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Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
Open accessAbstract
In order to assess the effect of genome size and number of 16S rRNA genes (rDNAs) on the quantities of PCR-generated partial 16S rDNA fragments, equimolar amounts of DNA from pairs of different species for which these parameters are known were subjected to gene amplification. The experimentally determined ratio of PCR products obtained, as determined by image analysis of SYBR-Green I-stained amplification products, corresponded well with the predicted ratio calculated from the number of rrn genes per equimolar amounts of DNA in mixtures of Escherichia coli and "Thermus thermophilus" and of Pseudomonas aeruginosa and "T. thermophilus." The values for the pair of Bacillus subtilis and "T. thermophilus" showed greater deviations from the predicted value. The dependence of the amount of 16S rDNA amplification product on these two parameters makes it impossible to quantify the number of species represented in 16S rDNA clone libraries of environmental samples as long as these two parameters are unknown for the species present.
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Cited by
Bias in template-to-product ratios in multitemplate PCR
Polz, M. F., & Cavanaugh, C. M. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.10.3724-3730.1998 · Cited by 1,484
Větrovský, T., & Baldrian, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057923 · Cited by 1,208
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134
Dowd, 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
“Although molecular approaches can also introduce their own forms of bias such as the ability to detect both viable and non-viable bacteria [18-20] they currently provide the most powerful tools available for elucidating the diversity of animal microbiomes [4,11,12,15].”
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Metadata
- Authors
- Farrelly, V, Rainey, F. A., & Stackebrandt, E.
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 1995-07
- Volume
- 61
- Issue
- 7
- Pages
- 2798-2801
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- OpenAlex
- W2081411589
- Cited by
- 714
- References
- 0
- FWCI
- 45.03
- Type
- journal article
- Language
- en
- Open access
- green
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- Farrelly, V, Rainey, F. A., & Stackebrandt, E. (1995). Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Applied and Environmental Microbiology. https://doi.org/10.1128/aem.61.7.2798-2801.1995
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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.
