High-throughput automated microfluidic sample preparation for accurate microbial genomics.
Soohong KimJoachim De JongheAnthony B KulesaDavid FeldmanTommi VatanenRoby P BhattacharyyaBrittany BerdyJames GomezJill NolanSlava EpsteinPaul C BlaineyPublished in: Nature communications (2017)
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.
Keyphrases
- high throughput
- single cell
- mycobacterium tuberculosis
- induced apoptosis
- pseudomonas aeruginosa
- molecularly imprinted
- low cost
- microbial community
- circulating tumor cells
- cell cycle arrest
- cystic fibrosis
- circulating tumor
- cell death
- single molecule
- high resolution
- escherichia coli
- cell proliferation
- endoplasmic reticulum stress
- oxidative stress
- drug resistant
- cell free
- deep learning
- staphylococcus aureus
- candida albicans
- big data
- mass spectrometry
- nucleic acid
- simultaneous determination