Cited by 1,000

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Accurate determination of microbial diversity from 454 pyrosequencing data

Open access

Quince, Christopher, Lanzén, Anders, Curtis, Thomas P, Davenport, Russell J, Hall, Neil, Head, Ian M, Read, L Fiona, Sloan, William T·2009·Nature Methods

DOI 10.1038/nmeth.1361

Open this paper in CoChat — free account

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1038/nmeth.1361

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
A general method applicable to the search for similarities in the amino acid sequence of two proteins
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227

Show all 3 references

UPARSE: highly accurate OTU sequences from microbial amplicon reads
Edgar, R. C. (2013) · Nature Methods · doi:10.1038/nmeth.2604 · Cited by 16,707
Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
Schloss, P. D., Gevers, D., & Westcott, S. L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027310 · Cited by 2,112
Distinct soil microbial diversity under long-term organic and conventional farming
Hartmann, M., Frey, B., Mayer, J., Mäder, P., & Widmer, F. (2015) · The ISME Journal · doi:10.1038/ismej.2014.210 · Cited by 1,496
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346
The oral microbiome in health and disease
Wade, W. G. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.11.006 · Cited by 1,347
Defining the healthy “core microbiome” of oral microbial communities
Zaura, E., Keijser, B. J., Huse, S. M., & Crielaard, W. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-259 · Cited by 1,323
Defining the human microbiome
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012) · Nutrition Reviews · doi:10.1111/j.1753-4887.2012.00493.x · Cited by 1,255
Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags
Wang, Y., Sheng, H.-F., He, Y., Wu, J.-Y., Jiang, Y.-X., Tam, N. F.-Y., & Zhou, H.-W. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.01821-12 · Cited by 892
Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide
Lindahl, B. D., Nilsson, R. H., Tedersoo, L., Abarenkov, K., Carlsen, T., Kjøller, R., Kõljalg, U., Pennanen, T., Rosendahl, S., Stenlid, J., et al. (2013) · New Phytologist · doi:10.1111/nph.12243 · Cited by 892
The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery
Cabrera-Rubio, R., Collado, M. C., Laitinen, K., Salminen, S., Isolauri, E., & Mira, A. (2012) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.037382 · Cited by 886
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017) · Nature Communications · doi:10.1038/s41467-017-01312-x · Cited by 835
The Rare Bacterial Biosphere
Pedrós-Alió, C. (2012) · Annual Review of Marine Science · doi:10.1146/annurev-marine-120710-100948 · Cited by 760
Low gut microbiota diversity in early infancy precedes asthma at school age
Abrahamsson, T. R., Jakobsson, H. E., Andersson, A. F., Björkstén, B., Engstrand, L., & Jenmalm, M. C. (2014) · Clinical & Experimental Allergy · doi:10.1111/cea.12253 · Cited by 750
A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy
Aagaard, K., Riehle, K., Ma, J., Segata, N., Mistretta, T.-A., Coarfa, C., Raza, S., Rosenbaum, S., Van den Veyver, I., Milosavljevic, A., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036466 · Cited by 709
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D., & Konstantinidis, K. T. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093827 · Cited by 684
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
Reeder, J., & Knight, R. (2010) · Nature Methods · doi:10.1038/nmeth0910-668b · Cited by 678
Genomic insights into the marine sponge microbiome
Hentschel, U., Piel, J., Degnan, S. M., & Taylor, M. W. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2839 · Cited by 658
The Gut Microbiome Modulates Colon Tumorigenesis
Zackular, J. P., Baxter, N. T., Iverson, K. D., Sadler, W. D., Petrosino, J. F., Chen, G. Y., & Schloss, P. D. (2013) · mBio · doi:10.1128/mbio.00692-13 · Cited by 629
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2536 · Cited by 621
The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis
Molyneaux, P. L., Cox, M. J., Willis-Owen, S. A. G., Mallia, P., Russell, K. E., Russell, A.-M., Murphy, E., Johnston, S. L., Schwartz, D. A., Wells, A. U., et al. (2014) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201403-0541oc · Cited by 567
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
Tedersoo, L., Nilsson, R. H., Abarenkov, K., Jairus, T., Sadam, A., Saar, I., Bahram, M., Bechem, E., Chuyong, G., & Kõljalg, U. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03373.x · Cited by 549
Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh
Sarker, S. A., Sultana, S., Reuteler, G., Moine, D., Descombes, P., Charton, F., Bourdin, G., McCallin, S., Ngom-Bru, C., Neville, T., et al. (2016) · EBioMedicine · doi:10.1016/j.ebiom.2015.12.023 · Cited by 533
