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 101–200 of 1,000
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
Roux, S., Solonenko, N., Dang, V. T., Poulos, B. T., Schwenck, S. M., Goldsmith, D. B., Coleman, M. L., Breitbart, M., & Sullivan, M. B. (2016) · PeerJ · doi:10.7717/peerj.2777 · Cited by 220
“, 2016), as well as elucidate the ecological and evolutionary roles of lesser-studied microbial lineages (Wrighton et al., 2012; Castelle et al., 2013; Brown et al., 2015).”
BackgroundOlm, M. R., Bhattacharya, N., Crits‐Christoph, A., Firek, B., Baker, R. W., Song, Y. S., Morowitz, M. J., & Banfield, J. F. (2019) · Science Advances · doi:10.1126/sciadv.aax5727 · Cited by 195
Self-citationMultiple levels of the unknown in microbiome research
Thomas, A. M., & Segata, N. (2019) · BMC Biology · doi:10.1186/s12915-019-0667-z · Cited by 176
DESMAN: a new tool for de novo extraction of strains from metagenomes
Quince, C., Connelly, S., Raguideau, S., Alneberg, J., Shin, S. G., Collins, G., & Eren, A. M. (2017) · Genome biology · doi:10.1186/s13059-017-1309-9 · Cited by 191
“This situation is unlikely to change, particularly given the great diversity of microbes that are elusive to standard culti-vation techniques [3].”
BackgroundThe multi-omics promise in context: from sequence to microbial isolate
Gutleben, J., Mares, M. C. D., van Elsas, J. D., Smidt, H., Overmann, J., & Sipkema, D. (2017) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2017.1332003 · Cited by 227
“…microorganisms in natural or man-made ecosystems (Tyson et al. 2004; Siegl et al. 2011; Hug et al. 2012; Albertsen et al. 2013; Wilson & Piel 2013; McLean et al. 2013; Narihiro et al. 2014; Nielsen et al. 2014; Urich et al. 2014; Walker et al. 2014; Afshinnekoo et al. 2015; Brown et al. 2015).”
BackgroundWurch, L. L., Giannone, R., Belisle, B. S., Swift, C., Utturkar, S., Hettich, R., Reysenbach, A., & Podar, M. (2016) · Nature Communications · doi:10.1038/ncomms12115 · Cited by 174
“7 and Supplementary Data 1).”
InfluentialBacterial RNA Biology on a Genome Scale
Hör, J., Gorski, S. A., & Vogel, J. (2018) · Molecular Cell · doi:10.1016/j.molcel.2017.12.023 · Cited by 191
Microbial decomposition of biodegradable plastics on the deep-sea floor
Omura, T., Isobe, N., Miura, T., Ishii, S., Mori, M., Ishitani, Y., Kimura, S., Hidaka, K., Komiyama, K., Suzuki, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-023-44368-8 · Cited by 202
“The gene encoding ribosomal protein S3 ( rpsC , K02981), a key marker single-copy housekeeping gene for the phylogeny of microorganisms 55 , was used for the metagenome-based population analysis 56 .”
Nanopore sequencing and its application to the study of microbial communities
Ciuffreda, L., Rodríguez‐Pérez, H., & Flores, C. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.02.020 · Cited by 209
“…advent of next-generation sequencing (NGS) technologies has unquestionably led to a real revolution in the area of microbiology, with major break-throughs the complete characterization of the human gut micro-biome [3] or the identification of novel phyla with undiscovered biology [4], to name a few.”
BackgroundMetagenomic tools in microbial ecology research
Taş, N., de Jong, A. E. E., Li, Y., Trubl, G., Xue, Y., & Dove, N. C. (2021) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2021.01.019 · Cited by 206
Liu, J., Meng, Z., Liu, X., & Zhang, X. (2019) · Marine Life Science & Technology · doi:10.1007/s42995-019-00004-3 · Cited by 203
Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges
Blaser, M. J., Cardon, Z. G., Cho, M. K., Dangl, J. L., Donohue, T. J., Green, J. L., Knight, R. D., Maxon, M. E., Northen, T. R., Pollard, K. S., et al. (2016) · mBio · doi:10.1128/mbio.00714-16 · Cited by 181
Hubbard, S. S., Williams, K. H., Agarwal, D., Banfield, J. F., Beller, H. R., Bouskill, N., Brodie, E., Carroll, R., Dafflon, B., Dwivedi, D., et al. (2018) · Vadose Zone Journal · doi:10.2136/vzj2018.03.0061 · Cited by 232
“Research included consideration of the floodplain microbial community diversity (Castelle et al., 2015; Brown et al., 2015; Hug et al., 2016a, 2016b; Long et al., 2016; Anantharaman et al., 2016) and metabolic potential (Jewell et al., 2016); the contribution of vadose zone microbial respiration to…”
BackgroundSelf-citationFrom cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems
Garza, D. R., & Dutilh, B. E. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-2004-1 · Cited by 190
“It was suggested that the commonly used primers for 16S amplicon sequencing would miss a large fraction of these bacteria due to primer mismatching and the presence of these introns [34].”
