Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water

Peng Luo; Chaoqun Hu; Lüping Zhang; Chunhua Ren; Qi Shen

doi:10.1007/s00343-007-0310-7

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Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water

Updated：2023-05-16

- Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water
- Journal of Oceanology and Limnology Vol. 25, Issue 3, Pages: 310-316(2007)
- Affiliations：
  
  The Key Laboratory of Applied Marine Biology of Guangdong Province and Chinese Academy of Sciences South China Sea Institute of Oceanology Chinese Academy of Sciences
- Author bio：
- Funds：
- DOI：10.1007/s00343-007-0310-7
  CLC：
- Published：2007
- Accepted：
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Luo, P., Hu, C., Zhang, L. et al. Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water., Chin. J. Ocean. Limnol. 25, 310–316 (2007). https://doi.org/10.1007/s00343-007-0310-7
DOI：

Luo, P., Hu, C., Zhang, L. et al. Effects of DNA extraction and universal primers on 16S rRNA gene-based DGGE analysis of a bacterial community from fish farming water., Chin. J. Ocean. Limnol. 25, 310–316 (2007). https://doi.org/10.1007/s00343-007-0310-7 DOI：

摘要

Abstract

Among many reports investigating microbial diversity from environmental samples with denaturing gradient gel electrophoresis (DGGE)

limited attention has been given to the effects of universal primers and DNA extraction on the outcome of DGGE analysis. In this study

these effects were tested with 16S rRNA gene-based DGGE on a bacterial community from farming water samples. The results indicate that the number of discernable bands in the DGGE fingerprint differed with the primer pairs used; the bands produced by 63f/518r

341f/926r and 933f/1387r primer pairs were obviously fewer than those by 968f/1401r. Also

we found that each DNA extraction method resulted in different community profiles

reflected by the number and intensity of bands in the DGGE fingerprint. Furthermore

the main bands (theoretically representing dominant bacteria) differed with the extraction methods applied. It is therefore believed that the effects of universal primers and DNA extraction should be given more attention and carefully chosen before performing an investigation into a new environment with DGGE.

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references

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