DEVELOPING AND APPLYING A MICRODROPLET CO-CULTIVATION AND OMICS TOOLBOX FOR ELUCIDATING COMPLEX MICROBIOMES

摘要

We have been developing, expanding, and applying a technological pipeline, based on nanoliter-scale microfluidic droplets, to co-cultivate and dissect subsets of complex microbial communities in order to elucidate molecular mechanisms underlying their structures and functions. The pipeline consists of droplet generation, co-cultivation, isolation, and analysis such as metagenomic sequencing. We apply this technological framework to the study of a range of microbial communities closely related to human health or the environment. For instance, we demonstrate the anaerobic co-cultivation of diverse sub-communities from a human fecal sample and the de novo reconstruction of genomes from a microdroplet. We observe that many of the cultivated bacteria in these encapsulated sub-communities represent the microbial "dark matter". In particular, we have constructed the draft genome of a novel Neisseriaceae, representing a new candidate genus with potential contributions to fatty acid utilization and biosynthesis of proatherogenic intermediates.