Applied Microbiology and Biotechnology

, Volume 82, Issue 3, pp 579–586

Potential natural product discovery from microbes through a diversity-guided computational framework

  • Eakasit Pacharawongsakda
  • Sunai Yokwai
  • Supawadee Ingsriswang
Methods

DOI: 10.1007/s00253-008-1847-x

Cite this article as:
Pacharawongsakda, E., Yokwai, S. & Ingsriswang, S. Appl Microbiol Biotechnol (2009) 82: 579. doi:10.1007/s00253-008-1847-x

Abstract

As the occurrence of natural compounds is related to the spatial distribution and evolution of microorganisms for biological and ecological relevance, the data integration of chemistry, geography, and phylogeny within an analytical framework is needed to make better decisions on sourcing the microbes for drug discovery. Such a framework should help researcher to decide on (a) which microorganisms are capable to produce the structurally diverse-bioactive compounds and (b) where those microbes could be found. Here, we present GIST (Geospatial Integrated Species, sites and bioactive compound relationships Tracking tool), a computational framework that could describe and compare how the chemical and genetic diversity varied among microbes in different areas. GIST mainly exploits the measures of bioactive diversity (BD) and phylogenetic diversity (PD), derived from the branch length of bioactive dendrogram and phylogenetic tree, respectively. Based on BD and PD, our framework could provide guidance and tools for measuring, monitoring, and evaluating of patterns and changes in biodiversity of microorganisms to improve the success rate of drug discovery.

Keywords

Bioactive diversityPhylogenetic diversityMicrobial collectionNatural productsDendrogramDrug discovery

Supplementary material

253_2008_1847_MOESM1_ESM.doc (100 kb)
ESM 1(DOC 99.5 kb)

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Eakasit Pacharawongsakda
    • 1
  • Sunai Yokwai
    • 1
  • Supawadee Ingsriswang
    • 1
  1. 1.Information Systems Laboratory, Bioresource Technology UnitNational Center for Genetic Engineering and BiotechnologyPathumthaniThailand