InfluentialAedes spp. and Their Microbiota: A Review
Scolari, F., Casiraghi, M., & Bonizzoni, M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02036 · Cited by 163
“, 2017) and with the ultrasmall cell size of some aquatic bacteria (Brown et al., 2015; Luef et al., 2015).”
BackgroundA metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments
Vavourakis, C. D., Andrei, A., Mehrshad, M., Ghai, R., Sorokin, D. Y., & Muyzer, G. (2018) · Microbiome · doi:10.1186/s40168-018-0548-7 · Cited by 185
Song, W.-Z., Wemheuer, B., Zhang, S., Steensen, K., & Thomas, T. (2019) · Microbiome · doi:10.1186/s40168-019-0649-y · Cited by 160
“…rRNA gene, which is the most commonly used phylogenetic and taxonomic marker of bacterial and archaeal organisms, is often missing in genome bins [29 – 31], we build a phylogenetic tree for all input genomes using the protein sequences of 43 universal single-copy genes (SCGs) used by CheckM [32].”
MethodGraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Boyd, J. A., Woodcroft, B. J., & Tyson, G. W. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky174 · Cited by 162
“In recent years, improvements in sequencing technology and bioinformatic tools for handling metagenomic data, including novel genome binning approaches (2–4), have enabled the recovery of population genomes from a wide range of environments (5,6).”
BackgroundPeabody, M. A., Rossum, T. V., Lo, R., & Brinkman, F. S. L. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0788-5 · Cited by 166
“Furthermore, a notable subset of taxa cannot be captured by traditional 16S sequencing owing to divergent 16S rRNA gene sequences [4].”
BackgroundFrom Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
Weimann, A., Mooren, K., Frank, J. A., Pope, P. B., Bremges, A., & McHardy, A. C. (2016) · mSystems · doi:10.1128/msystems.00101-16 · Cited by 179
Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152
Ortiz, M., Leung, P. M., Shelley, G., Jirapanjawat, T., Nauer, P. A., Goethem, M. W. V., Bay, S. K., Islam, Z. F., Jordaan, K., Vikram, S., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2025322118 · Cited by 160
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles
Grossart, H., Massana, R., McMahon, K. D., & Walsh, D. A. (2019) · Limnology and Oceanography · doi:10.1002/lno.11382 · Cited by 189
“…bacterial MAG reconstructions from deep aquifers and other environments has dramatically increased known phylum level diversity by discovery of the Candidate Phylum Radiation within the bacterial domain (Brown et al. 2015; Hug et al. 2016), and a revised phylogeny of bacteria (Parks et al. 2018).”
BackgroundGlobal metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Eloe-Fadrosh, E., Páez-Espino, D., Jarett, J., Dunfield, P., Hedlund, B., Dekas, A., Grasby, S., Brady, A., Dong, H.-L., Briggs, B., et al. (2016) · Nature Communications · doi:10.1038/ncomms10476 · Cited by 151
Hernsdorf, A. W., Amano, Y., Miyakawa, K., Ise, K., Suzuki, Y., Anantharaman, K., Probst, A., Burstein, D., Thomas, B., & Banfield, J. (2017) · The ISME Journal · doi:10.1038/ismej.2017.39 · Cited by 150
“Interestingly, one complete (curated, closed) genome from a member of the recently described Candidate Phyla Radiation (Brown et al., 2015), HGW-Dojkabacteria-1 (the second complete genome of this phylum previously referred to as WS6; Wrighton et al., 2016), was found to harbor genes for both form…”
BackgroundMethodInfluentialSelf-citationGenome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Vanwonterghem, I., Jensen, P. D., Rabaey, K., & Tyson, G. W. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13382 · Cited by 157
“growing number of population genomes to be recovered from increasingly complex environments (Albertsen et al., 2013; Baker et al., 2015; Brown et al., 2015).”
