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A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

Abstract

The use of rrs (16S rRNA) gene is widely regarded as the “gold standard” for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4–7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.

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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 the Academy of Scientific & Innovative Research (AcSIR), New Delhi.

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Correspondence to Vipin Chandra Kalia.

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Kalia, V.C., Kumar, R., Kumar, P. et al. A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus . Indian J Microbiol 56, 46–58 (2016). https://doi.org/10.1007/s12088-015-0561-5

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  • DOI: https://doi.org/10.1007/s12088-015-0561-5

Keywords

  • Biomarkers
  • Diagnosis
  • Genome
  • In silico
  • Restriction endonuclease
  • Streptococcus