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Volumn 6, Issue , 2016, Pages

Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BETA GLUCOSIDASE; FLUORESCENT DYE; OIL; RNA 16S; SEA WATER; WATER;

EID: 84959387605     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep22259     Document Type: Article
Times cited : (32)

References (51)
  • 1
    • 79251494754 scopus 로고    scopus 로고
    • Enzymes and bioconversions of industrial, pharmaceutical, and biotechnological significance
    • Sanchez, S. & Demain, A. L. Enzymes and bioconversions of industrial, pharmaceutical, and biotechnological significance. Org. Process. Res. Dev. 15, 224-230 (2011).
    • (2011) Org. Process. Res. Dev. , vol.15 , pp. 224-230
    • Sanchez, S.1    Demain, A.L.2
  • 2
    • 10944226351 scopus 로고    scopus 로고
    • Metagenomics: Genomic analysis of microbial communities
    • Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525-552 (2004).
    • (2004) Annu. Rev. Genet. , vol.38 , pp. 525-552
    • Riesenfeld, C.S.1    Schloss, P.D.2    Handelsman, J.3
  • 3
    • 84859627968 scopus 로고    scopus 로고
    • Biocatalysts and small molecule products from metagenomic studies
    • Iqbal, H. A., Feng, Z. & Brady, S. F. Biocatalysts and small molecule products from metagenomic studies. Curr. Opin. Chem. Biol. 16, 109-116 (2012).
    • (2012) Curr. Opin. Chem. Biol. , vol.16 , pp. 109-116
    • Iqbal, H.A.1    Feng, Z.2    Brady, S.F.3
  • 4
    • 19144366814 scopus 로고    scopus 로고
    • Metagenomics and industrial applications
    • Lorenz, P. & Eck, J. Metagenomics and industrial applications. Nat. Rev. Microbiol. 3, 510- 516 (2005).
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 510-516
    • Lorenz, P.1    Eck, J.2
  • 5
    • 70449727646 scopus 로고    scopus 로고
    • Functional metagenomics for enzyme discovery: Challenges to efficient screening
    • Uchiyama, T. & Miyazaki, K. Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr. Opin. Biotechnol. 20, 616-622 (2009).
    • (2009) Curr. Opin. Biotechnol. , vol.20 , pp. 616-622
    • Uchiyama, T.1    Miyazaki, K.2
  • 6
    • 84856496549 scopus 로고    scopus 로고
    • Next generation sequencing and bioinformatic bottlenecks: The current state of metagenomic data analysis
    • Scholz, M. B., Lo, C. C. & Chain, P. S. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 23, 9- 15 (2012).
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 9-15
    • Scholz, M.B.1    Lo, C.C.2    Chain, P.S.3
  • 7
    • 64749114328 scopus 로고    scopus 로고
    • Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries
    • Waschkowitz, T., Rockstroh, S. & Daniel, R. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl. Environ. Microbiol. 75, 2506-2516 (2011).
    • (2011) Appl. Environ. Microbiol. , vol.75 , pp. 2506-2516
    • Waschkowitz, T.1    Rockstroh, S.2    Daniel, R.3
  • 8
    • 34547540925 scopus 로고    scopus 로고
    • Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
    • Marcy, Y. et al. 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 (2007).
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 11889-11894
    • Marcy, Y.1
  • 9
    • 80052479893 scopus 로고    scopus 로고
    • Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean
    • Swan, B. K. et al. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296- 1300 (2011).
    • (2011) Science , vol.333 , pp. 1296-1300
    • Swan, B.K.1
  • 10
    • 84861342496 scopus 로고    scopus 로고
    • Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage
    • Dupont, C. L. et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 6, 1186- 1199 (2012).
    • (2012) ISME J. , vol.6 , pp. 1186-1199
    • Dupont, C.L.1
  • 11
    • 84879517803 scopus 로고    scopus 로고
    • Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum
    • McLean, J. S. et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc. Natl. Acad. Sci. USA 110, E2390- 2399 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. E2390-2399
    • McLean, J.S.1
  • 12
    • 84881138595 scopus 로고    scopus 로고
    • Insights into the phylogeny and coding potential of microbial dark matter
    • Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431- 437 (2013).
    • (2013) Nature , vol.499 , pp. 431-437
    • Rinke, C.1
  • 13
    • 84893542053 scopus 로고    scopus 로고
    • An environmental bacterial taxon with a large and distinct metabolic repertoire
    • Wilson, M. C. et al. An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506, 58-62 (2014).
    • (2014) Nature , vol.506 , pp. 58-62
    • Wilson, M.C.1
  • 14
    • 0029832083 scopus 로고    scopus 로고
    • Flow cytometry and cell sorting of heterogeneous microbial populations: The importance of single-cell analyses
    • Davey, H. M. & Kell, D. B. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiol. Rev. 60, 641- 696 (1996).
