Prevailing methods of culturing gut bacterial strains are often time- and labor-intensive and do not scale to the diversity of microbes across human populations. An alternative approach, developed in the David Lab, is to culture gut bacteria in nano- to pico-liter volumes by encapsulating microbes in droplets of media separated by oils and surfactants. Within minutes, millions of distinct culture volumes can be created using accessible microfluidic techniques and equipment.

Using this microfluidic platform to culture gut bacteria, the David Lab has generated bacterial growth curves for dozens of distinct sequence variants which has furthered our understanding of the impact that species’ growth has on overall community composition. The David Lab has also used microfluidics to characterize complex carbohydrate degradation among hundreds of gut bacteria isolated from human stool in our investigation of inter-individual variation in prebiotic response.