粪肠、屎肠球菌及相近种部分持家基因的系统发育分析

Phylogenetic analysis of closely related Enterococcus faecalis, Enterococcus faecium species based on partial housekeeping genes

摘要:

【目的】利用16S rRNA、clpX和recA基因分子标记研究Enterococcus faecalis、Enterococcus faecium及相近种间的种系发育关系，并比较这些基因序列对E. faecalis、E. faecium及相近种的区分能力。【方法】以分离自传统乳制品中的9株E. faecium和1株E. durans分离株为研究对象，以clpX和recA基因片段为标记，通过PCR扩增、测序，结合已公布的近缘种相应序列构建系统发育树并与16S rRNA基因进行比较。【结果】在基于clpX和recA基因的进化树中，10株试验菌株与E. faecalis始终处于同一分支。与该物种这两个基因的平均相似性为99.6%和98.6%，与另一分支的Faecium-group (E. durans和E. faecium)的平均相似性仅为61.5%和33.5%。相近种E. durans和E. hirae间这两个基因的差异性为20.3%和39.0%；在基于16S rRNA基因的进化树中，试验菌株与Faecium-group (E. lactis、E. faecium、E. durans、E. hirae)处于同一分支。与这些成员间该基因的相似性大于99.6%，与E. faecalis基因的平均相似性可达98.4%。相近种间该基因相似性无明显差异。【结论】按照10株试验菌株clpX和recA基因的分析结果可将由传统生理生化和16S rRNA基因序列鉴定的9株E. faecium和1株E. durans归类为E. faecalis，clpX和recA基因可用于部分相近种的分类鉴定。

Abstract:

[Objective] Using the 16S rRNA, clpX and recA gene sequences to identify the phylogenetic relationship among closely related Enterococcus faecalis and Enterococcus faecium species. [Methods] Nine E. faecium and one E. durans strains originally isolated from traditional dairy products were characterized by PCR methods. The gene sequences, clpX and recA, were amplified and assessed for their suitability as phylogenetic markers. Phylogenetic trees were constructed with 16S rRNA and the aforementioned housekeeping genes obtained from this study and public gene databases. [Results] In the phylogenetic tree of clpX and recA genes, 10 tested strains and E. faecalis belonged to the same branch. The sequence similarity was 99.6% and 98.6% with E. faecalis, and 61.5% and 33.5% with the Faecium-group (E. durans and E. faecium), respectively. The differences of these two genes between the closely related strains of E. durans and E. hirae were 20.3% and 39.0%. Based on the phylogenetic tree of 16S rRNA, the tested strains and Faecium-group (E. lactis, E. faecium, E. durans and E. hirae) belonged to the same branch. These members shared a similarity of higher than 99.6%, while an average homology of 98.4% with E. faecalis. No obvious difference was observed between closely related strains. [Conclusion] Based on the analysis results of the housekeeping genes, clpX and recA, we propose that nine E. faecium and one E. durans, could be transferred to E. faecalis. Meanwhile, the clpX and recA genes are suitable for classification and identification of some closely related E. faecalis and E. faecium species.