메뉴 건너뛰기




Volumn 10, Issue 2, 2016, Pages 427-436

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

Author keywords

[No Author keywords available]

Indexed keywords

CELLS AND CELL COMPONENTS; GENE TRANSFER; GENETIC ANALYSIS; GENETIC MARKER; MICROBIAL COMMUNITY; PHYLOGENETICS; POLYMERASE CHAIN REACTION; SULFATE-REDUCING BACTERIUM;

EID: 84955180101     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2015.124     Document Type: Article
Times cited : (158)

References (38)
  • 2
    • 0242384034 scopus 로고    scopus 로고
    • Review and re-analysis of domain-specific 16 S primers
    • Baker GC, Smith JJ, Cowan DA (2003). Review and re-analysis of domain-specific 16 S primers. J Microbiol Methods 55: 541-555.
    • (2003) J Microbiol Methods , vol.55 , pp. 541-555
    • Baker, G.C.1    Smith, J.J.2    Cowan, D.A.3
  • 3
    • 84907020140 scopus 로고    scopus 로고
    • Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammoniaoxidizing bacteria in activated sludge
    • Baptista JDC, Lunn M, Davenport RJ, Swan DL, Read LF, Brown MR et al. (2014). Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammoniaoxidizing bacteria in activated sludge. Appl Environ Microbiol 80: 5901-5910.
    • (2014) Appl Environ Microbiol , vol.80 , pp. 5901-5910
    • Baptista, J.D.C.1    Lunn, M.2    Davenport, R.J.3    Swan, D.L.4    Read, L.F.5    Brown, M.R.6
  • 4
    • 84871649308 scopus 로고    scopus 로고
    • Genomic mining for novel FADH2-dependent halogenases in marine sponge-associated microbial consortia
    • Bayer K, Scheuermayer M, Fieseler L, Hentschel U (2013). Genomic mining for novel FADH2-dependent halogenases in marine sponge-associated microbial consortia. Mar Biotechnol 15: 63-72.
    • (2013) Mar Biotechnol , vol.15 , pp. 63-72
    • Bayer, K.1    Scheuermayer, M.2    Fieseler, L.3    Hentschel, U.4
  • 6
    • 2642535144 scopus 로고    scopus 로고
    • Substitution of 3'-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays
    • Cradic KW, Wells JE, Allen L, Kruckeberg KE, Singh RJ, Grebe SKG (2004). Substitution of 3'-phosphate cap with a carbon-based blocker reduces the possibility of fluorescence resonance energy transfer probe failure in real-time PCR assays. Clin Chem 50: 1080-1082.
    • (2004) Clin Chem , vol.50 , pp. 1080-1082
    • Cradic, K.W.1    Wells, J.E.2    Allen, L.3    Kruckeberg, K.E.4    Singh, R.J.5    Grebe, S.K.G.6
  • 8
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 9
    • 0038062821 scopus 로고    scopus 로고
    • Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm
    • Gieseke A, Bjerrum L, Wagner M, Amann R (2003). Structure and activity of multiple nitrifying bacterial populations co-existing in a biofilm. Environ Microbiol 5: 355-369.
    • (2003) Environ Microbiol , vol.5 , pp. 355-369
    • Gieseke, A.1    Bjerrum, L.2    Wagner, M.3    Amann, R.4
  • 10
    • 77951520879 scopus 로고    scopus 로고
    • Nested PCR and new primers for analysis of sulfate-reducing bacteria in low-cell-biomass environments
    • Giloteaux L, Goñi-Urriza M, Duran R (2010). Nested PCR and new primers for analysis of sulfate-reducing bacteria in low-cell-biomass environments. Appl Environ Microbiol 76: 2856-2865.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 2856-2865
    • Giloteaux, L.1    Goñi-Urriza, M.2    Duran, R.3
  • 11
    • 0025815236 scopus 로고
    • Estimation of polyacrylamide gel pore size from Ferguson plots of linear DNA fragments. II. Comparison of gels with different crosslinker concentrations, added agarose and added linear polyacrylamide
    • Holmes DL, Stellwagen NC (1991). Estimation of polyacrylamide gel pore size from Ferguson plots of linear DNA fragments. II. Comparison of gels with different crosslinker concentrations, added agarose and added linear polyacrylamide. Electrophoresis 12: 612-619.
    • (1991) Electrophoresis , vol.12 , pp. 612-619
    • Holmes, D.L.1    Stellwagen, N.C.2
  • 13
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • Stackebrandt E, Goodfellow M (eds). Chinchester, UK: Wiley
    • Lane DJ (1991). 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds). Nucleic Acid Techniques in Bacterial Systemantics. Chinchester, UK: Wiley, pp 115-175.
