The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
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.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
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?
In the citing paper
“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
Citations
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
Self-citation
Flagged first, then by citations
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
Cited by
Sorted by citations
Items 801–900 of 1,000
Vannier, P., Farrant, G. K., Klonowski, A., Gaidos, E., Thorsteinsson, T., & Marteinsson, V. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1122184 · Cited by 4
“Saccharibacteria sp. rDNA contigs show 94% identity (16S and 23S) with the genome of Candidatus Saccharibacteria bacterium GW2011_GWC2_44_17 (Brown et al., 2015), which belongs to the recently described phylum Saccharibacteria (Ferrari et al., 2014).”
BackgroundCulture-based approaches to studying “microbial dark matter”
He, X. (2023) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2219691120 · Cited by 4
Valentin-Alvarado, L., Fakra, S., Probst, A., Giska, J. R., Jaffe, A. L., Oltrogge, L., West-Roberts, J., Rowland, J., Manga, M., Savage, D., et al. (2022) · bioRxiv · doi:10.1101/2022.11.17.516901 · Cited by 4
Self-citationThe evolution of bacterial genome assemblies - where do we need to go next?
Altermann, E., Tegetmeyer, H. E., & Chanyi, R. (2022) · Microbiome Research Reports · doi:10.20517/mrr.2022.02 · Cited by 4
The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects
Takamiya, H., Kouduka, M., & Suzuki, Y. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.785743 · Cited by 5
Tamarit, D., Teakel, S. L., Marama, M., Aragão, D., Gerdes, S., Forwood, J. K., Ettema, T. J. G., & Cahill, M. A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.17.468889 · Cited by 6
“The newly identified class of MAPR-like cytb5MY proteins are unique to CPR bacteria, which typically have small genomes characteristic of symbionts (Brown et al., 2015; Castelle and Banfield, 2018; Castelle et al., 2018).”
BackgroundPreviously uncharacterized rectangular bacterial structures in the dolphin mouth
Dudek, N. K., Galaz-Montoya, J. G., Shi, H., Mayer, M. L., Danita, C., Celis, A. I., Viehboeck, T., Wu, G., Behr, B. R., Bulgheresi, S., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37638-y · Cited by 7
“Sequencing the genomes of newly discovered organisms has led to the discovery of new functional systems, types of protein variants, and lifestyles 11,14 – 17 , illustrating the correlation between phylogenetic diversity and functional potential 18 .”
Bacterial glycyl tRNA synthetase offers glimpses of ancestral protein topologiesPreprint
Dimas-Torres, J.-U., Rodríguez-Hernández, A., Valencia-Sánchez, M., Campos-Chávez, E., Godínez-López, V., Rodríguez-Chamorro, D. E., Grøtli, M., Fleming, C. L., Hernández-González, A., Arciniega, M., et al. (2021) · bioRxiv · doi:10.1101/2021.08.20.456953 · Cited by 4
“Table S3) are the class I anticodon binding-domain (ACBD or DALR domain, in particular with ArgRS and CysRS, Figure S8), phosphohydrolases possessing the HD domain (Figure S9) and the body-tail domains of archaeal tRNA CCA adding enzymes-eukaryotic rRNA processing enzymes (Figure 2A, PDB codes 1R89, 1SZ1 (10) (11) and…”
BackgroundRadványi, Á., & Kun, Á. (2021) · Scientific Reports · doi:10.1038/s41598-021-90440-y · Cited by 8
A human respiratory tract-associated bacterium with an extremely small genome
Fukuda, K., Yamasaki, K., Ogura, Y., Kawanami, T., Ikegami, H., Noguchi, S., Akata, K., Katsura, K., Yatera, K., Mukae, H., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02162-6 · Cited by 5
Colombet, J., Fuster, M., Billard, H., & Sime‐Ngando, T. (2020) · Viruses · doi:10.3390/v12080881 · Cited by 9
Poghosyan, L., Koch, H., Frank, J., van Kessel, M., Cremers, G., van Alen, T. V., Jetten, M., den Camp, H. O., & Lücker, S. (2020) · bioRxiv · doi:10.1101/2020.05.19.103440 · Cited by 4
Nema, P., Paul, D., Karmalkar, N. R., & Shouche, Y. S. (2019) · Geomicrobiology Journal · doi:10.1080/01490451.2019.1654041 · Cited by 5
“A number of uncultured species were detected in the samples including several members of recently described Candidate Phyla Radiation (Brown et al. 2015).”
