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

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 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.

肠道细菌的分离与培养，可用于探究微生物在疾病中的作用，亦有望催生新型治疗手段。然而，人类肠道微生物组（microbiota）的多样性，阻碍了对单个细菌类群的全面实验研究。在此研究中，我们结合液滴微流控技术（droplet microfluidics）与高通量DNA测序（high-throughput DNA sequencing）的进展，开发出一种可在皮升级液滴（picoliter droplets）中分离并检测微生物组成员的平台（MicDrop）。MicDrop平台可在单次实验中构建数百万个独立的细菌菌落，且其使用的市售部件体积小巧，可放入厌氧培养箱中。在概念验证实验中，我们利用该平台对来自9名粪便供体的数百株降解多糖的肠道细菌进行了个体间代谢差异表征。我们还利用MicDrop平台验证了如下假说：单个肠道细菌类群的生长动力学与人工肠道系统中的长期群落动态存在关联。上述演示表明，MicDrop平台可助力未来的诊断工作，以实现靶向微生物组治疗的个性化，同时还能为人类肠道微生物组的生态学研究提供全新的全面视角。