  We report a droplet microfluidic method to target and sort individual cells
directly from complex microbiome samples, and to prepare these cells for bulk
whole genome sequencing without cultivation. We characterize this approach by
recovering bacteria spiked into human stool samples at a ratio as low as 1:250
and by successfully enriching endogenous Bacteroides vulgatus to the level
required for de-novo assembly of high-quality genomes. While microbiome strains
are increasingly demanded for biomedical applications, the vast majority of
species and strains are uncultivated and without reference genomes. We address
this shortcoming by encapsulating complex microbiome samples directly into
microfluidic droplets and amplify a target-specific genomic fragment using a
custom molecular TaqMan probe. We separate those positive droplets by droplet
sorting, selectively enriching single target strain cells. Finally, we present
a protocol to purify the genomic DNA while specifically removing amplicons and
cell debris for high-quality genome sequencing.