Diversity of the human skin microbiome early in life
Capone, K. A., Dowd, S. E., Stamatas, G. N., & Nikolovski, J. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.168 · Cited by 532
Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers
Hadziavdic, K., Lekang, K., Lanzen, A., Jonassen, I., Thompson, E. M., & Troedsson, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087624 · Cited by 532
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
Vaginal Microbiome Consortium (additional members), Brooks, J. P., Edwards, D. J., Harwich, M. D., Rivera, M. C., Fettweis, J. M., Serrano, M. G., Reris, R. A., Sheth, N. U., Huang, B., et al. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0351-6 · Cited by 528
Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification
Berry, D., Ben Mahfoudh, K., Wagner, M., & Loy, A. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05220-11 · Cited by 518
Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Ochman, H., Worobey, M., Kuo, C.-H., Ndjango, J.-B. N., Peeters, M., Hahn, B. H., & Hugenholtz, P. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000546 · Cited by 494
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
Turnbaugh, P. J., Quince, C., Faith, J. J., McHardy, A. C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002355107 · Cited by 478
Self-citation
Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis
Bogaert, D., Keijser, B., Huse, S., Rossen, J., Veenhoven, R., van Gils, E., Bruin, J., Montijn, R., Bonten, M., & Sanders, E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017035 · Cited by 454
Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers
Charlson, E. S., Chen, J., Custers-Allen, R., Bittinger, K., Li, H., Sinha, R., Hwang, J., Bushman, F. D., & Collman, R. G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015216 · Cited by 437
The Human Nasal Microbiota and Staphylococcus aureus Carriage
Frank, D. N., Feazel, L. M., Bessesen, M. T., Price, C. S., Janoff, E. N., & Pace, N. R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0010598 · Cited by 422
A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
D’Amore, R., Ijaz, U. Z., Schirmer, M., Kenny, J. G., Gregory, R., Darby, A. C., Shakya, M., Podar, M., Quince, C., & Hall, N. (2016) · BMC Genomics · doi:10.1186/s12864-015-2194-9 · Cited by 405
Self-citation
Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease
Molyneaux, P. L., Mallia, P., Cox, M. J., Footitt, J., Willis-Owen, S. A. G., Homola, D., Trujillo-Torralbo, M.-B., Elkin, S., Kon, O. M., Cookson, W. O. C., et al. (2013) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201302-0341oc · Cited by 390
The Microbiome and Human Biology
Knight, R., Callewaert, C., Marotz, C., Hyde, E. R., Debelius, J. W., McDonald, D., & Sogin, M. L. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022438 · Cited by 373
Resistance and resilience of the forest soil microbiome to logging-associated compaction
Hartmann, M., Niklaus, P. A., Zimmermann, S., Schmutz, S., Kremer, J., Abarenkov, K., Lüscher, P., Widmer, F., & Frey, B. (2014) · The ISME Journal · doi:10.1038/ismej.2013.141 · Cited by 391
Changes in Abundance of Oral Microbiota Associated with Oral Cancer
Schmidt, B. L., Kuczynski, J., Bhattacharya, A., Huey, B., Corby, P. M., Queiroz, E. L. S., Nightingale, K., Kerr, A. R., DeLacure, M. D., Veeramachaneni, R., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098741 · Cited by 375
The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea
Endt, K., Stecher, B., Chaffron, S., Slack, E., Tchitchek, N., Benecke, A., Van Maele, L., Sirard, J.-C., Mueller, A. J., Heikenwalder, M., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001097 · Cited by 344
Association of the Vaginal Microbiota with Human Papillomavirus Infection in a Korean Twin Cohort
Lee, J. E., Lee, S., Lee, H., Song, Y.-M., Lee, K., Han, M. J., Sung, J., & Ko, G. (2013) · PLoS ONE · doi:10.1371/journal.pone.0063514 · Cited by 340
Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample
Luo, C., Tsementzi, D., Kyrpides, N., Read, T., & Konstantinidis, K. T. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030087 · Cited by 337
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
Pride, D. T., Salzman, J., Haynes, M., Rohwer, F., Davis-Long, C., White, R. A., Loomer, P., Armitage, G. C., & Relman, D. A. (2012) · The ISME Journal · doi:10.1038/ismej.2011.169 · Cited by 335
Robustness of Gut Microbiota of Healthy Adults in Response to Probiotic Intervention Revealed by High-Throughput Pyrosequencing
Kim, S.-W., Suda, W., Kim, S., Oshima, K., Fukuda, S., Ohno, H., Morita, H., & Hattori, M. (2013) · DNA Research · doi:10.1093/dnares/dst006 · Cited by 334
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
Gloor, G. B., Hummelen, R., Macklaim, J. M., Dickson, R. J., Fernandes, A. D., MacPhee, R., & Reid, G. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015406 · Cited by 330