BackgroundInfluentialStatus of the Archaeal and Bacterial Census: an Update
Schloss, P. D., Girard, R., Martin, T., Edwards, J., & Thrash, J. C. (2016) · mBio · doi:10.1128/mbio.00201-16 · Cited by 165
“) that would preclude detection with standard PCR-based approaches (37, 38).”
The distinction of CPR bacteria from other bacteria based on protein family content
Méheust, R., Burstein, D., Castelle, C. J., & Banfield, J. F. (2019) · Nature Communications · doi:10.1038/s41467-019-12171-z · Cited by 151
Self-citationThe trajectory of microbial single-cell sequencing
Woyke, T., Doud, D. F. R., & Schulz, F. (2017) · Nature Methods · doi:10.1038/nmeth.4469 · Cited by 176
Goltsman, D. S. A., Sun, C. L., Proctor, D. M., DiGiulio, D. B., Robaczewska, A., Thomas, B. C., Shaw, G. M., Stevenson, D. K., Holmes, S., Banfield, J. F., et al. (2018) · Genome Research · doi:10.1101/gr.236000.118 · Cited by 149
“0 (Gardner et al. 2015) was used to build phylogenetic trees from whole-genome SNP patterns in Lactobacillus iners, Lactobacillus crispatus, and Gardnerella vaginalis. iRep (with default parameters) was used to estimate the replication rate of genomes reconstructed from the vaginal metagenomic datasets as in Brown et…”
BackgroundMethodInfluentialSelf-citationDegrune, F., Theodorakopoulos, N., Colinet, G., Hiel, M.-P., Bodson, B., Taminiau, B., Daube, G., Vandenbol, M., & Hartmann, M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01127 · Cited by 166
“Several groups of the recently suggested candidate phyla radiation (CPR) (Brown et al., 2015) differed in abundance between the tillage regimes.”
BackgroundCultivation and genomics of the first freshwater SAR11 (LD12) isolate
Henson, M. W., Lanclos, V. C., Faircloth, B. C., & Thrash, J. C. (2018) · The ISME Journal · doi:10.1038/s41396-018-0092-2 · Cited by 163
Danczak, R., Johnston, M., Kenah, C., Slattery, M. T., Wrighton, K. C., & Wilkins, M. J. (2017) · Microbiome · doi:10.1186/s40168-017-0331-1 · Cited by 173
“rRNA gene databases [4, 6] using SINA on the SILVA website [43, 44].”
BackgroundMethodInfluentialSelf-citationThe microbial rare biosphere: current concepts, methods and ecological principles
Pascoal, F., Costa, R., & Magalhães, C. (2020) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiaa227 · Cited by 161
Starr, E. P., Shi, S.-J., Blazewicz, S., Probst, A., Herman, D., Firestone, M., & Banfield, J. (2017) · Microbiome · doi:10.1186/s40168-018-0499-z · Cited by 136
“45 Mb scaffold was recovered and was able to be circularized, then scaffolding errors and completeness were assessed as described in [1] and scaffolding gaps were fixed manually by mapping reads to the scaffold using Bowtie2 on default settings [48].”
