Kim, SoohongDe Jonghe, JoachimKulesa, Anthony B.Feldman, DavidVatanen, TommiBhattacharyya, RobyBerdy, BrittanyGomez, JamesNolan, JillEpstein, SlavaBlainey, Paul C.2017-03-282017Kim, S., J. De Jonghe, A. B. Kulesa, D. Feldman, T. Vatanen, R. P. Bhattacharyya, B. Berdy, et al. 2017. “High-throughput automated microfluidic sample preparation for accurate microbial genomics.” Nature Communications 8 (1): 13919. doi:10.1038/ncomms13919. http://dx.doi.org/10.1038/ncomms13919.http://nrs.harvard.edu/urn-3:HUL.InstRepos:31731799Low-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.en-USJournal Article2017-03-2810.1038/ncomms13919