    • (1996) Microbiol. Rev. , vol.60 , pp. 641-696
    • Davey, H.M.1    Kell, D.B.2
  • 15
    • 77953254182 scopus 로고    scopus 로고
    • Functional single-cell analyses: Flow cytometry and cell sorting of microbial populations and communities
    • Muller, S. & Nebe-von-Caron, G. Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol. Rev. 34, 554- 587 (2010).
    • (2010) FEMS Microbiol. Rev. , vol.34 , pp. 554-587
    • Muller, S.1    Nebe-Von-Caron, G.2
  • 16
    • 29244468315 scopus 로고    scopus 로고
    • Single-cell microarray for analyzing cellular response
    • Yamamura, S. et al. Single-cell microarray for analyzing cellular response. Anal. Chem. 77, 8050-8056 (2005).
    • (2005) Anal. Chem. , vol.77 , pp. 8050-8056
    • Yamamura, S.1
  • 17
    • 84873693589 scopus 로고    scopus 로고
    • An automated system for high-throughput single cell-based breeding
    • Yoshimoto, N. et al. An automated system for high-throughput single cell-based breeding. Sci. Rep. 3, 1191 (2013).
    • (2013) Sci. Rep. , vol.3 , pp. 1191
    • Yoshimoto, N.1
  • 18
    • 0031854986 scopus 로고    scopus 로고
    • Man-made cell-like compartments for molecular evolution
    • Tawfik, D. S. & Griffiths, A. D. Man-made cell-like compartments for molecular evolution. Nat. Biotechnol. 16, 652-656 (1998).
    • (1998) Nat. Biotechnol. , vol.16 , pp. 652-656
    • Tawfik, D.S.1    Griffiths, A.D.2
  • 19
    • 28844487473 scopus 로고    scopus 로고
    • High-throughput screening of enzyme libraries: In vitro evolution of a β-galactosidase by fluorescenceactivated sorting of double emulsions
    • Mastrobattista, E. et al. High-throughput screening of enzyme libraries: in vitro evolution of a β-galactosidase by fluorescenceactivated sorting of double emulsions. Chem. Biol. 12, 1291-1300 (2005).
    • (2005) Chem. Biol. , vol.12 , pp. 1291-1300
    • Mastrobattista, E.1
  • 20
    • 77749270677 scopus 로고    scopus 로고
    • Ultrahigh-throughput screening in drop-based microfluidics for directed evolution
    • Agresti, J. J. et al. Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc. Natl. Acad. Sci. USA 107, 4004-4009 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 4004-4009
    • Agresti, J.J.1
  • 21
    • 0037455351 scopus 로고    scopus 로고
    • Formation of dispersions using "flow focusing" in microchannels
    • Anna, S. L., Bontoux, N. & Stone, H. A. Formation of dispersions using "flow focusing" in microchannels. Appl. Phys. Lett. 82, 364-366 (2003).
    • (2003) Appl. Phys. Lett. , vol.82 , pp. 364-366
    • Anna, S.L.1    Bontoux, N.2    Stone, H.A.3
  • 22
    • 80052329244 scopus 로고    scopus 로고
    • Microfluidic active sorting of DNA molecules labeled with single quantum dots using flow switching by a hydrogel sol-gel transition
    • Haneoka et al. Microfluidic active sorting of DNA molecules labeled with single quantum dots using flow switching by a hydrogel sol-gel transition. Sensor Actuat. B-Chem. 159, 314- 320 (2011).
    • (2011) Sensor Actuat. B-Chem. , vol.159 , pp. 314-320
    • Haneoka1
  • 23
    • 34547373189 scopus 로고    scopus 로고
    • Screening of the effect of surface energy of microchannels on microfluidic emulsification
    • Li, W. et al. Screening of the effect of surface energy of microchannels on microfluidic emulsification. Langmuir 23, 8010- 8014 (2007).
    • (2007) Langmuir , vol.23 , pp. 8010-8014
    • Li, W.1
  • 24
    • 18344396798 scopus 로고    scopus 로고
    • Comprehensive human genome amplification using multiple displacement amplification
    • Dean, F. B. et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. USA 99, 5261- 5266 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5261-5266
    • Dean, F.B.1
  • 25
    • 84936160214 scopus 로고    scopus 로고
    • Random-primed, Phi29 DNA polymerase-based whole genome amplification
    • Nelson, J. R. Random-primed, Phi29 DNA polymerase-based whole genome amplification. Curr. Protoc. Mol. Biol. 105, 15.13.1-15.13.16 (2014).
    • (2014) Curr. Protoc. Mol. Biol. , vol.105 , pp. 15131-151316
    • Nelson, J.R.1
  • 27
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477 (2012).
