三种粪便总DNA提取方法的比较

目的比较不同粪便总DNA提取方法对肠道菌群多样性研究的影响。方法采用Bead beating法、化学裂解法和QIAamp DNA Stool Mini Kit提取同一份人粪便样品的总DNA，对比3种方法的DNA得率和16S rRNA基因V3区的变性梯度凝胶电泳（DGGE）图谱。结果Bead beating法的DNA得率约是其他2种方法的2倍；3种方法得到的DGGE图谱的Dice相似性为60％～70％，2条优势条带只出现在Bead beating法图谱中。在2～5min的Bead beating法击打时间里，DNA得率随击打时间的延长有一定的增加，但DGGE图谱无显著变化。结论不同的DNA提取方法会影响菌群的多样性分析。比较其他2种方法，Bead beating的裂解效率更高，能够检测到更多种类的细菌，更合适肠道菌群组成的分子研究。

A comparison of three protocols for the extraction of total fecal DNA

Objective To investigate the effects of different fecal DNA extraction methods on the molecular analysis of the diversity of gut microflora. Methods Three protocols-bead beating, chemical lysis method and QIAamp DNA Stool Mini Kit were used to extract total DNA from one fecal sample of an adult. The DNA yield and the DGGE profiles of the amplicons of 16S rRNA gene V3 region of the three DNA isolation protocols were compared. Results The DNA yield of bead beating was 2 times higher than that of the other two protocols. The Dice coefficient between DGGE profiles of these three protocols was from 60% ～ 70%. Two predominant bands only appeared in the DGGE patterns obtained with the bead beating method. The DNA isolation experiments using 2～ 5 min duration of bead beating showed that DNA yield slightly increased with the increasing beating time but the DGGE patterns remained constant. Conclusion Different DNA isolation methods can affect the diversity analysis of the microbiota due to their different lysing efficiency, bead beating is more appropriate for DNA extraction from fecal samples because it can give higher DNA yield and recover more diversity.