BackgroundMethodSelf-citationMetagenomic Approaches for Understanding New Concepts in Microbial Science
Alves, L. D. F., Westmann, C. A., Lovate, G. L., de Siqueira, G. M. V., Borelli, T. C., & Guazzaroni, M. (2018) · International Journal of Genomics · doi:10.1155/2018/2312987 · Cited by 167
Hu, P., Tom, L., Singh, A., Thomas, B., Baker, B., Piceno, Y., Andersen, G., & Banfield, J. (2016) · mBio · doi:10.1128/mbio.01669-15 · Cited by 135
Self-citationUnifying the known and unknown microbial coding sequence space
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife · doi:10.7554/elife.67667 · Cited by 134
“Patescibacteria, more commonly known as Candidate Phyla Radiation (CPR), a phylum that has raised considerable interest due to its unusual biology (Brown et al., 2015) and for which we provide an extensive catalog of 283,874 linegage- specific genes of unknown function at different taxonomic level resolutions, which w…”
BackgroundRoadmap for naming uncultivated Archaea and Bacteria
Murray, A., Freudenstein, J., Gribaldo, S., Hatzenpichler, R., Hugenholtz, P., Kämpfer, P., Konstantinidis, K., Lane, C. E., Papke, R., Parks, D., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0733-x · Cited by 132
Self-citationTree of motility – A proposed history of motility systems in the tree of life
Miyata, M., Robinson, R. C., Uyeda, T. Q. P., Fukumori, Y., Fukushima, S., Haruta, S., Homma, M., Inaba, K., Ito, M., Kaito, C., et al. (2020) · Genes to Cells · doi:10.1111/gtc.12737 · Cited by 174
“According to the latest data analyses, life on the Earth can be divided into two or three groups (Brown et al., 2015; Castelle & Banfield, 2018; Hug et al., 2016; Williams, Foster, Cox, & Embley, 2013): Bacteria, which includes the subgroup of Candidate Phyla Radiation (CPR), species whose…”
MethodThe fourth wave of biocatalysis is approaching
Bornscheuer, U. T. (2017) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2017.0063 · Cited by 161
“As an example of the ‘information content’ now accessible by next-generation sequencing technology, the Banfield group identified 8 complete and 789 draft genomes in a single metagenome library from an aquifer water sample [32].”
BackgroundMilici, M., Deng, Z.-L., Tomasch, J., Decelle, J., Wos‐Oxley, M. L., Wang, H., Jáuregui, R., Plumeier, I., Giebel, H., Badewien, T. H., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00649 · Cited by 146
“However, this number refers only to the domains of bacteria and archaea without taking into account eukaryotic microorganisms (Caron et al., 2012; de Vargas et al., 2015), viruses (Suttle, 2005; Brum et al., 2015) or the ultra-small bacteria discovered recently (Brown et al., 2015).”
BackgroundGenomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota
Hua, Z., Qu, Y.-N., Zhu, Q., Zhou, E.-M., Qi, Y.-L., Yin, Y.-R., Rao, Y.-Z., Tian, Y., Li, Y.-X., Liu, L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05284-4 · Cited by 133
Self-citationGroundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths
Maamar, S. B., Aquilina, L., Quaiser, A., Pauwels, H., Michon-Coudouel, S., Vergnaud, V., Labasque, T., Roques, C., Abbott, B. W., & Dufresne, A. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01457 · Cited by 154
“Keywords: aquifers, hydrology, 16S rRNA, pyrosequencing, groundwater, bacterial communities, iron oxidation, nitrate Frontiers in Microbiology | www.frontiersin.org 1 December 2015 | Volume 6 | Article 1457”
MethodRuiz-Pérez, C. A., Conrad, R. E., & Konstantinidis, K. T. (2021) · BMC Bioinformatics · doi:10.1186/s12859-020-03940-5 · Cited by 141
Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain.
Yabusaki, S., Wilkins, M., Fang, Y.-L., Williams, K., Arora, B., Bargar, J., Beller, H., Bouskill, N., Brodie, E., Christensen, J., et al. (2017) · Environmental Science and Technology · doi:10.1021/acs.est.6b04873 · Cited by 123
Self-citationSporulation, bacterial cell envelopes and the origin of life
Tocheva, E. I., Ortega, D. R., & Jensen, G. J. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.85 · Cited by 121
Yuan, L., Wang, Y., Zhang, L., Palomo, A., Zhou, J. Z., Smets, B. F., Bürgmann, H., & Ju, F. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c02483 · Cited by 142
Large freshwater phages with the potential to augment aerobic methane oxidation
Chen, L.-X., Méheust, R., Crits-Christoph, A., McMahon, K., Nelson, T., Slater, G. F., Warren, L., & Banfield, J. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0779-9 · Cited by 121
Self-citationCulturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review
Sarhan, M. S., Hamza, M. A., Youssef, H. H., Patz, S., Becker, M., Elsawey, H., Nemr, R. A., Daanaa, H.-S. A., Mourad, E. F., Morsi, A., et al. (2019) · Journal of Advanced Research · doi:10.1016/j.jare.2019.04.002 · Cited by 161
“Moreover, phyla composed exclusively of uncultured representatives are referred to as Candidate Phyla (CP) [27,28].”
