Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
- University of Chicago, United States
- 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
William J Watterson
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.
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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Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
eLife 9:e56998.
https://doi.org/10.7554/eLife.56998
