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Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
Open accessAbstract
After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.
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Citations
Cites
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Roberts, J. D., Bebenek, K., & Kunkel, T. A. (1988) · Science · doi:10.1126/science.2460925 · Cited by 997
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Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Garbeva, P., van Veen, J. A., & van Elsas, J. D. (2004) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.42.012604.135455 · Cited by 1,458
SAR11 clade dominates ocean surface bacterioplankton communities
Morris, R. M., Rappé, M. S., Connon, S. A., Vergin, K. L., Siebold, W. A., Carlson, C. A., & Giovannoni, S. J. (2002) · Nature · doi:10.1038/nature01240 · Cited by 1,129
Metadata
- Authors
- v. Wintzingerode, F.
- Venue
- FEMS Microbiology Reviews
- Publisher
- Wiley
- Published
- 1997-11
- Volume
- 21
- Issue
- 3
- Pages
- 213-229
- ISSN
- 0168-6445 (ISSN-L)
- OpenAlex
- W2125862549
- Cited by
- 2,063
- References
- 1
- FWCI
- 44.42
- Type
- journal article
- Language
- en
- Open access
- bronze
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- v. Wintzingerode, F. (1997). Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews. https://doi.org/10.1016/s0168-6445(97)00057-0
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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.