BackgroundOrigin of microbial biomineralization and magnetotaxis during the Archean
Lin, W., Paterson, G. A., Zhu, Q., Wang, Y., Kopylova, E., Li, Y., Knight, R. D., Bazylinski, D. A., Zhu, R., Kirschvink, J. L., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1614654114 · Cited by 134
“Recent advances in high-throughput sequencing combined with improving computational methods are enabling the successful recovery of high-quality population genomes directly from metagenomic data (19, 20).”
BackgroundAssembling metagenomes, one community at a time
van der Walt, A. J., Goethem, M. W. V., Ramond, J., Makhalanyane, T. P., Reva, O. N., & Cowan, D. A. (2017) · BMC Genomics · doi:10.1186/s12864-017-3918-9 · Cited by 128
“However, within the scope of metagenome assembly, essential details are often omitted when describing methods [56].”
BackgroundWrighton, K., Castelle, C., Varaljay, V., Satagopan, S., Brown, C., Wilkins, M., Thomas, B., Sharon, I., Williams, K., Tabita, F., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.53 · Cited by 119
“Phylogenetic analyses that include these and other recently reported sequences (Rinke et al., 2014; Brown et al., 2015) support the identification of this lineage as a separate phylum (Candidatus Peregrinibacteria).”
BackgroundMethodResultInfluentialSelf-citationUndinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
Dombrowski, N., Williams, T. A., Sun, J., Woodcroft, B. J., Lee, J.-H., Minh, B. Q., Rinke, C., & Spang, A. (2020) · Nature Communications · doi:10.1038/s41467-020-17408-w · Cited by 127
Bäckström, D., Yutin, N., Jørgensen, S. L., Dharamshi, J. E., Homa, F., Zaremba-Niedźwiedzka, K., Spang, A., Wolf, Y. I., Koonin, E. V., & Ettema, T. J. G. (2019) · mBio · doi:10.1128/mbio.02497-18 · Cited by 155
Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota
Chen, L.-X., Méndez-García, C., Dombrowski, N., Servín-Garcidueñas, L. E., Eloe-Fadrosh, E., Fang, B.-Z., Luo, Z.-H., Tan, S., Zhi, X.-Y., Hua, Z., et al. (2017) · The ISME Journal · doi:10.1038/s41396-017-0002-z · Cited by 115
The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together
Dacks, J. B., Field, M. C., Buick, R., Eme, L., Gribaldo, S., Roger, A. J., Brochier‐Armanet, C., & Devos, D. P. (2016) · Journal of Cell Science · doi:10.1242/jcs.178566 · Cited by 131
“However, as the clustering of fast-evolving lineages in molecular phylogenies is a well-known artefact (Gribaldo and Philippe, 2002), the branching of the DPANN in the archaeal tree, or even their very existence, is another issue that requires resolution.”
BackgroundAcquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
McLean, J. S., Bor, B., Kerns, K. A., Liu, Q., To, T. T., Solden, L., Hendrickson, E. L., Wrighton, K. C., Shi, W., & He, X. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107939 · Cited by 138
“The environmental genomes RAAC3 and GWC2 are found in deep groundwater, where the vast majority of other new CPR members occur (Brown et al., 2015).”
InfluentialSelf-citationEcogenomics and Taxonomy of Cyanobacteria Phylum
Walter, J. M., Coutinho, F. H., Dutilh, B. E., Swings, J., Thompson, F. L., & Thompson, C. C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02132 · Cited by 124
“The CGT system should maintain all of the existing information, integrating it with new data on DNA, genomes, isolates/strains, cultured and uncultured, “Candidatus” cases and reconstructed genomes from metagenomes (Brown et al., 2015; Hugerth et al., 2015).”
BackgroundInfluentialTowards a balanced view of the bacterial tree of life
Schulz, F., Eloe‐Fadrosh, E. A., Bowers, R. M., Jarett, J. K., Nielsen, T., Ivanova, N., Kyrpides, N. C., & Woyke, T. (2017) · Microbiome · doi:10.1186/s40168-017-0360-9 · Cited by 128
“The underrepresentation of these so-called “blind spots” in PCR-based studies is thus not surprising [4, 7].”
