Bioinformatics-Based Tools and Software in Clinical Research: A New Emerging Area

  • Parveen Bansal
  • Malika Arora
  • Vikas Gupta
  • Mukesh Maithani
Part of the Methods in Molecular Biology book series (MIMB, volume 1939)


Nowadays, drug discovery is a long process which includes target identification, validation, lead optimization, and many other major/minor steps. The huge flow of data has necessitated the need for computational support for collection, storage, retrieval, analysis, and correlation of data sets of complex information. At the beginning of the twentieth century, it was cumbersome to elaborate the experimental findings in the form of clinical outcomes, but current research in the field of bioinformatics clearly shows ongoing unification of experimental findings and clinical outcomes. Bioinformatics has made it easier for researchers to overcome various challenges of time-consuming and expensive procedures of evaluation of safety and efficacy of drugs at a much faster and economic way. In the near future, it may be a major game player and trendsetter for personalized medicine, drug discovery, drug standardization, as well as food products. Due to rapidly increasing commercial interest, currently probiotic-based industries are flooding the market with a range of probiotic products under the banner of dietary supplements, natural health products, food supplements, or functional foods. Most of the consumers are attracted toward probiotic formulations due to the rosy picture provided by the media and advertisements about high beneficial claims. These products are not regulated by pharmaceutical regulatory authorities in different countries of origin and are rather regulated as per their intended use. Lack of stipulated quality standard is a major challenge for probiotic industry; hence there would always be a possibility of marketing of ineffective and unsafe products with false claims. Hence it is very important and pertinent to ensure the safety of probiotic formulations available as over-the-counter (OTC) products for ignorant society. At the same time, probiotic industry, being in its initial stages in developing and underdeveloped countries, requires to ensure safe, swift, and successful usage of probiotics. In the absence of harmonized regulatory guidelines, safety, quality, as well as the efficacy of the probiotic strain does not remain a mandate but becomes a choice for the manufacturer. Hence there is an urgent need to screen already marketed probiotic formulations for their safety with respect to specific strains of probiotic. Various conventional methods used by the manufacturers for the identification of probiotic microbes create a blurred image about their status as probiotics. The present manuscript focuses on a bioinformatics-based technique for validation of marketed probiotic formulation using 16s rRNA sequencing and strain-level identification of bacterial species using Ez Texan and laser gene software. This technique gives a clear picture about the safety of the product for human use.

Key words

Bioinformatics Probiotics Ez Texan Laser gene Drug discovery 16s rRNA Strain-level identification Pathogenic strain Safety and efficacy 


  1. 1.
    Zerhouni EA (2006) Clinical research at a crossroads: the NIH roadmap. J Investig Med 54:171–173Google Scholar
  2. 2.
    DiMasi JA, Hansen RW, Grabowski HG (2003) The price of innovation: new estimates of drug development costs. J Health Econ 22:151–185Google Scholar
  3. 3.
    Gill SK, Christopher AF, Gupta V et al (2016) Emerging role of bioinformatics tools and software in evolution of clinical research. Perspect Clin Res 7(3):115–119Google Scholar
  4. 4.
    PWC United States (2017) Medical Cost Trend. Accessed on 26 Sep 2018
  5. 5.
    Clark DE, Pickett SD (2000) Computational methods for the prediction of drug-likeness. Drug Discov Today 5:49–58Google Scholar
  6. 6.
    Drews J (1996) Genomic sciences and the medicine of tomorrow. Nat Biotechnol 14:1516–1518Google Scholar
  7. 7.
    Luscombe NM, Greenbaum D, Gerstein M (2001) What is bioinformatics? An introduction and overview. Yearb Med Inform 10(01), 83–100Google Scholar
  8. 8.
    Isea R (2015) The present-day meaning of the word bioinformatics. Global J Adv Res 2:70–73Google Scholar
  9. 9.
    Pyar HA, Peh K (2014) Characterization and identification of Lactobacillus acidophilus using biolog rapid identification system. Int J Pharm Pharm Sci 6(1):189–193Google Scholar
  10. 10.
    Stanton C, Gardiner G, Meehan H et al (2001) Market potential for probiotics. Am J Clin Nutr 73(2):476s–483sGoogle Scholar
  11. 11.
    Arora M, Baldi A (2017) Selective identification and characterization of potential probiotic strains: a review on comprehensive Polyphasic approach. App Clin Res Clin Trials Reg Aff 4(1):60–76Google Scholar
  12. 12.
    Ennis V (2008) Microbiology handouts. Int J Food Microbiol 91:305–313Google Scholar
  13. 13.
    Hiu SF, Holt RA, Sriranganathan N (1984) Lactobacillus piscicola, a new species from salmonid fish. Int J Syst Evol Microbiol 34(4):393–400Google Scholar
  14. 14.
    Taylor WI, Achanzar D (1972) Catalase test as an aid to the identification of Enterobacteriaceae. Appl Microbiol 24(1):58–61Google Scholar
  15. 15.
    Miller JM, Wright JW (1982) Spot Indole test: evaluation of four reagents. J Clin Microbiol 15(4):589–592Google Scholar
  16. 16.
    Tarrand JJ, Gröschel DH (1982) Rapid modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 16(4):772–774Google Scholar
  17. 17.
    Barry G (2011) Probiotics and health: from history to future. In: Wolfgang K (ed) Probiotics and health claim, 1st edn. Blackwell Publishing Ltd, New JeresyGoogle Scholar
  18. 18.
    Kateete DP, Kimani CN, Katabazi FA et al (2010) Identification of Staphylococcus aureus: Dnase and Mannitol salt agar improve the efficiency of the tube coagulase test. Ann Clin Microbiol Antimicrob 9(1):23–25Google Scholar
  19. 19.
    Miller JM, Rhoden DL (1991) Preliminary evaluation of biolog, a carbon source utilization method for bacterial identification. J Clin Microbiol 29(6):1143–1147Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Parveen Bansal
    • 1
  • Malika Arora
    • 2
  • Vikas Gupta
    • 1
  • Mukesh Maithani
    • 2
  1. 1.University Centre of Excellence in ResearchBaba Farid University of Health SciencesFaridkotIndia
  2. 2.Multidisciplinary Research UnitGuru Gobind Singh Medical CollegeFaridkotIndia

Personalised recommendations