Highly parallelized droplet cultivation and prioritization on antibiotic producers from natural microbial communities

  1. Lisa Mahler
  2. Sarah P Niehs
  3. Karin Martin
  4. Thomas Weber
  5. Kirstin Scherlach
  6. Christian Hertweck
  7. Martin Roth
  8. Miriam A Rosenbaum  Is a corresponding author
  1. Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Germany

Abstract

Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while the majority of microbial and with that chemical compound diversity remains inaccessible for cultivation and exploration. Culturing recalcitrant bacteria is a stochastic process. But conventional methods are limited to low throughput. By increasing (i) throughput and (ii) sensitivity by miniaturization, we innovate microbiological cultivation to comply with biological stochasticity. Here, we introduce a droplet-based microscale-cultivation system, which is directly coupled to a high-throughput screening for antimicrobial activity prior to strain isolation. We demonstrate that highly parallelized in-droplet cultivation starting from single cells results in the cultivation of yet uncultured species and a significantly higher bacterial diversity than standard agar plate cultivation. Strains able to inhibit intact reporter strains were isolated from the system. A variety of antimicrobial compounds were detected for a selected potent antibiotic producer.

Data availability

- Amplicon sequence data were deposited to NCBI under the BioProject accession numbers PRJNA623865. For isolated axenic strains, 16S rRNA gene sequences were deposited to GenBank under the accession numbers MT320111 - MT320533.- Source data, encompassing numerical and or taxonomical data and R-analysis files, are provided as RData objects and R scripts for graphs: Fig 2ab, Fig 3abc, Fig 5, Fig 6.Figures 1ab, 4 and 7 do not contain analyzed experimental data but depict workflows and overview information.

The following data sets were generated

Article and author information

Author details

  1. Lisa Mahler

    Bio Pilot Plant, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Sarah P Niehs

    Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Karin Martin

    Bio Pilot Plant, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Thomas Weber

    Bio Pilot Plant, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Kirstin Scherlach

    Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Christian Hertweck

    Department of Biomolecular Chemistry, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Martin Roth

    Bio Pilot Plant, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Miriam A Rosenbaum

    Bio Pilot Plant, Leibniz Institute for Natural Products Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
    For correspondence
    miriam.rosenbaum@leibniz-hki.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4566-8624

Funding

Thuringian Ministry of Eduction, Scienc and Culture (13008-715)

  • Lisa Mahler
  • Karin Martin
  • Martin Roth

Thuringian Ministry of Economy, Labor and Technology (2014FE9037)

  • Lisa Mahler
  • Thomas Weber
  • Martin Roth

German Center for Infection Research DZIF (TTU 09.811)

  • Lisa Mahler
  • Karin Martin

Deutsche Forschungsgemeinschaft (GSC 214)

  • Lisa Mahler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Bavesh D Kana, University of the Witwatersrand, South Africa

Publication history

  1. Received: November 10, 2020
  2. Accepted: March 19, 2021
  3. Accepted Manuscript published: March 25, 2021 (version 1)
  4. Version of Record published: April 28, 2021 (version 2)

Copyright

© 2021, Mahler 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. Lisa Mahler
  2. Sarah P Niehs
  3. Karin Martin
  4. Thomas Weber
  5. Kirstin Scherlach
  6. Christian Hertweck
  7. Martin Roth
  8. Miriam A Rosenbaum
(2021)
Highly parallelized droplet cultivation and prioritization on antibiotic producers from natural microbial communities
eLife 10:e64774.
https://doi.org/10.7554/eLife.64774

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