BackgroundResultInfluentialRokubacteria: Genomic Giants among the Uncultured Bacterial Phyla
Becraft, E., Woyke, T., Jarett, J., Ivanova, N., Godoy-Vitorino, F., Poulton, N., Brown, J. M., Brown, J., Lau, M., Onstott, T., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02264 · Cited by 111
“Also displayed are the estimated genome sizes for Candidate Phyla Radiation (CPR) genomes (green; R2 = 0.02) and candidate phyla genomes not a part of the CPR lineage (orange; R2 = 0.25).”
BackgroundInfluentialLemos, L. N., Medeiros, J. D., Dini‐Andreote, F., Fernandes, G. D. R., Varani, A. M., Oliveira, G., & Pylro, V. S. (2019) · Molecular Ecology · doi:10.1111/mec.15208 · Cited by 127
“Recent advances in metagenomics with respect to in silico recon‐ struction of metagenome‐assembled genomes (MAGs) have en‐ abled a deeper investigation of unculturable organisms, such as the new bacterial superphyla Candidate Phyla Radiation (CPR)/ Patescibacteria (Brown et al., 2015).”
BackgroundReductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
Moreira, D., Zivanovic, Y., López‐Archilla, A. I., Iniesto, M., & López‐García, P. (2021) · Nature Communications · doi:10.1038/s41467-021-22762-4 · Cited by 126
Delmont, T. O., Kiefl, E., Kilinc, O., Esen, Ö. C., Uysal, I., Rappé, M. S., Giovannoni, S. J., & Eren, A. M. (2019) · eLife · doi:10.7554/elife.46497 · Cited by 142
“While advances in genome-resolved metagenomics have made microbial clades more accessible without cultivation (Spang et al., 2015; Brown et al., 2015; Anantharaman et al., 2016), reconstructing SAR11 genomes from the surface ocean remains a difficult endeavor, as evident in recent comprehensive surveys of metagenome-a…”
BackgroundWang, Y., Gallagher, L. A., Andrade, P. A., Liu, A., Humphreys, I. R., Turkarslan, S., Cutler, K. J., Arrieta-Ortiz, M. L., Li, Y., Radey, M. C., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.017 · Cited by 108
Donhauser, J., Qi, W., Pinto, B. B., & Frey, B. (2020) · Global Change Biology · doi:10.1111/gcb.15492 · Cited by 134
“A primer bias is a likely cause for the discrimination against Patescibacteria in amplicon sequencing data (Brown et al., 2015; Dudek et al., 2017; Eloe-Fadrosh et al., 2016; Klindworth et al., 2013), while the lack of matches in the functional databases is likely explained by the fact that the…”
BackgroundKocur, C. M. D., Lomheim, L., Molenda, O., Weber, K. P., Austrins, L. M., Sleep, B. E., Boparai, H. K., Edwards, E. A., & O’Carroll, D. M. (2016) · Environmental Science & Technology · doi:10.1021/acs.est.6b01745 · Cited by 126
Chipashvili, O., Utter, D. R., Bedree, J. K., Ma, Y., Schulte, F., Mascarin, G., Alayyoubi, Y., Chouhan, D., Hardt, M., Bidlack, F. B., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.09.009 · Cited by 116
Farag, I., Youssef, N. H., & Elshahed, M. S. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.00521-17 · Cited by 119
High-quality genome sequences of uncultured microbes by assembly of read clouds
Bishara, A., Moss, E. L., Kolmogorov, M., Parada, A. E., Weng, Z., Sidow, A., Dekas, A., Batzoglou, S., & Bhatt, A. S. (2018) · Nature Biotechnology · doi:10.1038/nbt.4266 · Cited by 115
Proctor, C. R., Besmer, M. D., Langenegger, T., Beck, K., Walser, J., Ackermann, M., Bürgmann, H., & Hammes, F. (2018) · The ISME Journal · doi:10.1038/s41396-018-0070-8 · Cited by 119
“with small genomes and have similarities with symbiotic bacteria [18, 56].”
