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

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

    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

    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

    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

    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

    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

    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

    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

    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

    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

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

Reviewing Editor

  1. Jon Clardy, Harvard Medical School, United States

Version 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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  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
(2015)
Global biogeographic sampling of bacterial secondary metabolism
eLife 4:e05048.
https://doi.org/10.7554/eLife.05048

Share this article

https://doi.org/10.7554/eLife.05048

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