BackgroundTowards a systematic understanding of differences between archaeal and bacterial diversity
Spang, A., & Offre, P. (2018) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12701 · Cited by 4
“We expect continuing discoveries of novel archaeal and bacterial taxa but also wonder whether broader taxonomic groups such as the CPR (Brown et al., 2015), DPANN (Rinke et al., 2013; Castelle et al., 2015) and Asgard archaea (Spang et al., 2015; Zaremba-Niedzwiedzka et al., 2017) still await discovery.”
BackgroundForensic microbiology in built environments
Lax, S. M., & Gilbert, J. A. (2017) · Wiley eBooks · doi:10.1002/9781119062585.ch13 · Cited by 4
Proposal of a new genome-based taxonomy for CyanobacteriaPreprint
Walter, J. M., Coutinho, F., Dutilh, B., Thompson, F., & Thompson, C. (2017) · doi:10.7287/peerj.preprints.2676v1 · Cited by 4
In Situ Replication Rates for Uncultivated Bacteria in Microbial Communities
Brown, C., Olm, M., Thomas, B., & Banfield, J. (2016) · bioRxiv · doi:10.1101/057992 · Cited by 4
“Reads from the GWC2 sample from Brown et al.12 were used to conduct the analysis (Fig.”
MethodInfluentialSelf-citationDickinson, I., Walker, G., & Pearce, D. A. (2016) · Advances in environmental microbiology · doi:10.1007/978-3-319-28071-4_9 · Cited by 5
A Practical Guide to Studying the Microbiology of Karst Aquifers
Hershey, O., Kallmeyer, J., & Barton, H. (2019) · The handbook of environmental chemistry · doi:10.1007/978-3-319-77368-1_7 · Cited by 4
Metagenomics a modern approach to reveal the secrets of unculturable microbes
Shamim, K., Mujawar, S. Y., & Mutnale, M. C. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-817497-5.00012-4 · Cited by 7
Hug, L. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8728-3_14 · Cited by 4
Self-citationBacteria in Indoor and Occupational Settings
Barnes, M. A. (2017) · Springer eBooks · doi:10.1007/978-3-319-61688-9_2 · Cited by 4
The horse gut microbiota genome represents a vast novel reservoir of CAZymes.
He, H., Han, L., Ni, W., Yu, J., Liu, K., Li, W., Li, C., Hu, S.-W., Li, C.-Y., & Li, X.-Y. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.150042 · Cited by 3
Wang, C., Narayanasamy, S., Shaabad, M., Dallol, A., Hala, S., & Hong, P. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.5c11553 · Cited by 4
Complex effects of a prescribed burn on a prairie soil bacterial community
Uppal, S., Woolet, J., Venkateshwaran, M., Baxer, C., Johnson, Y., Tung, A., Yu, C. S., Whitman, T., & Kwan, J. C. (2025) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2025.110047 · Cited by 3
Ferreira, C. M., de Affonseca, D. B., Barbosa, F. A. S., Campos, A. B., Menezes, R., Brait, L. A. S., Viana, P. A. B., Silva, A. E. T., Loiola, M., de Azevedo, A. R., et al. (2025) · Microbial Ecology · doi:10.1007/s00248-025-02595-0 · Cited by 3
“(3 ) By connecting Similarity Percent-age (SIMPER) analysis of dissimilarity contributions [22] to CPR and DPANN genomic traits [23, 24], we explored if their streamlined metabolisms drive ecosystem differentiation more than abundant taxa.”
