A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 20, 2012, Pages 7665-7670

  Leung, Kaston ^a   Zahn, Hans ^a   Leaver, Timothy ^a   Konwar, Kishori M ^a   Hanson, Niels W ^a   Pagé, Antoine P ^a   Lo, Chien Chi ^b,c   Chain, Patrick S ^b,c   Hallam, Steven J ^a   Hansen, Carl L ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Droplet wetting; Environmental genomics; qPCR; Single cell analysis; Two phase flow

Indexed keywords

ARTICLE; CELL COMPARTMENTALIZATION; CELL SELECTION; COCULTURE; COMPUTER; GENE AMPLIFICATION; GENE IDENTIFICATION; GENOME; GENOME ANALYSIS; MICROBIAL COMMUNITY; MICROFLUIDICS; MICROORGANISM; NONHUMAN; PHYSICS; PRIORITY JOURNAL; PROGRAM DEVELOPMENT; TAXONOMY;

BASE SEQUENCE; DNA PRIMERS; GENOTYPE; GEOLOGIC SEDIMENTS; HUMANS; HYDRODYNAMICS; IMAGE PROCESSING, COMPUTER-ASSISTED; METAGENOME; METAGENOMICS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MICROSCOPY, FLUORESCENCE; MOLECULAR SEQUENCE DATA; MOUTH; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SURFACE-ACTIVE AGENTS; WETTABILITY;

BACTERIA (MICROORGANISMS);

EID: 84861212790     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1106752109     Document Type: Article

References (37)

1. Marcy Y, et al. (2007) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3:1702-1708. (Pubitemid 47510262)
2. White AK, et al. (2011) High-throughput microfluidic single-cell RT-qPCR. Proc Natl Acad Sci USA 108:13999-14004.
3. Tice JD, Song H, Lyon AD, Ismagilov RF (2003) Formation of droplets and mixing in multiphase microfluidics at low values of the Reynolds and the capillary numbers. Langmuir 19:9127-9133.
4. Hansen CL, Skordalakes E, Berger JM, Quake SR (2002) A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc Natl Acad Sci USA 99:16531-16536. (Pubitemid 36034007)
5. Thorsen T, Maerkl SJ, Quake SR (2002) Microfluidic large-scale integration. Science 298:580-584. (Pubitemid 35215308)
6. Xia YN, Whitesides GM (1998) Soft lithography. Annu Rev Mater Sci 28:153-184.
7. Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315:233-237. (Pubitemid 46166367)
8. Singhai A, Haynes CA, Hansen CL (2010) Microfluidic measurement of antibody-antigen binding kinetics from low-abundance samples and single cells. Anal Chem 82:8671-8679.
9. Marcy Y, et al. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104:11889-11894. (Pubitemid 47185600)
10. Fan HC, Wang J, Potanina A, Quake SR (2011) Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29:51-57.
11. Agresti JJ, et al. (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci USA 107:4004-4009.
12. Tewhey R, et al. (2009) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27:1025-1031.
13. Shih SCC, et al. (2012) Dried blood spot analysis by digital microfluidics coupled to nanoelectrospray ionization mass spectrometry. Anal Chem 84:3731-3738.
14. Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006) Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314:1464-1467. (Pubitemid 44871954)
15. Fidalgo LM, Maerkl SJ (2011) A software-programmable microfluidic device for automated biology. Lab Chip 11:1612-1619.
16. Lau BTC, Baitz CA, Dong XP, Hansen CL (2007) A complete microfluidic screening platform for rational protein crystallization. J Am Chem Soc 129:454-455. (Pubitemid 46147723)
17. Hua Z, et al. (2006) A versatile microreactor platform featuring a chemical-resistant microvalve array for addressable multiplex syntheses and assays. J Micromech Microeng 16:1433-1443. (Pubitemid 44102288)
18. Bretherton FP (1961) The motion of long bubbles in tubes. J Fluid Mech 10:166-188.
19. Baldessari F, Homsy GM, Leal LG (2007) Linear stability of a draining film squeezed between two approaching droplets. J Colloid Interface Sci 307:188-202. (Pubitemid 46275714)
20. Niu X, Gulati S, Edel JB, deMello AJ (2008) Pillar-induced droplet merging in microfluidic circuits. Lab Chip 8:1837-1841.
21. Utada AS, Fernandez-Nieves A, Stone HA, Weitz DA (2007) Dripping to jetting transitions in coflowing liquid streams. Phys Rev Lett 99:094502.
22. Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA (2010) High-performance single cell genetic analysis using microfluidic emulsion generator arrays. Anal Chem 82:3183-3190.
23. Lee C, Lee S, Shin S, Hwang S (2007) Real-time PCR determination of rRNA gene copy number: absolute and relative quantification assays with Escherichia coli. Appl Microbiol Biotechnol 78:371-376.
24. Navin N, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472:90-94.
25. StarkM, Berger S, Stamatakis A, von Mering C (2010) MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 11:461.
26. Powell S, et al. (2011) eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 40:D284-D289.
27. Huson DH, Mitra S, Ruscheweyh H-J, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res 21:1552-1560.
28. Pernthaler A, et al., ed. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA pp:7052-7057.
29. Orphan VJ (2009) Methods for unveiling cryptic microbial partnerships in nature. Curr Opin Microbiol 12:231-237.
30. Lens P, O'Flaherty V, Moran AP, Stoodley P, Mahony T, eds. (2003) Biofilms in Medicine, Industry and Environmental Biotechnology: Characteristics, Analysis and Control (IWA, London).
31. Kolenbrander PE (1988) Intergeneric coaggregation among human oral bacteria and ecology of dental plaque. Annu Rev Microbiol 42:627-656.
32. Kolenbrander PE (1989) Surface recognition among oral bacteria: Multigeneric coaggregations and their mediators. Crit Rev Microbiol 17:137-159.
33. Lancy P, Jr, Appelbaum B, Holt SC, Rosan B (1980) Quantitative in vitro assay for "corncob"formation. Infect Immun 29:663-670.
34. Valm AM, et al. (2011) Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci USA 108:4152-4157.
35. Shim J-u, et al. (2007) Control and measurement of the phase behavior of aqueous solutions using microfluidics. J Am Chem Soc 129:8825-8835.
36. Schmitz CHJ, Rowat AC, Koster S, Weitz DA (2009) Dropspots: A picoliter array in a microfluidic device. Lab Chip 9:44-49.
37. Huebner A, et al. (2009) Static microdroplet arrays: A microfluidic device for droplet trapping, incubation and release for enzymatic and cell-based assays. Lab Chip 9:692-698.