Amplicon study of microbial diversity after in-droplet cultivation

Here we established a microscale cultivation system in which we encapsulate bacterial cells of an environmental microbial community in microfluidic droplets. We demonstrate the merits of the in-droplet cultivation by comparing the cultivation outcome to cultivations on conventional agar plates for a bacterial soil community by 16S rRNA gene amplicon sequencing. Since the cultivation outcome with our new microscale cultivation system was significantly higher in microbial diversity than the outcome of the conventional approach, in-droplet cultivation is highly relevant for research fields requiring the isolation of new bacterial strains, like antibiotic discovery.