of the oral microbiome
Wade, W. G. (2021) · Periodontology 2000 · doi:10.1111/prd.12365 · Cited by 205 · see citing works
He, C., Keren, R., Whittaker, M., Farag, I., Doudna, J. A., Cate, J. H. D., & Banfield, J. F. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00840-5 · Cited by 221 · see citing works
Self-citationSequence-based classification and identification of Fungi
Hibbett, D., Abarenkov, K., Kõljalg, U., Öpik, M., Chai, B., Cole, J., Wang, Q., Crous, P., Robert, V., Helgason, T., et al. (2016) · Mycologia · doi:10.3852/16-130 · Cited by 203 · see citing works
“Given the restrictions on naming uncultured species, microbiologists have made wide use of informal names for new species, as well as phyla and divisions (Brown et al. 2015, Spang et al. 2015).”
BackgroundSaccharibacteria (TM7) in the Human Oral Microbiome
Bor, B., Bedree, J. K., Shi, W., McLean, J. S., & He, X. (2019) · Journal of Dental Research · doi:10.1177/0022034519831671 · Cited by 228 · see citing works
Probst, A., Castelle, C., Singh, A., Brown, C., Anantharaman, K., Sharon, I., Hug, L., Burstein, D., Emerson, J., Thomas, B., et al. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13362 · Cited by 200 · see citing works
“The phylogenetic analyses also identified a new highly divergent lineage that branches as a sibling lineage to the CPR in the concatenated ribosomal protein tree (Fig.”
BackgroundInfluentialSelf-citationA distinct abundant group of microbial rhodopsins discovered using functional metagenomics
Pushkarev, A., Inoue, K., Larom, S., Flores‐Uribe, J., Singh, M. P., Konno, M., Tomida, S., Ito, S., Nakamura, R., Tsunoda, S. P., et al. (2018) · Nature · doi:10.1038/s41586-018-0225-9 · Cited by 230 · see citing works
Self-citationKarst, S. M., Dueholm, M. S., McIlroy, S. J., Kirkegaard, R. H., Nielsen, P. H., & Albertsen, M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4045 · Cited by 218 · see citing works
Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Olm, M., Crits-Christoph, A., Diamond, S., Lavy, A., Carnevali, P. B. M., & Banfield, J. (2020) · mSystems · doi:10.1128/msystems.00731-19 · Cited by 195 · see citing works
“Absent dramatic improvements in sequencing technologies, complex communities can be more fully characterized through analysis of assembled and unbinned single-copy marker genes, for example, the 16S rRNA gene, ribosomal genes, or tRNA-ligase genes (27–30).”
Self-citationBeresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194 · see citing works
“For example, genomes of the large clade of uncultured bacteria, candidate phyla radiation (CPR), cannot be assigned a high-quality genome status using current single copy number gene methods (Brown et al., 2015).”
A decade of irrigation transforms the soil microbiome of a semi‐arid pine forest
Hartmann, M., Brunner, I., Hagedorn, F., Bardgett, R., Stierli, B., Herzog, C., Chen, X.-M., Zingg, A., Graf-Pannatier, E., Rigling, A., et al. (2017) · Molecular Ecology · doi:10.1111/mec.13995 · Cited by 194 · see citing works
“Members of these uncultured groups of bacteria have only recently been 337 characterized in more detail and feature small streamlined genomes with limited metabolic capabilities 338 and potentially symbiotic lifestyles (Brown et al. 2015; Youssef et al. 2015).”
BackgroundA census-based estimate of Earth's bacterial and archaeal diversity
Louca, S., Mazel, F., Doebeli, M., & Parfrey, L. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000106 · Cited by 193 · see citing works
Megaphages infect Prevotella and variants are widespread in gut microbiomes
Devoto, A. E., Santini, J. M., Olm, M. R., Anantharaman, K., Munk, P., Tung, J., Archie, E. A., Turnbaugh, P. J., Seed, K. D., Blekhman, R., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0338-9 · Cited by 210 · see citing works
Self-citationThe last universal common ancestor between ancient Earth chemistry and the onset of genetics
Weiss, M. C., Preiner, M., Xavier, J. C., Zimorski, V., & Martin, W. F. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007518 · Cited by 186 · see citing works
“New insights about microbial phylogeny are emerging from concatenated alignments [24,29,30,42,48,68].”
BackgroundStepanauskas, R., Fergusson, E. A., Brown, J., Poulton, N. J., Tupper, B., Labonté, J., Becraft, E. D., Brown, J. M., Pachiadaki, M., Povilaitis, T., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00128-z · Cited by 196 · see citing works
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples
Lear, G., Dickie, I. A., Banks, J. C., Boyer, S., Buckley, H. L., Buckley, T. R., Cruickshank, R., Dopheide, A., Handley, K. M., Hermans, S. M., et al. (2018) · New Zealand Journal of Ecology · doi:10.20417/nzjecol.42.9 · Cited by 181 · see citing works
“Results can also generate clues about the lifestyle of candidate phyla that elude cultivation efforts (Wrighton et al. 2012; Kantor et al. 2013; Brown et al. 2015).”
BackgroundHug, L., Thomas, B., Sharon, I., Brown, C., Sharma, R., Hettich, R., Wilkins, M., Williams, K., Singh, A., & Banfield, J. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.12930 · Cited by 185 · see citing works
Self-citation
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
