The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes
Open accessAbstract
rRNA-based studies, which have become the most common method for assessing microbial communities, rely upon faithful amplification of the corresponding genes from the original DNA sample. We report here an analysis and reevaluation of commonly used primers for amplifying the DNA between positions 27 and 1492 of bacterial 16S rRNA genes (numbered according to the Escherichia coli rRNA). We propose a formulation for a forward primer (27f) that includes three sequences not usually present. We compare our proposed formulation to two common alternatives by using linear amplification—providing an assessment that is independent of a reverse primer—and in combination with the 1492 reverse primer (1492r) under the PCR conditions appropriate for making community rRNA gene clone libraries. For analyses of DNA from human vaginal samples, our formulation was better at maintaining the original rRNA gene ratio of Lactobacillus spp. to Gardnerella spp., particularly under stringent amplification conditions. Because our 27f formulation remains relatively simple, having seven distinct primer sequences, there is minimal loss of overall amplification efficiency and specificity.
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Basic local alignment search tool
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Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
Molecular Identification of Bacteria Associated with Bacterial Vaginosis
Fredricks, D. N., Fiedler, T. L., & Marrazzo, J. M. (2005) · New England Journal of Medicine · doi:10.1056/nejmoa043802 · Cited by 1,303
Database resources of the National Center for Biotechnology Information
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734
Cited by
Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C. R., Yu, W.-H., Lakshmanan, A., & Wade, W. G. (2010) · Journal of Bacteriology · doi:10.1128/jb.00542-10 · Cited by 3,352
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
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity
Markle, J. G. M., Frank, D. N., Mortin-Toth, S., Robertson, C. E., Feazel, L. M., Rolle-Kampczyk, U., von Bergen, M., McCoy, K. D., Macpherson, A. J., & Danska, J. S. (2013) · Science · doi:10.1126/science.1233521 · Cited by 2,025
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2010.118 · Cited by 1,632
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
Metadata
- Authors
- Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., & Olsen, G. J.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2008-04-15
- Volume
- 74
- Issue
- 8
- Pages
- 2461-2470
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W2159480438
- Cited by
- 1,912
- References
- 4
- FWCI
- 21.47
- Type
- journal article
- Language
- en
- Open access
- green
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- Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., & Olsen, G. J. (2008). Critical Evaluation of Two Primers Commonly Used for Amplification of Bacterial 16S rRNA Genes. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.02272-07
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