Helmholtz Gemeinschaft

Search
Browse
Statistics
Feeds

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

[thumbnail of Original Article]
Preview
PDF (Original Article) - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
3MB
[thumbnail of Supplemental Information] Other (Supplemental Information)
3MB

Item Type:Article
Title:Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics
Creators Name:Pryszlak, A., Wenzel, T., Seitz, K.W., Hildebrand, F., Kartal, E., Cosenza, M.R., Benes, V., Bork, P. and Merten, C.A.
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.
Keywords:Droplet Microfluidics, Single-Cell Analysis, Genomics, Genome, Gut Microbiome, Functional Analysis, Metagenomics, Bacteria
Source:Cell Reports Methods
ISSN:2667-2375
Publisher:Elsevier
Volume:2
Number:1
Page Range:100137
Date:24 January 2022
Official Publication:https://doi.org/10.1016/j.crmeth.2021.100137
PubMed:View item in PubMed

Repository Staff Only: item control page

Downloads

Downloads per month over past year

Open Access
MDC Library