RT Journal Article SR Electronic T1 High-throughput isolation and culture of human gut bacteria with droplet microfluidics JF bioRxiv FD Cold Spring Harbor Laboratory SP 630822 DO 10.1101/630822 A1 Max M Villa A1 Rachael J Bloom A1 Justin D Silverman A1 Heather K Durand A1 Sharon Jiang A1 Anchi Wu A1 Shuqiang Huang A1 Lingchong You A1 Lawrence A David YR 2019 UL http://biorxiv.org/content/early/2019/05/07/630822.abstract AB Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. However, the diversity of human gut microbial communities (microbiota) impedes comprehensive experimental studies of individual bacterial taxa. Here, we combine advances in droplet microfluidics and high-throughput DNA sequencing to develop a platform for isolating and assaying microbiota members in picoliter droplets (MicDrop). MicDrop can be used to create millions of distinct bacterial colonies in a single experiment while using off-the-shelf parts compact enough to fit in an anaerobic chamber. In proof-of-concept experiments, we used the platform to characterize inter-individual metabolic variation among hundreds of polysaccharide-degrading gut bacteria from nine stool donors. We also used MicDrop to test the hypothesis that growth kinetics of individual gut bacterial taxa are associated with longterm community dynamics in an artificial gut. These demonstrations suggest the MicDrop platform could support future diagnostic efforts to personalize microbiota-directed therapies, as well as to provide comprehensive new insights into the ecology of human gut microbiota.