High-throughput isolation and culture of human gut bacteria with droplet microfluidics

Abstract

Isolation and culture of gut bacteria enable testing for microbial roles in disease and may also lead to novel therapeutics. However, characterization of these microbes represents a complex and substantial problem in the diversity (hundreds of microbes unique to an individual) and magnitude (up to billions of microbes within one gram of stool) of microbes present in the human gut. While microbiologists have been working on this problem for decades, the diversity and number of microbes present in the human gut 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 antibiotic sensitivity in a set of gut microbes. We also used MicDrop to test the hypothesis that growth kinetics of individual gut bacterial taxa are associated with long-term 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.