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Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.


ABSTRACT: 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. Although microbiome strains are increasingly demanded for biomedical applications, a 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 amplifying 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.

SUBMITTER: Pryszlak A 

PROVIDER: S-EPMC8787643 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.

Pryszlak Anna A   Wenzel Tobias T   Seitz Kiley West KW   Hildebrand Falk F   Kartal Ece E   Cosenza Marco Raffaele MR   Benes Vladimir V   Bork Peer P   Merten Christoph A CA  

Cell reports methods 20220124 1


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 <i>Bacteroides vulgatus</i> to the level required for de novo assembly of high-quality genomes. Although microbiome strains are increasingly demanded  ...[more]

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