变性梯度凝胶电泳技术在微生态学研究中应用的进展

变性梯度凝胶电泳(Denaturing gradient gel electrophoresis,DGGE)技术具有无需进行微生物培养、检测率高、分辨率高、重复性好等优点,现已逐渐成为微生态学研究中的强有力工具.本研究介绍了变性梯度凝胶电泳(DGGE)的基本原理和实验步骤中的系统优化,重点介绍和讨论了DGGE在微生态学研究中应用以及进展情况,并对该技术的应用前景进行了展望.     

DGGE/TGGE技术及其在微生物分子生态学中的应用

变性梯度凝胶电泳(DGGE)和温度梯度凝胶电泳(TGGE)是近些年微生物分子生态学研究中的热点技术之一。由于DGGE／TGGE技术具有可靠性强、重现性高、方便快捷等优点,被广泛地应用于微生物群落多样性和动态性分析。文章对DGGE／TGGE技术原理与关键环节、局限性和应用前景进行了综述。     

PCR-DGGE技术及其在植物微生态研究中的应用

植物中微生物种类较为丰富,在植物微生态系统中发挥重要作用.变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)技术作为研究微生物物种多样性和种群动态变化的分子检测工具之一,广泛应用于植物微生物群落多样性和群落动态变化研究中.概述了DGGE技术的原理,及其在植物微生物生态学中的应用以及在该领域研究中导致DGGE偏差的因素和相应解决方法,对DGGE检测结果的分析提供参考,为进一步研究植物微生物相互作用提供帮助.     

DGGE/TGGE技术在土壤微生物分子生态学研究中的应用

传统的微生物生态学研究方法只限于环境样品中极少部分(0.1%￣1%)可培养的微生物类群,极大程度地限制了对土壤微生物群落结构的研究。综述了以16S rDNA为主要研究对象的DGGE/TGGE(Denaturing gradientgel electrophoresis,DGGE/Temperature gradient gel electrophoresis,TGGE)技术原理,以其为主要手段结合PCR扩增、克隆建库、序列测定以及种系分析对土壤微生物的群落结构和多样性研究的最新动态。DGGE/TGGE技术极大地推动了土壤微生物分子生态学的发展,同时也为实际问题的诊断、作物生长跟踪监测等提供了技术支撑,在土壤微生物分子生态学研究和生产实践中起着越来越重要的作用。     

DGGE技术在微生物生态学研究中的应用

简要介绍了DGGE（denaturing gradient gel electrophorests）的基本原理,及其在研究微生物类群多样性,环境中微生物变化的动态监测,微生物新物种的发现,不同DNA提取方法效果的比较和功能基因多样性研究等微生物生态学领域中的应用,并对该技术自身存在的缺陷进行了评价。     

应用DGGE研究微生物群落时的常见问题分析

变性梯度凝胶电泳(DGGE)是通过核酸片段对微生物群落进行研究,可以监测未培养细菌及其功能基因,被广泛地应用于微生物群落多样性和动态分析,并成为微生物分子生态学研究中的重要手段之一。文中论述了DGGE操作过程中遇到的常见问题,并提出了相应的解决方法。全面分析了样品预处理过程和PCR扩增效果对DGGE分析的影响,探讨了DGGE图谱的优化过程和图谱分析方法,并对DGGE的应用前景进行了综述。     

不同DGGE谱带信息提取方法对分析结果的影响

自1993年Muyzer,et al.[1]将变性梯度凝胶电泳技术(Denaturing gradient gel electrophoresis,DGGE)引入到微生物生态学研究以来,DGGE已被广泛应用于各种生态系统(如淡水、海洋、土壤、动物消化道等)的微生物群落结构分析[2—6]。但对于DGGE凝胶的分析至今仍没有统一的方法,     

PCR-DGGE技术在农田土壤微生物多样性研究中的应用

变性梯度凝胶电泳技术(DGGE)在微生物生态学领域有着广泛的应用。研究采用化学裂解法直接提取出不同农田土壤微生物基因组DNA,并以此基因组DNA为模板,选择特异性引物F357GC和R515对16S rRNA基因的V3区进行扩增,长约230bp的PCR产物经变性梯度凝胶电泳(DGGE)进行分离后,得到不同数目且分离效果较好的电泳条带。结果说明,DGGE能够对土壤样品中的不同微生物的16S rRNA基因的V3区的DNA扩增片断进行分离,为这些DNA片断的定性和鉴定提供了条件。与传统的平板培养方法相比,变性梯度凝胶电泳(DGGE)技术能够更精确的反映出土壤微生物多样性,它是一种有效的微生物多样性研究技术。     

益生菌DGGE Marker的制备及验证

目的 制备指示益生菌标准菌株的DGGE marker并对其可靠性进行验证.方法 分别利用乳杆菌、双歧杆菌特异性引物和细菌V3区通用引物对选取的乳杆菌、双歧杆菌标准菌株DNA进行扩增,利用DGGE检测每个标准菌株条带位置是否与利用这些标准菌株制备的DGGE marker条带相对应.结果 DGGE图谱显示,乳杆菌和双歧杆菌特异性引物或V3区通用引物扩增后的每个标准菌株优势条带,与乳杆菌、双歧杆菌DGGE marker均有对应关系.结论 常见益生菌菌株的DGGE marker可以指示相应菌株的存在;其研制成功,可为微生物生态学中应用DGGE技术检测特定微生物种类的动态变化,提供新的思路.     

