title: A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities.
abstract: We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.
authors.affiliation: Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Kaston
authors.initials: K
authors.lastname: Leung
authors.forename: Hans
authors.initials: H
authors.lastname: Zahn
authors.forename: Timothy
authors.initials: T
authors.lastname: Leaver
authors.forename: Kishori M
authors.initials: KM
authors.lastname: Konwar
authors.forename: Niels W
authors.initials: NW
authors.lastname: Hanson
authors.forename: Antoine P
authors.initials: AP
authors.lastname: Pagé
authors.forename: Chien-Chi
authors.initials: CC
authors.lastname: Lo
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Chain
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Hallam
authors.forename: Carl L
authors.initials: CL
authors.lastname: Hansen
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D005838:Genotype; D019015:Geologic Sediments / Q000382:microbiology; D006801:Humans; D057446:Hydrodynamics; D007091:Image Processing, Computer-Assisted; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation* / Q000379:methods*; D008856:Microscopy, Fluorescence; D008969:Molecular Sequence Data; D009055:Mouth / Q000382:microbiology; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013501:Surface-Active Agents; D017155:Wettability
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D013501:Surface-Active Agents