    • (2012) J. Comput. Biol. , vol.19 , pp. 455-477
    • Bankevich, A.1
  • 28
    • 84891763855 scopus 로고    scopus 로고
    • The Carbohydrate-active enzymes database (CAZy) in 2013
    • Lombard, V. et al. The Carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490-D495 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D490-D495
    • Lombard, V.1
  • 29
    • 77955563148 scopus 로고    scopus 로고
    • Microdroplets in microfluidics: An evolving platform for discoveries in chemistry and biology
    • Theberge, A. B. et al. Microdroplets in microfluidics: an evolving platform for discoveries in chemistry and biology. Angew Chem. Int. Ed. Engl. 49, 5846- 5868 (2010).
    • (2010) Angew Chem. Int. Ed. Engl. , vol.49 , pp. 5846-5868
    • Theberge, A.B.1
  • 30
    • 84862212456 scopus 로고    scopus 로고
    • Droplet microfluidics for high-throughput biological assays
    • Guo, M. T., Rotem, A., Heyman, J. A. & Weitz, D. A. Droplet microfluidics for high-throughput biological assays. Lab Chip 12, 2146- 2155 (2012).
    • (2012) Lab Chip , vol.12 , pp. 2146-2155
    • Guo, M.T.1    Rotem, A.2    Heyman, J.A.3    Weitz, D.A.4
  • 31
    • 84919883694 scopus 로고    scopus 로고
    • Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms
    • Najah, M. et al. Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms. Chem. Biol. 21, 1722- 1732 (2014).
    • (2014) Chem. Biol. , vol.21 , pp. 1722-1732
    • Najah, M.1
  • 32
    • 84876122754 scopus 로고    scopus 로고
    • The future is now: Single-cell genomics of bacteria and archaea
    • Blainey, P. C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407-427 (2013).
    • (2013) FEMS Microbiol. Rev. , vol.37 , pp. 407-427
    • Blainey, P.C.1
  • 33
    • 84920645442 scopus 로고    scopus 로고
    • A quantitative comparison of single-cell whole genome amplification methods
    • de Bourcy, C. F. et al. A quantitative comparison of single-cell whole genome amplification methods. PLoS ONE 9, e105585 (2014).
    • (2014) PLoS ONE , vol.9
    • De Bourcy, C.F.1
  • 34
    • 0036448608 scopus 로고    scopus 로고
    • Microbial β-glucosidases: Cloning, properties, and applications
    • Bhatia, Y., Mishra, S. & Bisaria, V. S. Microbial β-glucosidases: cloning, properties, and applications. Crit. Rev. Biotechnol. 22, 375-407 (2002).
    • (2002) Crit. Rev. Biotechnol. , vol.22 , pp. 375-407
    • Bhatia, Y.1    Mishra, S.2    Bisaria, V.S.3
  • 36
    • 0027202563 scopus 로고
    • An in situ study of beta-glucosidase activity in normal and Gaucher fibroblasts with fluorogenic probes
    • Kohen, E. et al. An in situ study of beta-glucosidase activity in normal and Gaucher fibroblasts with fluorogenic probes. Cell Biochem. Funct. 11, 167-177 (1993).
    • (1993) Cell Biochem. Funct. , vol.11 , pp. 167-177
    • Kohen, E.1
  • 37
    • 0031149907 scopus 로고    scopus 로고
    • A flow cytometric assay for lysosomal glucocerebrosidase
    • van Es, H. H., Veldwijk, M., Havenga, M. & Valerio, D. A flow cytometric assay for lysosomal glucocerebrosidase. Anal. Biochem. 247, 268-271 (1997).
    • (1997) Anal. Biochem. , vol.247 , pp. 268-271
    • Van Es, H.H.1    Veldwijk, M.2    Havenga, M.3    Valerio, D.4
  • 38
    • 46149091744 scopus 로고    scopus 로고
    • Drop-based microfluidic devices for encapsulation of single cells
    • Koster, S. et al. Drop-based microfluidic devices for encapsulation of single cells. Lab Chip 8, 1110-1115 (2008).
    • (2008) Lab Chip , vol.8 , pp. 1110-1115
    • Koster, S.1
  • 39
    • 34547468984 scopus 로고    scopus 로고
    • Screening and characterization of an enzyme with β-glucosidase activity from environmental DNA
    • Kim, S. J. et al. Screening and characterization of an enzyme with β-glucosidase activity from environmental DNA. J. Microbiol. Biotechnol. 17, 905-912 (2007).
    • (2007) J. Microbiol. Biotechnol. , vol.17 , pp. 905-912
    • Kim, S.J.1
  • 40
    • 71049146248 scopus 로고    scopus 로고
    • Characterization of a novel β-glucosidase-like activity from a soil metagenome
    • Jiang, C. et al. Characterization of a novel β-glucosidase-like activity from a soil metagenome. J. Microbiol. 47, 542-548 (2009).