Gao, S., Páez-Espino, D., Li, J., Ai, H., Liang, J., Luo, Z., Zheng, J. H., Chen, H. H., Shu, W., & Huang, L. (2022) · Nature Communications · doi:10.1038/s41467-022-30049-5 · Cited by 109
Functional and evolutionary significance of unknown genes from uncultivated taxa
del Río, Á. R., Giner‐Lamia, J., Cantalapiedra, C. P., Botas, J., Deng, Z., Hernández-Plaza, A., Palmer, M. M., Santamaría‐Hernando, S., Rodríguez‐Herva, J. J., Ruscheweyh, H., et al. (2023) · Nature · doi:10.1038/s41586-023-06955-z · Cited by 110
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
Trubl, G., Kimbrel, J. A., Liquet-Gonzalez, J., Nuccio, E., Weber, P., Pett-Ridge, J., Jansson, J., Waldrop, M., & Blazewicz, S. (2021) · Microbiome · doi:10.1186/s40168-021-01154-2 · Cited by 98
“12 [64], using the CPR marker set [65].”
MethodRosselli, R., Romoli, O., Vitulo, N., Vezzi, A., Campanaro, S., Pascale, F. D., Schiavon, R., Tiarca, M., Poletto, F., Concheri, G., et al. (2016) · Scientific Reports · doi:10.1038/srep32165 · Cited by 102
Permafrost Meta-Omics and Climate Change
Mackelprang, R., SALESKA, S. R., Jacobsen, C. S., Jansson, J. K., & Taş, N. (2016) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev-earth-060614-105126 · Cited by 99
Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’
Villanueva, L., Stefan Schouten, A., & Damsté, J. S. S. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13361 · Cited by 98
“newly proposed Parcubacteria group (Brown et al., 2015),”
BackgroundCastelle, C., Brown, C., Thomas, B., Williams, K., & Banfield, J. (2017) · Scientific Reports · doi:10.1038/srep40101 · Cited by 96
Self-citationAn estimate of the deepest branches of the tree of life from ancient vertically evolving genes
Moody, E. R., Mahendrarajah, T. A., Dombrowski, N., Clark, J. W., Petitjean, C., Offre, P., Szöllősi, G. J., Spang, A., & Williams, T. A. (2022) · eLife · doi:10.7554/elife.66695 · Cited by 95
“In particular, 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.”
MethodResultInfluentialPredicted microbial secretomes and their target substrates in marine sediment
Orsi, W., Richards, T., & Francis, W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0047-9 · Cited by 95
Xiang, G., Li, Y., Sun, J., Huo, Y., Cao, S., Cao, Y., Guo, Y., Yang, L., Cai, Y., Zhang, Y. E., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01857-x · Cited by 106
“One possible reason is that these bacteria are less studied, and no TnpB systems have been annotated 27,28 .”
STRONG: metagenomics strain resolution on assembly graphs
Quince, C., Nurk, S., Raguideau, S., James, R., Soyer, O. S., Summers, J., Limasset, A., Eren, A. M., Chikhi, R., & Darling, A. (2021) · Genome Biology · doi:10.1186/s13059-021-02419-7 · Cited by 94
Bor, B., Poweleit, N., Bois, J. S., Cen, L., Bedree, J. K., Zhou, Z. H., Gunsalus, R. P., Lux, R., McLean, J. S., He, X., et al. (2015) · Microbial Ecology · doi:10.1007/s00248-015-0711-7 · Cited by 98
Highly active rubiscos discovered by systematic interrogation of natural sequence diversity
Davidi, D., Shamshoum, M., Guo, Z., Bar‐On, Y. M., Prywes, N., Oz, A., Jabłońska, J., Flamholz, A. I., Wernick, D. G., Antonovsky, N., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019104081 · Cited by 105
“…(i) the non-redundant database from NCBI (Benson et al , 2013), (ii) TARA ocean metagenomics (assemblies of 244 samples) (Pesant et al , 2015), and (iii) a database of candidate phyla radiation genomes recovered from sediment metagenomes (Brown et al , 2015); data were downloaded on April 2017.”
Self-citationMicrobial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers
Danczak, R., Johnston, M., Kenah, C., Slattery, M. T., & Wilkins, M. J. (2018) · mSystems · doi:10.1128/msystems.00066-18 · Cited by 99
Self-citationThe importance of designating type material for uncultured taxa
Chuvochina, M. S., Rinke, C., Parks, D. H., Rappé, M. S., Tyson, G. W., Yilmaz, P., Whitman, W. B., & Hugenholtz, P. (2018) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2018.07.003 · Cited by 95
“Some studies aimed to designate type species for higher taxa [2,35] but many uncultured lineages are only named at the phylum-level [1,3,8,14,17].”
