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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: Human gut metagenomics research based on next-generation sequencing technology has become the most active and potential disciplinary direction in microbiology and even the whole biology. At this stage most of the intestinal flora as the target of the study is mainly based on 16S rRNA gene variable region sequencing. This study focuses on the similarities and differences between the diversity and species composition information of 16S rRNA gene sequences selected by V1-V3 and V3-V5 after the development of sequencing technology makes the sequence read-out extend. Methods Based on the full-length Sanger sequencing data of two real 16S rRNA genes, the two fragments of V1-V3 and V3-V5 were analyzed by simulated data and compared with the full-length fragment of 16S rRNA gene in OTU Diversity level and species composition information. The results showed that the genotypes V1-V3 were closer to the full-length sequence than the V3-V5 region in OTU diversity. Most of the genus abundances and full-length sequences identified by the two variable regions The results are consistent, but there are differences between the abundance results of minority genera and the results of full-length sequence abundance. Conclusion In the analysis of diversity, the results of selecting V1-V3 region fragments are more similar to the full-length ones. However, in the compositional analysis of the strains, the V1-V3 region and the V3-V5 region have their limitations.