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Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

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Abstract

Bacteria possessing multiple copies of 16S rRNA (rrs) gene demonstrate high intragenomic heterogeneity. It hinders clear distinction at species level and even leads to overestimation of the bacterial diversity. Fifty completely sequenced genomes belonging to 19 species of Lactobacillus species were found to possess 4–9 copies of rrs each. Multiple sequence alignment of 268 rrs genes from all the 19 species could be classified into 20 groups. Lactobacillus sanfranciscensis TMW 1.1304 was the only species where all the 7 copies of rrs were exactly similar and thus formed a distinct group. In order to circumvent the problem of high heterogeneity arising due to multiple copies of rrs, 19 additional genes (732–3645 nucleotides in size) common to Lactobacillus genomes, were selected and digested with 10 Type II restriction endonucleases (RE), under in silico conditions. The following unique gene—RE combinations: recA (1098 nts)—HpyCH4 V, CviAII, BfuCI and RsaI were found to be useful in identifying 29 strains representing 17 species. Digestion patterns of genes—ruvB (1020 nts), dnaA (1368 nts), purA (1290 nts), dnaJ (1140 nts), and gyrB (1944 nts) in combination with REs—AluI, BfuCI, CviAI, Taq1, and Tru9I allowed clear identification of an additional 14 strains belonging to 8 species. Digestion pattern of genes recA, ruvB, dnaA, purA, dnaJ and gyrB can be used as biomarkers for identifying different species of Lactobacillus.

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Acknowledgments

We are thankful to the Director of CSIR-Institute of Genomics and Integrative Biology (IGIB), and CSIR projects GENESIS (BSC0121) and INDEPTH (BSC0111) 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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  1. Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007, India

    Shikha Koul & Vipin Chandra Kalia

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

    Shikha Koul & Vipin Chandra Kalia

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  1. Shikha Koul
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Correspondence to Vipin Chandra Kalia.

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Koul, S., Kalia, V.C. Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species. Indian J Microbiol 56, 265–276 (2016). https://doi.org/10.1007/s12088-016-0605-5

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