BackgroundBernard, G., Pathmanathan, J. S., Lannes, R., Lopez, P., & Bapteste, E. P. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy031 · Cited by 114
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing
Donati, C., Zolfo, M., Albanese, D., Truong, D. T., Asnicar, F., Iebba, V., Cavalieri, D., Jousson, O., Filippo, C. D., Huttenhower, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.70 · Cited by 93
Carbon fixation rates in groundwater similar to those in oligotrophic marine systems
Overholt, W. A., Trumbore, S. E., Xu, X., Bornemann, T. L. V., Probst, A. J., Krüger, M., Herrmann, M., Thamdrup, B., Bristow, L. A., Taubert, M., et al. (2022) · Nature Geoscience · doi:10.1038/s41561-022-00968-5 · Cited by 103
Zhou, Y., Liu, M., & Yang, J. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127023 · Cited by 109
Diversity and ecology of and biomineralization by magnetotactic bacteria
Lin, W., Pan, Y., & Bazylinski, D. A. (2017) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12550 · Cited by 130
“The rapid development of metagenomic methods, high-throughput DNA sequencing and efficient computational tools now allows for the rapid assembly of reliable DNA reads and binning of genomic contigs/scaffolds directly from metagenome datasets (Brown et al., 2015; Evans et al., 2015).”
BackgroundUnifying the known and unknown microbial coding sequence spacePreprint
Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.30.180448 · Cited by 15
Zambrano, M. C., Pawlak, J. J., Daystar, J., Ankeny, M., Goller, C., & Venditti, R. A. (2020) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2019.110826 · Cited by 114
Méheust, R., Castelle, C. J., Carnevali, P. B. M., Farag, I., He, C., Chen, L.-X., Amano, Y., Hug, L. A., & Banfield, J. F. (2020) · The ISME Journal · doi:10.1038/s41396-020-0716-1 · Cited by 110
Self-citationOn the Origin of Isoprenoid Biosynthesis
Hoshino, Y., & Gaucher, E. (2018) · Molecular biology and evolution · doi:10.1093/molbev/msy120 · Cited by 88
“CPR is taxonomically divided into two major groups: microgenomates (previously known as OP11) and parcubacteria (OD1) (Rinke et al. 2013; Brown et al. 2015).”
BackgroundTechnological Microbiology: Development and Applications
Vitorino, L. C., & Bessa, L. A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00827 · Cited by 116
“CPR bacteria have small genomes and unusual ribosomal compositions, in addition to lacking numerous biosynthetic pathways (Brown et al., 2015), whereas DPANN has been defined as a function of the metabolic capacity (Rinke et al., 2013; Castelle et al., 2015).”
BackgroundSequencing-based analysis of microbiomes
Pinto, Y., & Bhatt, A. S. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00746-6 · Cited by 109
“…metagenomic studies have identified a new taxon of archaea that was posited to bridge the evolutionary gap between prokaryotes and eukaryotes 64 and a new phylum (named candidate phyla radiation) with unique genomic characteristics such as compact genomes and proteins encoded within rRNA genes 65 .”
Kuroda, K., Yamamoto, K., Nakai, R., Hirakata, Y., Kubota, K., Nobu, M., & Narihiro, T. (2022) · mBio · doi:10.1128/mbio.01711-22 · Cited by 87
“One major lineage of the domain Bacteria, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) (1, 2), is a highly diverse”
BackgroundHosokawa, S., Kuroda, K., Narihiro, T., Aoi, Y., Ozaki, N., Ohashi, A., & Kindaichi, T. (2021) · Water · doi:10.3390/w13020208 · Cited by 87
“The numbers in square brackets on the horizontal axis represent the following genes: [1] ammonia oxidation (amoA and amoBC, pmmo), [2] hydroxylamine oxidation (hao), [3] nitrite oxidation (nxrAB), [4] dissimilatory nitrate reduction (narGH and/or napAB), [5] DNRA (nirBD and/or nrfAH), [6] nitrite reduction (nirK or ni…”
BackgroundMethodInfluentialChen, L., Qin, Y.-J., Chen, B., Wu, C., Zheng, S., Chen, R., Yang, S.-H., Yang, L., & Liu, Z. (2020) · Environmental Research · doi:10.1016/j.envres.2020.109743 · Cited by 87
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
