Natural product drug discovery in the genomic era: realities, conjectures, misconceptions, and opportunities

J Ind Microbiol Biotechnol. 2019 Mar;46(3-4):281-299. doi: 10.1007/s10295-018-2115-4. Epub 2018 Nov 27.


Natural product discovery from microorganisms provided important sources for antibiotics, anti-cancer agents, immune-modulators, anthelminthic agents, and insecticides during a span of 50 years starting in the 1940s, then became less productive because of rediscovery issues, low throughput, and lack of relevant new technologies to unveil less abundant or not easily detected drug-like natural products. In the early 2000s, it was observed from genome sequencing that Streptomyces species encode about ten times as many secondary metabolites as predicted from known secondary metabolomes. This gave rise to a new discovery approach-microbial genome mining. As the cost of genome sequencing dropped, the numbers of sequenced bacteria, fungi and archaea expanded dramatically, and bioinformatic methods were developed to rapidly scan whole genomes for the numbers, types, and novelty of secondary metabolite biosynthetic gene clusters. This methodology enabled the identification of microbial taxa gifted for the biosynthesis of drug-like secondary metabolites. As genome sequencing technology progressed, the realities relevant to drug discovery have emerged, the conjectures and misconceptions have been clarified, and opportunities to reinvigorate microbial drug discovery have crystallized. This perspective addresses these critical issues for drug discovery.

Keywords: Actinomycetes; Biosynthetic gene clusters; Combinatorial biosynthesis; Genome mining; Gifted microbes; Myxobacteria; Natural products; Proteobacteria; Secondary metabolites; Streptomyces.

MeSH terms

  • Anti-Bacterial Agents / chemistry
  • Biological Products / chemistry*
  • Biosynthetic Pathways / genetics
  • Computational Biology
  • Drug Discovery*
  • Genome, Bacterial
  • Genomics*
  • Multigene Family
  • Phylogeny
  • Sequence Analysis, DNA
  • Streptomyces / genetics
  • Streptomyces / metabolism


  • Anti-Bacterial Agents
  • Biological Products