16S rRNA基因两个可变区对反映肠道菌群多样性与物种鉴定能力的比较分析  

Two hypervariable regions of 16S rRNA gene in revealing the diversity and genus composition of gut microbiota: a comparative study

作　　者：王国洋[1] 王景[1] 赵立平[1] 张晓君[1] 张梦晖[1] 

机构地区：[1]上海交通大学 生命科学与技术学院微生物代谢国家重点实验室,上海200240

出　　处：《中国微生态学杂志》2013年第9期1005-1009,共5页Chinese Journal of Microecology

基　　金：国家自然科学基金项目(20875061;21177086);上海市国际合作项目(12230706800)

摘　　要：目的目前基于新一代测序技术开展的人类肠道元基因组学研究已成为微生物学乃至整个生物学中最活跃和最有潜力的学科方向。现阶段绝大部分以肠道菌群为靶标的研究主要基于16S rRNA基因可变区测序。本研究关注的是测序技术发展使得序列的读长能力延长后,选择16S rRNA基因V1-V3区与V3-V5区进行测序所反映的多样性与物种组成信息的异同点。方法以两个真实的16S rRNA基因全长Sanger测序数据为基础,对其中的V1-V3和V3-V5两种片段进行了模拟数据的分析,将它们分别与16S rRNA基因的全长片段在OTU多样性水平和物种组成信息方面进行比较。结果结果显示V1-V3区在OTU多样性上较V3-V5区更为接近全长序列;在物种组成表现上,两个可变区鉴定出的大部分的属的丰度与全长序列分析结果一致,但是各自有少数属的丰度结果与全长序列丰度结果存在差异。结论在多样性分析上,选择V1-V3区片段能得到与全长更为接近的结果;而具体到菌种的组成分析中,V1-V3区和V3-V5区都有其局限性。Objective This study focused on comparison of the 16S rRNA gene V1-V3 and V3-V5 hypervariable regions in revea- ling the diversity and species composition information of gut microbiota. Methods Based on the data of two full-length 16S rRNA se- quencing reads obtained with Sanger sequencing, we simulated the sequence sets representing V1-V3 and V3-V5 hypervariable regions, respectively. The OTU diversity on different similarity levels and the composition at genus level of the two simulated data sets were com- pared with those of the full length data sets. Results The OTU diversity of V1-V3 region was more similar to that of the full length re- gion. The majorities of the composition at genus level of the two simulated data sets were consistant with that of their corresponding genus of the full length data; however, each data had some genuses behaving differently. Conclusion V1-V3 region is superior to V3-V5 region in revealing OTU diversity; but both regions have its own limitation in reflecting correct mirobiome composition.

关 键 词：454焦磷酸测序 16S RRNA基因 V1-V3可变区 V3-V5可变区 

分 类 号：R378[医药卫生—病原生物学]