The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Short pyrosequencing reads suffice for accurate microbial community analysis
Open accessAbstract
Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been possible. However, results from different studies using pyrosequencing and traditional sequencing are often difficult to compare, because amplicons covering different regions of the rRNA might yield different conclusions. We used sequences from over 200 globally dispersed environments to test whether studies that used similar primers clustered together mistakenly, without regard to environment. We then tested whether primer choice affects sequence-based community analyses using UniFrac, our recently-developed method for comparing microbial communities. We performed three tests of primer effects. We tested whether different simulated amplicons generated the same UniFrac clustering results as near-full-length sequences for three recent large-scale studies of microbial communities in the mouse and human gut, and the Guerrero Negro microbial mat. We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) resembling those produced by pyrosequencing. The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced.
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Citations
Cites
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
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
Self-citationObesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
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Klindworth, A., Pruesse, E., Schweer, T., Peplies, J., Quast, C., Horn, M., & Glöckner, F. O. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks808 · Cited by 8,850
Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774
Self-citationLauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Self-citationDethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
The Long-Term Stability of the Human Gut Microbiota
Faith, J. J., Guruge, J. L., Charbonneau, M., Subramanian, S., Seedorf, H., Goodman, A. L., Clemente, J. C., Knight, R., Heath, A. C., Leibel, R. L., et al. (2013) · Science · doi:10.1126/science.1237439 · Cited by 2,058
Self-citationBest practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Self-citationHigh-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity
Hildebrandt, M. A., Hoffmann, C., Sherrill–Mix, S. A., Keilbaugh, S. A., Hamady, M., Chen, Y., Knight, R., Ahima, R. S., Bushman, F., & Wu, G. D. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.08.042 · Cited by 1,576
Self-citationError-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J., & Knight, R. (2008) · Nature Methods · doi:10.1038/nmeth.1184 · Cited by 1,310
Self-citationMetagenomic discovery of biomass-degrading genes and genomes from cow rumen
Hess, M., Sczyrba, A., Egan, R., Kim, T.-W., Chokhawala, H., Schroth, G., Luo, S., Clark, D. S., Chen, F., Zhang, T., et al. (2011) · Science · doi:10.1126/science.1200387 · Cited by 1,319
Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · The ISME Journal · doi:10.1038/ismej.2008.127 · Cited by 1,230
Self-citationDowd, S. E., Callaway, T. R., Wolcott, R. D., Sun, Y., McKeehan, T., Hagevoort, R. G., & Edrington, T. S. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-125 · Cited by 1,121
“The use of rapid sequencing technologies combined with molecular methods is becoming a gold standard for evaluating the microbiomes of animals [21-25].”
MethodCharacterization of fecal microbial communities in patients with liver cirrhosis
Chen, Y., Yang, F., Lu, H., Wang, B., Chen, Y., Lei, D., Wang, Y., Zhu, B., & Li, L. (2011) · Hepatology · doi:10.1002/hep.24423 · Cited by 1,038
Taur, Y., Xavier, J. B., Lipuma, L., Ubeda, C., Goldberg, J., Gobourne, A., Lee, Y. J., Dubin, K. A., Socci, N. D., Viale, A., et al. (2012) · Clinical Infectious Diseases · doi:10.1093/cid/cis580 · Cited by 1,020
Srinivasan, S., Hoffman, N. G., Morgan, M. T., Matsen, F. A., Fiedler, T. L., Hall, R. W., Ross, F. J., McCoy, C. O., Bumgarner, R., Marrazzo, J. M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037818 · Cited by 673
Pyrosequencing analysis of the oral microflora of healthy adults
Keijser, B. J. F., Zaura, E., Huse, S. M., van der Vossen, J. M. B. M., Schuren, F. H. J., Montijn, R. C., ten Cate, J. M., & Crielaard, W. (2008) · Journal of Dental Research · doi:10.1177/154405910808701104 · Cited by 669
Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596
The gut microbiome in human neurological disease: A review
Tremlett, H., Bauer, K. C., Appel‐Cresswell, S., Finlay, B. B., & Waubant, E. (2017) · Annals of Neurology · doi:10.1002/ana.24901 · Cited by 535
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
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
Self-citationA practical guide to the oral microbiome and its relation to health and disease
Krishnan, K., Chen, T., & Paster, B. (2017) · Oral Diseases · doi:10.1111/odi.12509 · Cited by 347
“The length of sequencing reads varies depending upon the primers used, but many studies utilize about 500 base-reads for a typical sequencing run, which allows for microbial community identification (Liu et al., 2007, Liu et al., 2008, Wang et al., 2007, Mougeot et al., 2016).”
BackgroundEstablishment of ruminal bacterial community in dairy calves from birth to weaning is sequential
Rey, M., Enjalbert, F., Combes, S., Cauquil, L., Bouchez, O., & Monteils, V. (2014) · Journal of Applied Microbiology · doi:10.1111/jam.12405 · Cited by 314
Bikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., Del Pozo-Yauner, L., & Ochoa-Leyva, A. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.06.001 · Cited by 263
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
The interaction between smoking, alcohol and the gut microbiome
Capurso, G., & Lahner, E. (2017) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2017.10.006 · Cited by 182
Stahringer, S. S., Clemente, J. C., Corley, R. P., Hewitt, J., Knights, D., Walters, W. A., Knight, R., & Krauter, K. S. (2012) · Genome Research · doi:10.1101/gr.140608.112 · Cited by 180
Self-citationDougal, K., de la Fuente, G., Harris, P. A., Girdwood, S. E., Pinloche, E., Geor, R. J., Nielsen, B. D., Schott, H. C., Elzinga, S., & Newbold, C. J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087424 · Cited by 165
Zhang, F., Xu, H., Shelobolina, E. S., Konishi, H., Converse, B., Shen, Z., & Roden, E. E. (2015) · American Mineralogist · doi:10.2138/am-2015-4999 · Cited by 81
“Total DNA from the enrichment culture was polymerase chain reaction-amplified using primers targeting variable regions 1 through 2 of the bacterial 16S rRNA gene (V1-2), gel purified, and sequenced using 454/Roche GS FLX technology (Liu et al. 2007).”
MethodDestrez, A., Grimm, P., & Julliand, V. (2019) · Physiology & Behavior · doi:10.1016/j.physbeh.2019.02.003 · Cited by 42
Metadata
- Authors
- Liu, Z., Lozupone, C., Hamady, M., Bushman, F. D., & Knight, R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-08-28
- Volume
- 35
- Issue
- 18
- Pages
- e120-e120
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1984474722
- Cited by
- 691
- References
- 3
- FWCI
- 27.01
- Type
- journal article
- Language
- en
- Open access
- gold
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