High-throughput automated microfluidic sample preparation for accurate microbial genomics

Soohong Kim, Joachim De Jonghe, Anthony B. Kulesa, David Feldman, Tommi Vatanen, Roby P. Bhattacharyya, Brittany Berdy, James Gomez, Jill Nolan, Slava Epstein, Paul C. Blainey*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

47 Citations (Scopus)
178 Downloads (Pure)

Abstract

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.

Original languageEnglish
Article number13919
Pages (from-to)1-10
JournalNature Communications
Volume8
DOIs
Publication statusPublished - 27 Jan 2017
MoE publication typeA1 Journal article-refereed

Fingerprint Dive into the research topics of 'High-throughput automated microfluidic sample preparation for accurate microbial genomics'. Together they form a unique fingerprint.

Cite this