Huang, W.-C., Dombrowski, N., Mahendrarajah, T., Wahl, N. A., Stamatakis, A., Szöllősi, G. J., Williams, T. A., & Spang, A. (2026) · Nature Communications · doi:10.1038/s41467-026-76386-7 · Cited by 7
“To estimate the ancestral optimal growth temperature of LACA, we reconstructedancestralsequencesbasedonthesupermatrixusingthe LG+G4+COaLA[2] model (best-fi tting model from LG+G4+COaLA[1-3] 107 based on BIC; [x] refers to the number of independent axis…”
InfluentialMartinez-Mercado, M. A., Latisnere-Barragán, H., Ramírez-Arenas, P. J., Vázquez-Juárez, R., García-Maldonado, J. Q., & López-Cortés, A. (2025) · Environmental Microbiology · doi:10.1111/1462-2920.70199 · Cited by 3
Liu, Y., Wu, X.-J., Wegner, C., Ma, K., Xu, G., Cui, Z.-L., Zhang, F.-S., Liesack, W., & Peng, J.-J. (2025) · Molecular Ecology · doi:10.1111/mec.70156 · Cited by 3
Wang, R., Pu, P., Huang, D., Du, X., Xiang, R., Li, G., & Jiaka, L.-T. (2025) · Polish Journal of Microbiology · doi:10.33073/pjm-2025-030 · Cited by 3
“Bioinformatics tools, including USEARCH (Edgar 2010) and QIIME (Caporaso et al. 2010) were employed for data processing, while R, Python, and Java used for statistical analysis and visualization (Brown et al. 2015).”
A practical guide on environmental genomics for prokaryotic systematics
Ernster, N. M., & Rodriguez‐R, L. M. (2025) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2025.126643 · Cited by 4
Microbial dark matter spearheading the biogeochemical cycle in the Solar Lake of Taba, Egypt
Abdallah, R., Elbehery, A., Ouf, A. A., & Siam, R. (2025) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2025.100433 · Cited by 3
“They are thought to play essential roles in carbon and hydrogen cycling (Brown et al., 2015; Castelle et al., 2018).”
Peng, S.-X., Gao, S.-M., Lin, Z.-L., Luo, Z.-H., Zhang, S.-Y., Shu, W.-S., Meng, F.-G., & Huang, L.-N. (2025) · mBio · doi:10.1128/mbio.00705-25 · Cited by 3
“in a wide variety of habitats including extreme environments (e.g., acid mine drainage [AMD] [5, 6], terrestrial geothermal springs [7], hypersaline habitats [8, 9], subsurface [2, 3, 10, 11], and deep sea [12, 13]).”
Rodríguez-Gijón, A., Pacheco-Valenciana, A., Milke, F., Dharamshi, J. E., Hampel, J. J., Damashek, J., Wienhausen, G., Rodriguez-R., L., & Garcia, S. (2025) · bioRxiv · doi:10.1101/2025.03.24.644981 · Cited by 3
“Custom marker gene sets for both phyla were provided by CheckM [74,81].”
Host habitat shapes the gut microbiomes of insular reptilian hosts in the Philippines
Smith, S. N., Fernandez, J. B., & Siler, C. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf141 · Cited by 3
“…microbiome, but no other studies to date have reported Patescibacteria within reptilian gut microbiome samples, but members of this large microbial radiation are found in various aquatic environments such as groundwater [4] and seawater [5], and activated sludge collected from wastewater tanks [6].”
Thoron, radon and microbial community as supportive indicators of seismic activity in groundwater
Kim, J., Kim, H., Kaown, D., & Lee, K.-K. (2024) · Scientific Reports · doi:10.1038/s41598-024-77011-7 · Cited by 3
Watanabe, K., Yamada, A., Masuda, H., Kashiwazaki, E., Nakayama, S., Kadokura, T., Sakai, K., & Tashiro, Y. (2024) · Scientific Reports · doi:10.1038/s41598-024-72936-5 · Cited by 3
“…set for the V4 region of the bacterial 16S rRNA gene and tailed sequences for MiSeq sequencing were used (1-515F, 5 ʹ - TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG GTG CCA GCM GCC GCG GTA A-3 ʹ and 1-806R, 5 ʹ -GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGG ACT ACH VGG GTW TCT AAT-3 ʹ ) 51 .”