    • (1991) Nucleic Acid Techniques in Bacterial Systemantics , pp. 115-175
    • Lane, D.J.1
  • 14
    • 0842265917 scopus 로고    scopus 로고
    • Molecular quantification of sulfate-reducing microorganisms (carrying dsrAB genes) by competitive PCR in estuarine sediments
    • Leloup J, Quillet L, Oger C, Boust D, Petit F (2004). Molecular quantification of sulfate-reducing microorganisms (carrying dsrAB genes) by competitive PCR in estuarine sediments. FEMS Microbiol Ecol 47: 207-214.
    • (2004) FEMS Microbiol Ecol , vol.47 , pp. 207-214
    • Leloup, J.1    Quillet, L.2    Oger, C.3    Boust, D.4    Petit, F.5
  • 15
    • 79960004119 scopus 로고    scopus 로고
    • Interactive Tree of Life v2: Online annotation and display of phylogenetic trees made easy
    • Letunic I, Bork P (2011). Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475-W478.
    • (2011) Nucleic Acids Res , vol.39 , pp. W475-W478
    • Letunic, I.1    Bork, P.2
  • 16
    • 78651338362 scopus 로고    scopus 로고
    • An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction
    • Liu J, Li J, Feng L, Cao H, Cui Z (2011). An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction. J Microbiol 48: 728-733.
    • (2011) J Microbiol , vol.48 , pp. 728-733
    • Liu, J.1    Li, J.2    Feng, L.3    Cao, H.4    Cui, Z.5
  • 17
    • 84355163060 scopus 로고    scopus 로고
    • High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton
    • Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME et al. (2012). High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J 6: 113-123.
    • (2012) ISME J , vol.6 , pp. 113-123
    • Martinez-Garcia, M.1    Swan, B.K.2    Poulton, N.J.3    Gomez, M.L.4    Masland, D.5    Sieracki, M.E.6
  • 18
    • 84928585812 scopus 로고    scopus 로고
    • Phylogenetic and environmental diversity of DsrABtype dissimilatory (bi)sulfite reductases
    • Müller AL, Kjeldsen KU, Rattei T, Pester M, Loy A (2015). Phylogenetic and environmental diversity of DsrABtype dissimilatory (bi)sulfite reductases. ISME J 9: 1152-1165.
    • (2015) ISME J , vol.9 , pp. 1152-1165
    • Müller, A.L.1    Kjeldsen, K.U.2    Rattei, T.3    Pester, M.4    Loy, A.5
  • 19
    • 43849095105 scopus 로고    scopus 로고
    • The ecology and biotechnology of sulphate-reducing bacteria
    • Muyzer G, Stams AJM (2008). The ecology and biotechnology of sulphate-reducing bacteria. Nat Rev Microbiol 6: 441-454.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 441-454
    • Muyzer, G.1    Stams, A.J.M.2
  • 20
    • 33845342557 scopus 로고    scopus 로고
    • Microfluidic digital PCR enables multigene analysis of individual environmental bacteria
    • Ottesen EA, Hong JW, Quake SR, Leadbetter JR (2006). Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science 314: 1464-1467.
    • (2006) Science , vol.314 , pp. 1464-1467
    • Ottesen, E.A.1    Hong, J.W.2    Quake, S.R.3    Leadbetter, J.R.4
  • 21
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2- approximately maximum-likelihood trees for large alignments
    • Price MN, Dehal PS, Arkin AP (2010). FastTree 2- approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
    • (2010) PLoS One , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 22
    • 84864134721 scopus 로고    scopus 로고
    • SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
    • Pruesse E, Peplies J, Glöckner FO. (2012). SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829.
    • (2012) Bioinformatics , vol.28 , pp. 1823-1829
    • Pruesse, E.1    Peplies, J.2    Glöckner, F.O.3
  • 23
    • 84873739311 scopus 로고    scopus 로고
    • The SILVA ribosomal RNA gene database project: Improved data processing and webbased tools
    • Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and webbased tools. Nucleic Acids Res 41: D590-D596.
    • (2013) Nucleic Acids Res , vol.41 , pp. D590-D596
    • Quast, C.1    Pruesse, E.2    Yilmaz, P.3    Gerken, J.4    Schweer, T.5    Yarza, P.6
  • 24
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The european molecular biology open software suite
    • Rice P, Longden I, Bleasby A (2000). EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 25
    • 78649723307 scopus 로고    scopus 로고
    • PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification
