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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.<\/jats:p>","DOI":"10.7554\/elife.56998","type":"journal-article","created":{"date-parts":[[2020,6,17]],"date-time":"2020-06-17T08:00:37Z","timestamp":1592380837000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.56998","source":"Crossref","is-referenced-by-count":138,"title":["Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes"],"prefix":"10.7554","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5065-9634","authenticated-orcid":true,"given":"William J","family":"Watterson","sequence":"first","affiliation":[{"name":"Pritzker School of Molecular Engineering, The University of Chicago, Chicago, United States"},{"name":"Institute for Genomics and Systems Biology, The University of Chicago, Chicago, United 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