分子生态学方法在微生物肥料质量监测中的应用

应用PCR—DGGE技术对某微生物肥料的质量进行了跟踪监测,并结合分离培养和克隆文库分析对其菌种组成进行了检测。结果表明,同一生产批次3个不同包装样品的细菌和真菌DGGE（denaturing gradient gel eleetrophoresis）图谱相似性为80％-100％,3个不同生产批次之间DGGE图谱相似性为80％-88％,表明该微生物肥料的菌种组成的稳定性较好。但分离培养和克隆文库分析结果显示样品的菌种组成与产品标签说明之间存在较大差异。对于产品标注的6种微生物组成,只有Lactobacillus属的微生物可与之对应,其他检测到的Bacillus、Monascus、Brevibacillus、Psudomonas和Penicillium属的微生物并未包括在产品说明中。研究表明用分子生态学方法可以比较客观准确的对微生物肥料质量进行评估和峪测。     

PCR-DGGE技术在细菌多样性研究中的条件优化

基于聚合酶链式反应的变性梯度凝胶电泳（Polymerase chain reaction denaturing gradient gel electrophoresis,PCR-DGGE）技术作为研究微生物物种多样性和动态变化的分子检测工具之一,具有可靠性强、重复性好、方便快捷等优点。该技术无需传统的微生物分离培养,便能快速、准确地获取复杂样品中微生物的菌群多样性、动态性及其功能菌的遗传信息,被广泛用于环境生态学的研究中。该文概述了PCR-DGGE技术的基本原理,并对该技术的各个环节如DNA提取、PCR扩增、DGGE条件以及图谱染色等条件的优化进行探讨,提出可能出现的影响因素,并对该技术自身存在的局限性和应用前景进行了评价。     

PCR-DGGE技术在微生物生态学中的应用

PCR-DGGE技术是随着现代分子生物学发展起来的一种很重要的分析手段,与传统的种群鉴定方法相比,PCR-DGGE技术具有快速和操作简便等优点,对于不可培养的微生物也能达到分离的效果,因而在微生物生态学中受到普遍关注与重视。介绍了该技术的基本原理、主要影响因素等研究动态以及在微生物生态学中的应用现状,并对其应用前景作了综述。     

PCR-DGGE技术及其在微生物生态学中的应用

现代分子生物学技术PCR-DGGE是一种分析微生物群落的有效工具,可以用于研究生态系统中微生物多样性和群落动态性。本文简要介绍了PCR-DGGE技术原理及其在微生物生态学领域的应用,并对该技术的局限性进行了评价。     

Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.     

Fluorophore-Labeled Primers Improve the Sensitivity, Versatility, and Normalization of Denaturing Gradient Gel Electrophoresis

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology. We tested the effect of fluorophore-labeled primers on DGGE band migration, sensitivity, and normalization. The fluorophores Cy5 and Cy3 did not visibly alter DGGE fingerprints; however, 6-carboxyfluorescein retarded band migration. Fluorophore modification improved the sensitivity of DGGE fingerprint detection and facilitated normalization of samples from multiple gels by the application of intralane standards.     

Application of Denaturing High-Performance Liquid Chromatography in Microbial Ecology: Fermentor Sludge, Compost, and Soil Community Profiling

Genetic fingerprinting methods, such as denaturing gradient gel electrophoresis (DGGE), are used in microbial ecology for the analysis of mixed microbial communities but are associated with various problems. In the present study we used a new alternative method: denaturing high-performance liquid chromatography (dHPLC). This method was previously shown to work with samples from water and gut flora but had not yet been applied to complex environmental samples. In contrast to other publications dealing with dHPLC, we used a commonly available HPLC system. Samples from different origins (fermentor sludge, compost, and soil), all ecologically significant, were tested, and the 16S rRNA gene was amplified via PCR. After optimization of the HPLC elution conditions, amplicons of pure cultures and mixed microbial populations could be separated successfully. Systematic differentiation was carried out by a cloning approach, since fraction collection of the peaks did not result in satisfactory fragment separation. dHPLC was evaluated as a tool for microbial community analysis on a genetic level and demonstrated major improvements compared to gel-based fingerprinting methods, such as DGGE, that are commonly used in microbial ecology.     

DGGE/TGGE a method for identifying genes from natural ecosystems.

Five years after the introduction of denaturing gradient gel electrophoresis(DGGE) and temperature gradient gel electrophoresis (TGGE) in environmental microbiology these techniques are now routinely used in many microbiological laboratories worldwide as molecular tools to compare the diversity of microbial communities and to monitor population dynamics. Recent advances in these techniques have demonstrated their importance in microbial ecology.     

PCR-Denaturing Gradient Gel Electrophoresis of Complex Microbial Communities: A Two-Step Approach to Address the Effect of Gel-to-Gel Variation and Allow Valid Comparisons Across a Large Dataset

Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis software package (TL120 v2006, Phoretix 1D Advanced) followed by a simple interpolation step in Matlab minimized the effect of gel-to-gel variation, allowing for comparisons between large numbers of samples with a high degree of confidence. At the same time, data were obtained in the form of whole densitometric curves, rather than as band presence/absence or intensity information, and could be readily analyzed by a collection of well-established multivariate methods. This work clearly demonstrates that there is still room for significant improvements as to the way large DGGE datasets are processed and statistically interrogated.