1. Genomics and Evolutionary Biology
  2. Microbiology and Infectious Disease
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Global biogeographic sampling of bacterial secondary metabolism

  1. Zachary Charlop-Powers
  2. Jeremy G Owen
  3. Boojala Vijay B Reddy
  4. Melinda A Ternei
  5. Denise O Guimarães
  6. Ulysses A de Frias
  7. Monica T Pupo
  8. Prudy Seepe
  9. Zhiyang Feng
  10. Sean F Brady Is a corresponding author
  1. Howard Hughes Medical Institute, Rockefeller University, United States
  2. Universidade Federal do Rio de Janeiro, Brazil
  3. University of São Paulo, Brazil
  4. Nelson R Mandela School of Medicine, South Africa
  5. Nanjing Agricultural University, China
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Cite as: eLife 2015;4:e05048 doi: 10.7554/eLife.05048

Abstract

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.

Article and author information

Author details

  1. Zachary Charlop-Powers

    1. Laboratory for Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Jeremy G Owen

    1. Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Boojala Vijay B Reddy

    1. Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Melinda A Ternei

    1. Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Denise O Guimarães

    1. Laboratório de Produtos Naturais, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  6. Ulysses A de Frias

    1. School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  7. Monica T Pupo

    1. School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
    Competing interests
    The authors declare that no competing interests exist.
  8. Prudy Seepe

    1. KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R Mandela School of Medicine, Durban, South Africa
    Competing interests
    The authors declare that no competing interests exist.
  9. Zhiyang Feng

    1. College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
    Competing interests
    The authors declare that no competing interests exist.
  10. Sean F Brady

    1. Laboratory of Genetically Encoded Small Molecules, Howard Hughes Medical Institute, Rockefeller University, New York, United States
    For correspondence
    1. sbrady@rockefeller.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Jon Clardy, Reviewing Editor, Harvard Medical School, United States

Publication history

  1. Received: October 5, 2014
  2. Accepted: January 7, 2015
  3. Accepted Manuscript published: January 19, 2015 (version 1)
  4. Version of Record published: February 13, 2015 (version 2)

Copyright

© 2015, Charlop-Powers et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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