凝胶条带内DNA回收测序评估DGGE可靠性
ASSESSING THE RELIABILITY OF DGGE BY RETRIEVING AND SEQUENCING DNA FRAGMENTS IN GEL BANDS
查看参考文献17篇
文摘
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为了评估DGGE的可靠性, 对DGGE条带中回收的DNA片段进行了测序比较分析, 并引入了DGGE可靠性指数的概念评价其可靠性。结果显示同一条DGGE条带回收的DNA来自同一属的概率为64.7%, 相同位置的DGGE条带可以被认为是同一OTU; 不同的DGGE条带回收到类似的DNA序列(16S rDNA V3区差异小于4 bp)的概率为10.5%; DGGE可靠性指数为74.8%。以上结果表明尽管DGGE技术与理论预期存在一定的差距, 但是DGGE技术基本能够反映微生物群落的多样性。 |
其他语种文摘
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To assess the reliability of DGGE, the V3 region fragments of prokaryotic 16S rDNA sequences were amplified by PCR and separated by DGGE with 40%-70% denaturing gradient in present study, and the differences of DNA sequences retrieved from DGGE bands were compared, and the concept of DGGE reliable index (RI) that was calculated by the equation RI = (N_(ss) - N_(sd) + N_(dd) - N_(ds))/N_s, was introduced. The results showed that the probability of a single band retrieving similar sequences (the sequence diversity of the V3 region of 16S rDNA is less than 4 bp) was 64.7%, and that the bands located at the same level of denaturing gradient could be considered as the same OTU. The probability that different bands retrieve similar sequences was 10.5%. The DGGE reliable index was 74.8%. Therefore, the results of DGGE still reflect the molecular diversity of environmental microbiota, although there was a disparity comparing with theoretical expectations. |
来源
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水生生物学报
,2014,38(3):454-458 【核心库】
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关键词
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DGGE可靠性指数
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DNA指纹
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变性梯度凝胶电泳
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微生物群落结构
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地址
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中国科学院水生生物研究所, 中国科学院水生生物多样性与保护重点实验室, 武汉, 430072
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语种
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中文 |
文献类型
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研究性论文 |
ISSN
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1000-3207 |
基金
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国家973计划
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国家自然科学基金
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文献收藏号
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CSCD:5146579
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参考文献 共
17
共1页
|
1.
Muyzer G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction- amplified genes coding for 16S rRNA.
Applied and Environmental Microbiology,1993,59(3):695-700
|
被引
1226
次
|
|
|
|
2.
Gelsomino A. Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis.
Journal of Microbiological Methods,1999,38(1):1-15
|
被引
39
次
|
|
|
|
3.
Yang C H. 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and Phytophthora infected avocado roots.
FEMS Microbiology Ecology,2001,35(2):129-136
|
被引
24
次
|
|
|
|
4.
Yan Q Y. Genetic diversity of plankton community as depicted by PCR-DGGE fingerprinting and its relation to morphological composition and environmental factors in Lake Donghu.
Microbial Ecology,2007,54(2):290-297
|
被引
29
次
|
|
|
|
5.
Bell T. Larger islands house more bacterial taxa.
Science,2005,308(5730):1884
|
被引
21
次
|
|
|
|
6.
倪加加. 钉螺体内细菌群落结构PCR.DGGE分析方法的建立.
四川动物,2010,29(5):546-549
|
被引
4
次
|
|
|
|
7.
Ni J J. Impacts of algal blooms removal by chitosan-modified soils on zooplankton community in Taihu Lake, China.
Journal of Environmental Sciences,2010,22(10):1500-1507
|
被引
7
次
|
|
|
|
8.
Ni J J. Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats.
Chinese Journal of Oceanology and Limnology,2012,30(5):757-765
|
被引
11
次
|
|
|
|
9.
Boon N. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants.
FEMS Microbiology Ecology,2002,39(2):101-112
|
被引
42
次
|
|
|
|
10.
Gafan G P. Denaturing gradient gel electrophoresis gel expansion (DGGEGE) - an attempt to resolve the limitations of co-migration in the DGGE of complex polymicrobial communities.
FEMS Microbiology Letters,2005,253(2):303-307
|
被引
4
次
|
|
|
|
11.
Sanchez O. Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities.
Applied and Environmental Microbiology,2007,73(18):5962-5967
|
被引
9
次
|
|
|
|
12.
Muhling M. Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities.
ISME Journal,2008,2(4):379-392
|
被引
6
次
|
|
|
|
13.
倪加加. 不同DGGE谱带信息提取方法对分析结果的影响.
水生生物学报,2012,36(5):1009-1011
|
被引
3
次
|
|
|
|
14.
Muyzer G. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology.
Antonie van Leeuwenhoek,1998,73(1):127-141
|
被引
175
次
|
|
|
|
15.
Ercolini D. Bacterial community structure and location in Stilton cheese.
Applied and Environmental Microbiology,2003,69(6):3540-3548
|
被引
26
次
|
|
|
|
16.
Ercolini D. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food.
Journal of Microbiological Methods,2004,56(3):297-314
|
被引
64
次
|
|
|
|
17.
Fischer S G. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory.
Proceedings of the National Academy of Sciences of the United States of America,1983,80(6):1579-1583
|
被引
72
次
|
|
|
|
|