MethodSussfeld, D., Lannes, R., Corel, E., Bernard, G., Martin, P., Bapteste, E., Pelletier, E., & Lopez, P. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00697-3 · Cited by 3
“…of microbial adaptations and interactions in numerous environments [9–12] to the characterisation of multiple novel major taxonomic groups [13–17] – most notably CPR bacteria [13, 18, 19], DPANN archaea [18, 20, 21] and Asgard archaea [22–24], profoundly reshaping the structure of the Tree of Life.”
Wu, L., Lin, H., Zhang, L., Kiet, T. Q., Liu, P., Song, J., Duan, Y., Hu, C., Yang, H., Duan, W., et al. (2024) · Scientific Data · doi:10.1038/s41597-024-03379-w · Cited by 3
The Structure of Evolutionary Model Space for Proteins across the Tree of Life
Scolaro, G. E., & Braun, E. L. (2023) · Biology · doi:10.3390/biology12020282 · Cited by 3
“indicates members of the candidate phyla radiation [35,53,54].”
BackgroundChen, 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) · bioRxiv · doi:10.1101/2022.04.20.488981 · Cited by 3
“Other studies have reported 241 success enriching ultra-small microbes this way (1, 26, 28).”
BackgroundMethodResultInfluentialSelf-citationCornish, K. A. S., Lange, J., Aevarsson, A., & Pohl, E. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101919 · Cited by 10
“As these sequences are the key for uncovering new species by PCR techniques, it is estimated that at least half of the organisms sampled from the CPR would remain undetected in typical PCR surveys (10).”
BackgroundFuster, M., Billard, H., Bronner, G., Sime-Ngando, T., & Colombet, J. (2022) · Microbial Ecology · doi:10.1007/s00248-022-01974-1 · Cited by 3
“Attempts to evaluate the quantitative and qualitative importance of CPR/DPANN [11, 12], BMOPs [13], and EVs [14] underscore this necessity.”
BackgroundRates of primary production in groundwater rival those in oligotrophic marine systems
Overholt, W., Trumbore, S., Xu, X.-M., Bornemann, T., Probst, A., Krüger, M., Herrmann, M., Thamdrup, B., Bristow, L., Taubert, M., et al. (2021) · bioRxiv · doi:10.1101/2021.10.13.464073 · Cited by 3
Whaley-Martin, K., Chen, L.-X., Nelson, T., Gordon, J., Kantor, R. S., Twible, L. E., Marshall, S., Rossi, L., Bessette, B., Baron, C., et al. (2021) · bioRxiv · doi:10.1101/2021.09.16.460096 · Cited by 3
Self-citationDelwiche, C. F. (2021) · Current Biology · doi:10.1016/j.cub.2021.05.059 · Cited by 2
Jaffe, A. L., He, C., Keren, R., Valentin-Alvarado, L., Munk, P., Bouma-Gregson, K., Farag, I. F., Amano, Y., Sachdeva, R., West, P., et al. (2021) · bioRxiv · doi:10.1101/2021.03.03.433784 · Cited by 3
Self-citationGhuneim, L.-A. J., Distaso, M. A., Chernikova, T. N., Bargiela, R., Lunev, E. A., Korzhenkov, A. A., Toshchakov, S. V., Rojo, D., Barbas, C., Ferrer, M., et al. (2020) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaa244 · Cited by 5
“For instance, a lack of biosynthetic pathways like for the synthesis of nucleic acids, vitamins and lipids, and mechanisms for DNA repair is commonplace for many symbiont species (Brown et al. 2015; Nelson and Stegen 2015).”
BackgroundLamont, E., Hendrickson, E., McLean, J., He, X., & Bor, B. (2020) · Microbiology Resource Announcements · doi:10.1128/mra.00810-20 · Cited by 3
“CPR organisms comprise 25% of all bacterial diversity and have an ultrasmall cell size and reduced genome (1, 3).”
BackgroundMeng, P., Lu, C., Lou, X., Zhang, Q., Jia, P., Yan, Z., Lin, J., & Chen, F. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/358812 · Cited by 8
Migrating SSU rRNA gene surveys to the metagenomics era.
