The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
Polymerase chain reaction primers miss half of rRNA microbial diversity
Abstract
The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this—yet to be used—approach may still leave an unknown number of species and higher taxa undetected.
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Cites
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Cited by
Apprill, A., McNally, S., Parsons, R., & Weber, L. (2015) · Aquatic Microbial Ecology · doi:10.3354/ame01753 · Cited by 2,707
Turner, T. R., James, E. K., & Poole, P. S. (2013) · Genome Biology · doi:10.1186/gb-2013-14-6-209 · Cited by 1,349
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D. M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T. J., Clayton, J. B., Johnson, T. J., Hunter, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3601 · Cited by 819
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
Metadata
- Authors
- Hong, S., Bunge, J., Leslin, C., Jeon, S., & Epstein, S. S.
- Venue
- The ISME Journal
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-08-20
- Volume
- 3
- Issue
- 12
- Pages
- 1365-1373
- ISSN
- 1751-7362 (ISSN-L)
- 1751-7370
- OpenAlex
- W1971536609
- Cited by
- 278
- References
- 36
- FWCI
- 17.65
- Type
- journal article
- Language
- en
- Open access
- closed
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- Hong, S., Bunge, J., Leslin, C., Jeon, S., & Epstein, S. S. (2009). Polymerase chain reaction primers miss half of rRNA microbial diversity. The ISME Journal. https://doi.org/10.1038/ismej.2009.89
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