| CVTree在454高通量测序分析菌群结构中的应用 |
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| 引用本文： | 华蔚颖,徐昭,张梦晖,李旻,张晨虹,赵立平.CVTree在454高通量测序分析菌群结构中的应用[J].中国微生态学杂志,2010,22(4):312-316. |
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| 作者姓名： | 华蔚颖 徐昭 张梦晖 李旻 张晨虹 赵立平 |
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| 作者单位： | 1. 上海交通大学生命科学技术学院,微生物分子生态与生态基因组学实验室,上海,200240
2. 复旦大学,理论生命研究中心,上海,200433 |
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| 基金项目： | 致谢：本文工作得到郝柏林院士的悉心指导,在此谨表诚挚谢意.同时,感谢863专题项目（2008AA02Z315）和自然基金项目（30730005、20875061）、上海市科委国际合作项目（075407001）对本项目的资助. |
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| 摘 要： | 目的探究将基于短串频度的CVTree方法用于反映菌群结构的16S rRNA基因的454高通量测序数据分析的可行性,为快速分析高通量菌群结构数据提供新的方法。方法对一个四世同堂的中国家庭7名成员肠道菌群和不同基因型及饮食类型的小鼠肠道菌群用454高通量方法获得16S rRNA基因的V3区的测序数据,用CVTree的方法进行菌群结构的比较分析。结果通过选取合适的短串长度,CVTree的方法能准确检测到各样本间的聚类关系,其结果与之前文献报道的基于Unifrac算法的结果相一致。结论CVTree能快速、有效地处理16S rRNA基因的454高通量测序数据,实现对不同菌群结构相似性的比较分析。
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| 关 键 词： | CVTree 454高通量测序 菌群结构 |
The application of CVTree in structural analysis of microbial communities by 454 pyrosequencing |
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| HUA Wei-ying,XU Zhao,ZHANG Meng-hui,LI Min,ZHANG Chen-hong,ZHAO Li-ping.The application of CVTree in structural analysis of microbial communities by 454 pyrosequencing[J].Chinese Journal of Microecology,2010,22(4):312-316. |
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| Authors: | HUA Wei-ying XU Zhao ZHANG Meng-hui LI Min ZHANG Chen-hong ZHAO Li-ping |
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| Affiliation: | 1.Lab of Molecular Microbial Ecology and Ecogenomics,School of Life Science and Technology,Shanghai Jiaotong University,Shanghai 200240,China;2.The T-Life Research Center,Fudan University,Shanghai 200433,China) |
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| Abstract: | Objective To explore the feasibility of CVTree application in structural analysis of microbial communities by 454 pyrosequencing.Method The CVTree was applied to two datasets to perform structural comparison of microbial communities：（1） 454 pyrosequencing data of gut microbiomes of a four-generation,seven-member Chinese family; （2） 454 pyrosequencing data of gut microbiomes of mice with different genotypes and diets.Result When suitable K-tuple length was selected,the CVTree reflected the relationship among the samples which were in good agreement with those reported in the previous studies based on Unifrac analysis. Conclusion Our study shows the ability of CVTree in structural analysis of microbial communities based on 454 pyrosequencing with high efficiency and effectiveness. |
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| Keywords: | CVTree |
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