Neufeld, J. (2017) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12493 · Cited by 3
Delmont, T., & Eren, A. M. (2016) · bioRxiv · doi:10.1101/058750 · Cited by 3
“To explore microbial systems using metagenomeassembled genomes (MAGs), researchers often rely on functional annotations, phylogenetically informative conserved gene families, or distribution patterns to identify metabolic potentials [8], evolutionary relatedness [9, 10], or co-occurrence of genomic collections [11].”
BackgroundThe status of the microbial census: an update
Schloss, P., Girard, R., Martin, T. M., Edwards, J., & Thrash, J. (2016) · bioRxiv · doi:10.1101/038646 · Cited by 3
“preclude detection with standard PCR-based approaches (37, 38).”
MethodBacterial evolution: An intriguing new bacterial phylum
Attar, N. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3534 · Cited by 3
Bioremediation and Biotechnology, Vol 4: Techniques for Noxious Substances Remediation
Bhat, R., & Hakeem, K. R. (2020) · doi:10.1007/978-3-030-48690-7 · Cited by 3
Extremophile Microorganisms and Their Industrial Applications
Malik, K., Kumari, N., Ahlawat, S., Kumar, U., & Sindhu, M. (2020) · Springer eBooks · doi:10.1007/978-981-15-4099-8_10 · Cited by 3
Wang, E. T., & Young, J. P. W. (2019) · Springer eBooks · doi:10.1007/978-981-32-9555-1_2 · Cited by 5
Diversity, biogeography and assembly mechanisms of groundwater microbiomes
Wu, Z., Ning, D., Fields, M. W., Hazen, T. C., Adams, P. D., Arkin, A. P., & Zhou, J. Z. (2026) · Nature Reviews Earth & Environment · doi:10.1038/s43017-026-00813-y · Cited by 2
“It provides comprehensive genetic information of almost all microorganisms, thereby revealing functional potentials and phylogenetic taxonomy of bacteria, archaea and viruses in groundwater 9,10,22,126 .”
InfluentialRethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?
Pellegrinetti, T., Molligan, J., Mendes, L. W., Pedrinho, A., & Pérez-López, E. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1884628 · Cited by 2
Hendrickson, E., Bor, B., He, X.-S., & McLean, J. S. (2026) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.007162 · Cited by 2
Parks, D., Chaumeil, P., Chuvochina, M., & Hugenholtz, P. (2026) · bioRxiv · doi:10.64898/2025.12.01.691617 · Cited by 2
“These 35 MAGs came from 27 SRA runs which have a minimum estimated CAVGFB01 or JAUNQF01 coverage of 6.8x and abundance of 0.17%.”
InfluentialMalina, N., Tollerson, R., Monami, S. J., Rivera, E., Lee, M.-K., Bilenker, L., & Ojeda, A. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.00988-25 · Cited by 2
Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type
Lane, K. R., Jones, S. E., Osborne, T. H., Geller‐McGrath, D., Nwaobi, B. C., Chen, L.-X., Thomas, B. C., Hudson-Edwards, K. A., Banfield, J. F., & Santini, J. M. (2025) · Environmental Microbiology Reports · doi:10.1111/1758-2229.70261 · Cited by 3
“Organisms were also binned automatically with ABAWACA (Brown et al. 2015) and metaBAT2 v2.”
Self-citationLv, Y.-X., Zhang, L.-Z., & Zhang, Y. (2025) · Microbiome · doi:10.1186/s40168-025-02192-w · Cited by 2
“Specifically, the quality of MAGs classified as Patescibacteria was based on the marker gene set [44].”
Viral ecogenomics across oxic and anoxic zones of the Yongle Blue Hole
Yang, M., Zhang, H., Zhou, Y.-L., Selvarajan, R., Xu, P., Gao, Z.-M., & Wang, Y. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00778-3 · Cited by 2
“Nota-bly, due to the simplified genomes of several prokaryotic hosts detected in YBH, such as Patescibacteria , Nanoar-chaeota , Aenigmatarchaeota and Altarchaeota [84, 86], viral infections may provide crucial AMGs that enhance its survival and adaptability in the relatively extreme environment.”
