Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
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.
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All data generated or analysed during this study are included in the manuscript and supporting files.
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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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