用于快速鉴定弧菌属物种的全基因组分析
Genome Wide Analysis for Rapid Identification of Vibrio Species.
作者信息
Kalia Vipin Chandra, Kumar Prasun, Kumar Ravi, Mishra Anjali, Koul Shikha
机构信息
Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India.
Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India.
出版信息
Indian J Microbiol. 2015 Dec;55(4):375-83. doi: 10.1007/s12088-015-0553-5. Epub 2015 Sep 7.
The highly conserved 16S rRNA (rrs) gene is generally used for bacterial identification. In organisms possessing multiple copies of rrs, high intra-genomic heterogeneity does not allow easy distinction among different species. In order to identify Vibrio species, a wide range of genes have been employed. There is an urgent requirement of a consensus gene, which can be used as biomarker for rapid identification. Eight sequenced genomes of Vibrio species were screened for selecting genes which were common among all the genomes. Out of 108 common genes, 24 genes of sizes varying from 0.11 to 3.94 kb were subjected to in silico digestion with 10 type II restriction endonucleases (RE). A few unique genes-dapF, fadA, hisD, ilvH, lpxC, recF, recR, rph and ruvB in combination with certain REs provided unique digestion patterns, which can be used as biomarkers. This protocol can be exploited for rapid diagnosis of Vibrio species.
高度保守的16S rRNA（rrs）基因通常用于细菌鉴定。在拥有多个rrs拷贝的生物体中，高基因组内异质性使得不同物种之间难以区分。为了鉴定弧菌属物种，人们采用了多种基因。迫切需要一种共识基因，可作为快速鉴定的生物标志物。对8个已测序的弧菌属物种基因组进行筛选，以选择在所有基因组中都常见的基因。在108个常见基因中，选择了24个大小从0.11到3.94 kb不等的基因，用10种II型限制性内切酶（RE）进行电子消化。一些独特的基因——dapF、fadA、hisD、ilvH、lpxC、recF、recR、rph和ruvB与某些RE结合，提供了独特的消化模式，可作为生物标志物。该方案可用于弧菌属物种的快速诊断。
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