Yagi, S., Fukui, H., Shiraishi, T., Kaku, K., Wakita, M., Takagi, Y., Ikenouchi, M., Sato, T., Kawai, M., Yokoyama, Y., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26199359 · Cited by 2
“…of Patescibacteria in human diseases is not fully understood, it represents a diverse group of bacteria accounting for a significant proportion of microbial dark matter [37] and is frequently detected in various environments, including groundwater, freshwater, and the human oral cavity [38–40].”
Gios, E., Mosley, O. E., Takeuchi, N., & Handley, K. M. (2025) · mSystems · doi:10.1128/msystems.00046-25 · Cited by 8
“…prokaryotes, genome completeness and contamination were assessed based on the presence of the following SCG sets: 43 SCGs for Patescibacteria (5), 51 bacterial single-copy genes (SCGs) for Dependentiae (89), and 38 archaeal SCGs for DPANN (89), using the method described by Brown et al. (5).”
Alibrandi, A., Plewka, J., Primio, R. D., Bartholomäus, A., Vuillemin, A., Probst, A. J., & Kallmeyer, J. (2025) · bioRxiv · doi:10.3389/fmicb.2026.1741638 · Cited by 2
“Scaolds with a minimum length of 1,000 bp were binned into MAGs using ABAWACA (v. 1.0.0) (Brown et al., 2015) and MaxBin2 (v. 2.2.7) (Wu et al., 2016) with default parameters.”
InfluentialYe, P.-Z., Yang, Q., Zhang, C.-Y., Yang, T.-T., Jiang, S.-F., Lan, R., Gao, S.-M., & Huang, L.-N. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.138862 · Cited by 2
Environmental diversity of Candidatus Babelota and their relationships with protists
Weisse, L., Martin, L., Moumen, B., Héchard, Y., & Delafont, V. (2025) · mSystems · doi:10.1128/msystems.00261-25 · Cited by 2
“matter (MDM) (5).”
Vigneron, A., Cloarec, L., Brochier-Armanet, C., Flandrois, J., Troussellier, M., Bernard, C., Agogué, H., Oger, P. M., & Hugoni, M. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00699-1 · Cited by 2
“…genomic, and functional diversities of the enigmatic Patescibacteria (bacterial Candidate Phyla Radiation) or DPANN archaea, has been significantly expanded by genome-centric metagenomics, revealing their ubiq-uity, abundance and complex entanglement with other microbial lineages [11, 12].”
Gunawardana, E. G., Sotelo, T. J., Oshima, K., Hattori, M., Mino, T., & Satoh, H. (2025) · Microbes and Environments · doi:10.1264/jsme2.me24082 · Cited by 2
“Bacteria in this group have been reported in ground‐ water filtrates (Nelson and Stegen, 2015; Brown et al. , 2015).”
InfluentialSchechter, M. S., Trigodet, F., Veseli, I., Miller, S. E., Klein, M. L., Sever, M., Maignien, L., Delmont, T. O., Light, S. H., & Eren, A. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.15.633187 · Cited by 4
“Indeed, the rapidly increasing number of microbial genomes (1) provides an evolutionary framework to resolve the branches of the Tree of Life (Brown et al. 2015; Spang et al. 2015), (2) enables hypothesis generation and testing through comparative genomics (Paoli et al. 2022; Al-Shayeb et al. 2022;…”
The right tool for the job: Chemical biology and microbiome science
Whidbey, C. (2025) · Cell chemical biology · doi:10.1016/j.chembiol.2024.12.004 · Cited by 2
Papaleo, S., Nodari, R., Sterzi, L., D'Auria, E., Cattaneo, C., Bettoni, G., Bonaiti, C., Pagliarini, E., Zuccotti, G., Panelli, S., et al. (2024) · PLoS ONE · doi:10.1371/journal.pone.0310675 · Cited by 2
Herbold, C. W., Noell, S. E., Lee, C. K., Vickers, C. J., Stott, M., Eisen, J., McDonald, I. R., & Cary, S. (2024) · Environmental Microbiome · doi:10.1186/s40793-024-00655-5 · Cited by 2
“Due to this distribution pattern and the fact that an accelerated evolutionary process is a hallmark feature of members of this lineage [31, 61, 62], we did not pursue further analysis of this genome, which would be best accomplished in a comprehensive comparison with other Ca. Patescibacteria.”
