Recent metabolomics and gene editing approaches for synthesis of microbial secondary metabolites for drug discovery and development

  • Rajeshwari Sinha
  • Babita Sharma
  • Arun Kumar Dangi
  • Pratyoosh ShuklaEmail author


Microbial secondary metabolites (SMs) have been identified as an important natural source of drugs for several metabolic and neurological diseases. Along with biomedical applications, SMs are also used in the food and biochemical industries. SMs include natural products such as pigments, alkaloids, toxins, antimicrobials obtained from cultured microorganisms, while other non-cultivable microorganisms have also acted as a rich source of SMs. But, the isolation of SMs from these sources is a very tedious task. Metabolomics provides complete identification and structural information about the entire cellular metabolome under specific conditions using highly sophisticated instrumentation. Further, gene editing techniques such as cloning and gene refactoring, including advanced CRISPR-Cas, can be used for engineering microbes that have the potential to produce natural SMs that were not produced in native microbial strain. The present review describes integrated metabolomics and gene editing approaches for the synthesis of novel microbial SMs and their potential application towards drug discovery and development.

Graphical abstract


Secondary metabolites Drug discovery Metabolomics Gene editing CRISPR-Cas Gene refactoring 



The author, Babita Sharma acknowledges Maharshi Dayanand University, Rohtak, India for providing University Research Fellowship (URS). PS acknowledges the infrastructural support from Department of Science and Technology, New Delhi, Govt. of India, through FIST grant (Grant No. 1196 SR/FST/LS-I/ 2017/4) and Department of Biotechnology, Government of India (Grant No. BT/PR27437/BCE/8/1433/2018) is duly acknowledged.

Compliance with ethical standards

Conflict of interest

The authors don’t have any conflict of interest.


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© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Independent ResearcherNew DelhiIndia
  2. 2.Enzyme Technology and Protein Bioinformatics Laboratory, Department of MicrobiologyMaharshi Dayanand UniversityRohtakIndia
  3. 3.Independent ResearcherRohtakIndia

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