Global biogeographic sampling of bacterial secondary metabolism

Elife. 2015 Jan 19:4:e05048. doi: 10.7554/eLife.05048.


Recent bacterial (meta)genome sequencing efforts suggest the existence of an enormous untapped reservoir of natural-product-encoding biosynthetic gene clusters in the environment. Here we use the pyro-sequencing of PCR amplicons derived from both nonribosomal peptide adenylation domains and polyketide ketosynthase domains to compare biosynthetic diversity in soil microbiomes from around the globe. We see large differences in domain populations from all except the most proximal and biome-similar samples, suggesting that most microbiomes will encode largely distinct collections of bacterial secondary metabolites. Our data indicate a correlation between two factors, geographic distance and biome-type, and the biosynthetic diversity found in soil environments. By assigning reads to known gene clusters we identify hotspots of biomedically relevant biosynthetic diversity. These observations not only provide new insights into the natural world, they also provide a road map for guiding future natural products discovery efforts.

Keywords: biogeography; biosynthesis; evolutionary biology; genomics; infectious disease; metagenomics; microbiology; natural products; none.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / enzymology
  • Bacteria / metabolism*
  • Base Sequence
  • Biodiversity
  • Biological Products / metabolism
  • Phylogeography*
  • Polyketide Synthases / chemistry
  • Polyketide Synthases / metabolism
  • Protein Structure, Tertiary
  • Secondary Metabolism*


  • Biological Products
  • Polyketide Synthases