Evolutionary Flexibility of Ribosome Biogenesis in Bacteria
Amikura, K., Ishii, S., Shimizu, Y., & Suzuki, S. (2024) · bioRxiv · doi:10.1093/molbev/msaf288 · Cited by 2
Unique Features of Extremely Halophilic Microbiota Inhabiting Solar Saltworks Fields of Vietnam
Cono, V. L., Spada, G. L., Smedile, F., Crisafi, F., Marturano, L., Modica, A., Huynh, K. H. N., Pham, T. D., Hang, C. T. T., Selivanova, E. A., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12101975 · Cited by 2
“Members of these newly discovered taxa are typically ultra-small in size, with an average cell diameter of 200–450 nm, and possess highly reduced genomes (average size 1 Mbp) and minimal cellular activities, including limited metabolic potential [31–33].”
BackgroundTrubl, G., Leleiwi, I., Campbell, A., Kimbrel, J. A., Bhattacharyya, A., Riley, R., Malmstrom, R., Blazewicz, S., & Pett-Ridge, J. (2024) · bioRxiv · doi:10.1101/2024.09.13.612973 · Cited by 2
Wong, M. L., Duckett, M., Hernandez, E. S., Rajaei, V., & Smith, K. J. (2024) · Perspectives of Earth and Space Scientists · doi:10.1029/2023cn000223 · Cited by 10
“The development of metagenomics and deep sequencing methods has revealed a more complete picture of the tree of life, unconstrained by culture methods previously predominant in microbiology (Al‐Shayeb et al., 2022; Brown et al., 2015; Hug et al., 2016; Shu & Huang, 2022).”
Analyzing microbial evolution through gene and genome phylogenies
Teichman, S., Lee, M. D., & Willis, A. (2023) · bioRxiv · doi:10.1101/2023.08.15.553440 · Cited by 2
“When pursuing phylogenomics, most microbial investigations estimate a single phylogeny that summarizes the evolution of a set of organisms (see, e.g., Brown et al. (2015); Parks et al. (2018); Imachi et al. (2020)).”
COBRA improves the quality of viral genomes assembled from metagenomesPreprint
Chen, L.-X., & Banfield, J. (2023) · bioRxiv · doi:10.1101/2023.05.30.542503 · Cited by 2
“To evaluate the performance of COBRA on non-viral genomes, we applied it to three published groundwater metagenomes, each containing hundreds of MAGs from Candidate Phyla Radiation (CPR) bacteria that typically have small genomes (~1 Mbp) 37 , as well as from other bacteria and archaea 38,39 .”
MethodSelf-citationAnaerobic Thermodesulfovibrio and Aerobic Meiothermus Coexist in Deep Thermal Water
Lukina, A., Kadnikov, V., Rusanov, I., Avakyan, M. R., Beletsky, A., Mardanov, A., Pimenov, N., Ravin, N., & Karnachuk, O. (2023) · Microbiology · doi:10.1134/s0026261723600234 · Cited by 2
“Patescibacteria possess small genomes (typically less than ~1 million nucleotides) and lack many essential biosynthetic pathways (Brown et al., 2015).”
BackgroundStructure and Seasonal Variability of Microbial Communities of Groundwater in the City of Moscow
Gruzdev, E. V., Begmatov, S., Beletsky, A., Mardanov, A. V., Ravin, N., & Kadnikov, V. (2023) · Microbiology · doi:10.1134/s0026261722603293 · Cited by 2
“Like Nanoarchaeota, Patescibacteria have small genomes (usually less than ~1 Mb) and lack many key biosynthetic pathways (Brown et al., 2015).”
