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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.

SUBMITTER: Watterson WJ 

PROVIDER: S-EPMC7351490 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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

Watterson William J WJ   Tanyeri Melikhan M   Watson Andrea R AR   Cham Candace M CM   Shan Yue Y   Chang Eugene B EB   Eren A Murat AM   Tay Savaş S  

eLife 20200617


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 b  ...[more]

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