Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

  1. William J Watterson  Is a corresponding author
  2. Melikhan Tanyeri
  3. Andrea R Watson
  4. Candace M Cham
  5. Yue Shan
  6. Eugene B Chang
  7. A Murat Eren  Is a corresponding author
  8. Savas Tay  Is a corresponding author
  1. University of Chicago, United States
  2. Duquesne University, United States

Abstract

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. William J Watterson

    Pritzker School of Molecular Engineering, University of Chicago, Chicago, United States
    For correspondence
    william.j.watterson@gmail.com
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5065-9634
  2. Melikhan Tanyeri

    Department of Engineering, Duquesne University, Pittsburgh, United States
    Competing interests
    No competing interests declared.
  3. Andrea R Watson

    Department of Medicine, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0128-6795
  4. Candace M Cham

    Department of Medicine, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
  5. Yue Shan

    Department of Medicine, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
  6. Eugene B Chang

    Department of Medicine, University of Chicago, Chicago, United States
    Competing interests
    No competing interests declared.
  7. A Murat Eren

    Medicine, University of Chicago, Chicago, United States
    For correspondence
    meren@uchicago.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9013-4827
  8. Savas Tay

    Institute of Molecular Engineering, University of Chicago, Chicago, United States
    For correspondence
    tays@uchicago.edu
    Competing interests
    Savas Tay, Savas Tay is a founder and equity holder of BiomeSense Inc..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1912-6020

Funding

National Institute of Diabetes and Digestive and Kidney Diseases (DK42086)

  • Eugene B Chang

National Institute of Diabetes and Digestive and Kidney Diseases (RC2 DK122394-01)

  • Eugene B Chang

Samuel and Emma Winters Foundation (2018-2019)

  • Melikhan Tanyeri

GI Research Foundation of Chicago

  • William J Watterson

James & Katie Mutchnik

  • A Murat Eren

National Institute of Diabetes and Digestive and Kidney Diseases (T32 DK07074)

  • William J Watterson

Duchossois Family Institute at the University of Chicago

  • Savas Tay

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

Reviewing Editor

  1. Vaughn S Cooper, University of Pittsburgh, United States

Version history

  1. Received: March 17, 2020
  2. Accepted: June 14, 2020
  3. Accepted Manuscript published: June 17, 2020 (version 1)
  4. Version of Record published: July 10, 2020 (version 2)

Copyright

© 2020, Watterson 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. William J Watterson
  2. Melikhan Tanyeri
  3. Andrea R Watson
  4. Candace M Cham
  5. Yue Shan
  6. Eugene B Chang
  7. A Murat Eren
  8. Savas Tay
(2020)
Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
eLife 9:e56998.
https://doi.org/10.7554/eLife.56998

Share this article

https://doi.org/10.7554/eLife.56998

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