BackgroundExpanded diversity of tfdA harboring bacteria across the natural and built environment
White, A., Vázquez, A. G. G., McDaniel, E., Peterson, B. D., Koch, P., Remucal, C., & McMahon, K. (2022) · bioRxiv · doi:10.1101/2022.09.28.509959 · Cited by 2
“Previous 204 work demonstrating uncultured microbes like Rokubacteria may use alternative metabolic 205 pathways that prevent their culturing under typical conditions (46, 51, 52) highlights the power of 206”
BackgroundHilts, A., Hunjan, M., & Hug, L. (2021) · bioRxiv · doi:10.1128/msystems.00790-21 · Cited by 2
Self-citationBaker, J. (2021) · Microbiology Resource Announcements · doi:10.1128/mra.00517-21 · Cited by 2
Reconstruction of Metagenome-Assembled Genomes from Aquaria
Ettinger, C., Bryan, J., Tokajian, S., Jospin, G., Coil, D., & Eisen, J. (2021) · bioRxiv · doi:10.1128/mra.00557-21 · Cited by 2
“CPR genome completion was then re-estimated using 43 single-copy marker genes, as CPR members are known to have missing single-copy genes (14).”
MethodDistinct hydrogenotrophic bacteria are stimulated by elevated H2 levels in upland and wetland soilsPreprint
Xu, Y.-F., Teng, Y., Dong, X.-Y., Wang, X.-M., Zhang, C., Ren, W.-J., Zhao, L., Luo, Y.-M., & Greening, C. (2020) · bioRxiv · doi:10.1101/2020.11.15.383943 · Cited by 2
“We also retrieved a surprising number of 180 Patescibacteria MAGs (17), supporting recent reports that these symbionts can be 181 abundant in oxygenated soils [78, 79].”
Moreira, D., Zivanovic, Y., López-Archilla, A., Iniesto, M., & López-García, P. (2020) · bioRxiv · doi:10.1101/2020.11.10.374967 · Cited by 2
Hwang, Y., Schulze-Makuch, D., Arens, F., Sáenz, J., Adam, P., Bornemann, T., Airo, A., Schloter, M., & Probst, A. (2020) · bioRxiv · doi:10.1101/2020.07.17.208546 · Cited by 2
Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution
Naumoff, D. G., & Dedysh, S. (2020) · Microbiology · doi:10.1134/s0026261720040098 · Cited by 2
Sieber, C., Paul, B., Castelle, C., Hu, P., Tringe, S., Valentine, D. L., Andersen, G., & Banfield, J. (2019) · bioRxiv · doi:10.1101/595074 · Cited by 2
“The absence of these pathways raises two questions (1) the nature of central carbon metabolism in these organisms, and (2) how ATP, NADH, NADPH and ferredoxin are reduced and recycled.”
BackgroundSelf-citationCell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human PrimatesPreprint
Kowarsky, M., Vlaminck, I. D., Okamoto, J., Neff, N., Lebreton, M., Nwobegabay, J., Tamoufe, U., LeDoux, J. E., Tafon, B., Kiyang, J. A., et al. (2018) · bioRxiv · doi:10.1101/481093 · Cited by 2
Chen, L.-X., Al-Shayeb, B., Méheust, R., Li, W.-J., Doudna, J., & Banfield, J. (2018) · doi:10.1101/448639 · Cited by 2
Self-citationQuantifying biosynthetic network robustness across the human oral microbiome
Bernstein, D. B., Dewhirst, F., & Segrè, D. (2018) · bioRxiv · doi:10.1101/392621 · Cited by 2
The Impact of Agriculture on Soil Microbial Community Composition and Diversity in Southeast Asia
Tripathi, B., Moroenyane, I., & Adams, J. (2017) · doi:10.1002/9781119276050.ch2 · Cited by 2
Archaea as components of forest microbiome
Yrjälä, K., & Lopez‐Echartea, E. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822542-4.00014-0
Virus Discovery by Metagenomics: The (Im)possibilities
Dutilh, B., Reyes, A., Hall, R. J., & Whiteson, K. (n.d.) · doi:10.3389/978-2-88945-308-5 · Cited by 2
“Second, this reflects the diversity in the microbial world itself that includes giant viruses (Halary et al., 2016), tiny bacteria (Brown et al., 2015), and everything in between.”
Long, Y., Sun, L., Han, Y., Paengkoum, P., Paengkoum, S., Taethaisong, N., Meethip, W., Sanlakhon, A., Konkrathok, S., Kotsanthia, S., et al. (2026) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2026.117068 · Cited by 1
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
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