Ancient and modern environmental DNA
Pedersen, M. W., Overballe-Petersen, S., Ermini, L., Sarkissian, C. D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., et al. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0383 · Cited by 329
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys
Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L., & Graf, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0094249 · Cited by 324
Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
Hartmann, M., Howes, C. G., VanInsberghe, D., Yu, H., Bachar, D., Christen, R., Henrik Nilsson, R., Hallam, S. J., & Mohn, W. W. (2012) · The ISME Journal · doi:10.1038/ismej.2012.84 · Cited by 320
PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences
Abarenkov, K., Tedersoo, L., Nilsson, R. H., Vellak, K., Saar, I., Veldre, V., Parmasto, E., Prous, M., Aan, A., Ots, M., et al. (2010) · Evolutionary Bioinformatics · doi:10.4137/ebo.s6271 · Cited by 301
Sources of PCR-induced distortions in high-throughput sequencing data sets
Kebschull, J. M., & Zador, A. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv717 · Cited by 299
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
Jumpstart Consortium Human Microbiome Project Data Generation Working Group (2012) · PLoS ONE · doi:10.1371/journal.pone.0039315 · Cited by 297
Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction
Laehnemann, D., Borkhardt, A., & McHardy, A. C. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbv029 · Cited by 296
The generation and maintenance of diversity in microbial communities
Fierer, N., & Lennon, J. T. (2011) · American Journal of Botany · doi:10.3732/ajb.1000498 · Cited by 288
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
Bragg, L. M., Stone, G., Butler, M. K., Hugenholtz, P., & Tyson, G. W. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003031 · Cited by 261
Analysis of plant microbe interactions in the era of next generation sequencing technologies
Knief, C. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00216 · Cited by 253
Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children
Laufer, A. S., Metlay, J. P., Gent, J. F., Fennie, K. P., Kong, Y., & Pettigrew, M. M. (2011) · mBio · doi:10.1128/mbio.00245-10 · Cited by 224
“Average-linkage clustering may yield more accurate estimates of diversity with regard to identifying rare microbiota in short amplicon (60-bp) data sets (32, 33).”
Background
Impact of next generation sequencing techniques in food microbiology.
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R., & Delgado, S. (2014) · Current Genomics · doi:10.2174/1389202915666140616233211 · Cited by 188
Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents.
Meier, D. V., Pjevac, P., Bach, W., Hourdez, S., Girguis, P. R., Vidoudez, C., Amann, R., & Meyerdierks, A. (2017) · The ISME Journal · doi:10.1038/ismej.2017.37 · Cited by 177
Sebum and Hydration Levels in Specific Regions of Human Face Significantly Predict the Nature and Diversity of Facial Skin Microbiome
Mukherjee, S., Mitra, R., Maitra, A., Gupta, S., Kumaran, S., Chakrabortty, A., & Majumder, P. P. (2016) · Scientific Reports · doi:10.1038/srep36062 · Cited by 153
Alterations in Vaginal Microbiota and Associated Metabolome in Women with Recurrent Implantation Failure
Fu, M., Zhang, X., Liang, Y., Lin, S., Qian, W., & Fan, S. (2020) · mBio · doi:10.1128/mbio.03242-19 · Cited by 130
Characteristics of 454 pyrosequencing data—enabling realistic simulation with flowsim
Balzer, S., Malde, K., Lanzén, A., Sharma, A., & Jonassen, I. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq365 · Cited by 124
Self-citation
Does Maternal Perinatal Probiotic Supplementation Alter the Intestinal Microbiota of Mother and Child?
Dotterud, C. K., Avershina, E., Sekelja, M., Simpson, M. R., Rudi, K., Storrø, O., Johnsen, R., & Øien, T. (2015) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000000781 · Cited by 112
Molecular diversity of bacteria in commercially available “Spirulina” food supplements
Vardaka, E., Kormas, K. A., Katsiapi, M., Genitsaris, S., & Moustaka-Gouni, M. (2016) · PeerJ · doi:10.7717/peerj.1610 · Cited by 48

Authors: Quince, C., Lanzén, A., Curtis, T. P., Davenport, R. J., Hall, N., Head, I. M., Read, L. F., & Sloan, W. T.
Venue: Nature Methods
Publisher: Springer Science and Business Media LLC
Published: 2009-08-09
Volume: 6
Issue: 9
Pages: 639-641
ISSN: 1548-7091 (ISSN-L)
1548-7105
DOI: 10.1038/nmeth.1361
OpenAlex: W2000072710
Cited by: 1,000
References: 3
FWCI: 34.57
Type: journal article
Language: en
Open access: green

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

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

Accurate determination of microbial diversity from 454 pyrosequencing data

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

About these checks

Data sources