Identification and classification of the genus Bacteroides by multilocus sequence analysis
Identification and classification of the genus Bacteroides by multilocus sequence analysis
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DOI：
10.1099/mic.0.052332-0
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发表时间：
2011-12-01
期刊：
影响因子：
2.8
通讯作者：
Ohkuma, Moriya
中科院分区：
文献类型：
--
作者：
Sakamoto, Mitsuo;Ohkuma, Moriya
对拟杆菌属的代表性物种进行多位点序列分析（MLSA）。采用直接PCR法对35个种的38株拟杆菌进行了dnaJ、gyrB、hsp60、recA、rpoB和16SrRNA基因的扩增和序列测定。比较了各基因的邻接（NJ）、最大似然（ML）和最大简约（MP）遗传性。这些数据证实，使用管家基因的MLSA比使用16S rRNA基因的MLSA区分拟杆菌属物种的潜力更大。在所分析的管家基因中，gyrB是最具信息性的，其次是dnaJ。所有6个基因的串联序列（4816 bp）的分析显示强大的系统发育关系不同的拟杆菌属物种相比，单基因树。NJ，ML和MP树是非常相似的，几乎完全解决了拟杆菌属物种的关系，据我们所知的第一次。此外，对dnaJ、gyrB和hsp60基因的串联（2457 bp）的分析产生了基本上相同的结果。使用SplitsTree4程序识别十个不同的进化枝。对于拟杆菌属，我们可以将种定义为基于5个蛋白编码管家基因和16S rRNA基因的片段具有至少97.5%基因序列相似性的一组菌株。这项研究表明，管家基因的MLSA是一个有价值的替代技术的细菌属的鉴定和分类。
Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.