    • (2009) J. Microbiol. , vol.47 , pp. 542-548
    • Jiang, C.1
  • 41
    • 75449115609 scopus 로고    scopus 로고
    • Identification of a metagenome-derived β-glucosidase from bioreactor contents
    • Jiang, C. et al. Identification of a metagenome-derived β-glucosidase from bioreactor contents. J. Mol. Catal. B Enzym. 63, 11-16 (2010).
    • (2010) J. Mol. Catal. B Enzym. , vol.63 , pp. 11-16
    • Jiang, C.1
  • 42
    • 84880056854 scopus 로고    scopus 로고
    • Characterization of a novel β-glucosidase from a compost microbial metagenome with strong transglycosylation activity
    • Uchiyama, T., Miyazaki, K. & Yaoi, K. Characterization of a novel β-glucosidase from a compost microbial metagenome with strong transglycosylation activity. J. Biol. Chem. 288, 18325-18334 (2013).
    • (2013) J. Biol. Chem. , vol.288 , pp. 18325-18334
    • Uchiyama, T.1    Miyazaki, K.2    Yaoi, K.3
  • 43
    • 84893020696 scopus 로고    scopus 로고
    • High-throughput screening for industrial enzyme production hosts by droplet microfluidics
    • Sjostrom, S. L. et al. High-throughput screening for industrial enzyme production hosts by droplet microfluidics. Lab Chip 14, 806-813 (2014).
    • (2014) Lab Chip , vol.14 , pp. 806-813
    • Sjostrom, S.L.1
  • 44
    • 84865492433 scopus 로고    scopus 로고
    • Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution
    • Kintses, B. et al. Picoliter cell lysate assays in microfluidic droplet compartments for directed enzyme evolution. Chem. Biol. 19, 1001-1009 (2012).
    • (2012) Chem. Biol. , vol.19 , pp. 1001-1009
    • Kintses, B.1
  • 45
    • 84856734748 scopus 로고    scopus 로고
    • Self-regulated, droplet-based sample chopper for microfluidic absorbance detection
    • Deal, K. S. & Easley, C. J. Self-regulated, droplet-based sample chopper for microfluidic absorbance detection. Anal. Chem. 84, 1510-1516 (2012).
    • (2012) Anal. Chem. , vol.84 , pp. 1510-1516
    • Deal, K.S.1    Easley, C.J.2
  • 46
    • 84877322586 scopus 로고    scopus 로고
    • A fully unsupervised compartment-on-demand platform for precise nanoliter assays of time-dependent steady-state enzyme kinetics and inhibition
    • Gielen, F. et al. A fully unsupervised compartment-on-demand platform for precise nanoliter assays of time-dependent steady-state enzyme kinetics and inhibition. Anal. Chem. 85, 4761-4769 (2013).
    • (2013) Anal. Chem. , vol.85 , pp. 4761-4769
    • Gielen, F.1
  • 47
    • 84885000015 scopus 로고    scopus 로고
    • Analysis of intracellular enzyme activity by surface enhanced Raman scattering
    • Stevenson, R. et al. Analysis of intracellular enzyme activity by surface enhanced Raman scattering. Analyst 138, 6331-6336 (2013).
    • (2013) Analyst , vol.138 , pp. 6331-6336
    • Stevenson, R.1
  • 48
    • 67650762821 scopus 로고    scopus 로고
    • Measuring rapid enzymatic kinetics by electrochemical method in droplet-based microfluidic devices with pneumatic valves
    • Han, Z., Li, W., Huang, Y. & Zheng, B. Measuring rapid enzymatic kinetics by electrochemical method in droplet-based microfluidic devices with pneumatic valves. Anal. Chem. 81, 5840-5845 (2009).
    • (2009) Anal. Chem. , vol.81 , pp. 5840-5845
    • Han, Z.1    Li, W.2    Huang, Y.3    Zheng, B.4
  • 49
    • 84861212790 scopus 로고    scopus 로고
    • A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities
    • Leung, K. et al. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl. Acad. Sci. USA 109, 7665-7670 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 7665-7670
    • Leung, K.1
  • 50
    • 84884572248 scopus 로고    scopus 로고
    • Optofluidic cell selection from complex microbial communities for single-genome analysis
    • Landry, Z. C., Giovanonni, S. J., Quake, S. R. & Blainey, P. C. Optofluidic cell selection from complex microbial communities for single-genome analysis. Methods Enzymol. 531, 61-90 (2013).
    • (2013) Methods Enzymol. , vol.531 , pp. 61-90
    • Landry, Z.C.1    Giovanonni, S.J.2    Quake, S.R.3    Blainey, P.C.4
  • 51
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. 7188-7196
    • Pruesse, E.1


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