Developing and applying a microdroplet co-cultivation and omics toolbox for elucidating complex microbiomes

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, cocultivation, isolation, and analysis such as metagenomic sequencing (Figure 1). 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.Please click Additional Files below to see the full abstract.