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Genome Wide Analysis for Rapid Identification of Vibrio Species

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Abstract

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.

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Acknowledgments

We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB), and CSIR project GENESIS (BSC0121) for providing the necessary funds, facilities and moral support. Authors are also thankful to Academy of Scientific & Innovative Research (AcSIR), New Delhi.

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Authors and Affiliations

  1. Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007, India

    Vipin Chandra Kalia, Prasun Kumar, Ravi Kumar, Anjali Mishra & Shikha Koul

  2. Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001, India

    Vipin Chandra Kalia & Shikha Koul

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  1. Vipin Chandra Kalia
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  2. Prasun Kumar
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Correspondence to Vipin Chandra Kalia.

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Kalia, V.C., Kumar, P., Kumar, R. et al. Genome Wide Analysis for Rapid Identification of Vibrio Species. Indian J Microbiol 55, 375–383 (2015). https://doi.org/10.1007/s12088-015-0553-5

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