    • Siegl A, Hentschel U (2010). PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification. Environ Microbiol Rep 2: 507-513.
    • (2010) Environ Microbiol Rep , vol.2 , pp. 507-513
    • Siegl, A.1    Hentschel, U.2
  • 26
    • 34547492897 scopus 로고    scopus 로고
    • Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    • Stepanauskas R, Sieracki ME (2007). Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci USA 104: 9052-9057.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 9052-9057
    • Stepanauskas, R.1    Sieracki, M.E.2
  • 27
    • 79959855149 scopus 로고    scopus 로고
    • Probing individual environmental bacteria for viruses by using microfluidic digital PCR
    • Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R (2011). Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science 333: 58-62.
    • (2011) Science , vol.333 , pp. 58-62
    • Tadmor, A.D.1    Ottesen, E.A.2    Leadbetter, J.R.3    Phillips, R.4
  • 28
    • 84927125749 scopus 로고    scopus 로고
    • Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells
    • Tamminen MV, Virta MPJ (2015). Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells. Front Microbiol 6: 195.
    • (2015) Front Microbiol , vol.6 , pp. 195
    • Tamminen, M.V.1    Virta, M.P.J.2
  • 30
    • 74949127401 scopus 로고    scopus 로고
    • High-throughput haplotype determination over long distances by haplotype fusion PCR and ligation haplotyping
    • Turner DJ, Hurles ME (2009). High-throughput haplotype determination over long distances by haplotype fusion PCR and ligation haplotyping. Nat Protoc 4: 1771-1783.
    • (2009) Nat Protoc , vol.4 , pp. 1771-1783
    • Turner, D.J.1    Hurles, M.E.2
  • 31
    • 81255146230 scopus 로고    scopus 로고
    • The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation
    • Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong S-H et al. (2011). The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell 44: 252-264.
    • (2011) Mol Cell , vol.44 , pp. 252-264
    • Umbarger, M.A.1    Toro, E.2    Wright, M.A.3    Porreca, G.J.4    Baù, D.5    Hong, S.-H.6
  • 32
    • 79952769971 scopus 로고    scopus 로고
    • Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
    • Valm AM, Welch JLM, Rieken CW, Hasegawa Y, Sogin ML, Oldenbourg R et al. (2011). Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci USA 108: 4152-4157.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 4152-4157
    • Valm, A.M.1    Welch, J.L.M.2    Rieken, C.W.3    Hasegawa, Y.4    Sogin, M.L.5    Oldenbourg, R.6
  • 33
    • 27644568639 scopus 로고    scopus 로고
    • Functional marker genes for identification of sulfate-reducing prokaryotes
    • Wagner M, Loy A, Klein M, Lee N, Ramsing NB, Stahl DA et al. (2005). Functional marker genes for identification of sulfate-reducing prokaryotes. Methods Enzymol 397: 469-489.
    • (2005) Methods Enzymol , vol.397 , pp. 469-489
    • Wagner, M.1    Loy, A.2    Klein, M.3    Lee, N.4    Ramsing, N.B.5    Stahl, D.A.6
  • 34
    • 0032463021 scopus 로고    scopus 로고
    • Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration
    • Wagner M, Roger AJ, Flax JL, Brusseau GA, Stahl DA (1998). Phylogeny of dissimilatory sulfite reductases supports an early origin of sulfate respiration. J Bacteriol 180: 2975-2982.
    • (1998) J Bacteriol , vol.180 , pp. 2975-2982
    • Wagner, M.1    Roger, A.J.2    Flax, J.L.3    Brusseau, G.A.4    Stahl, D.A.5
  • 35
    • 19444381961 scopus 로고    scopus 로고
    • Molecular haplotyping by linking emulsion PCR: Analysis of paraoxonase 1 haplotypes and phenotypes
    • Wetmur JG, Kumar M, Zhang L, Palomeque C, Wallenstein S, Chen J (2005). Molecular haplotyping by linking emulsion PCR: Analysis of paraoxonase 1 haplotypes and phenotypes. Nucleic Acids Res 33: 2615-2619.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2615-2619
    • Wetmur, J.G.1    Kumar, M.2    Zhang, L.3    Palomeque, C.4    Wallenstein, S.5    Chen, J.6
  • 37
    • 0024368864 scopus 로고
    • Precise gene fusion by PCR
    • Yon J, Fried M (1989). Precise gene fusion by PCR. Nucleic Acids Res 17: 4895.
    • (1989) Nucleic Acids Res , vol.17 , pp. 4895
    • Yon, J.1    Fried, M.2
  • 38
    • 77951080101 scopus 로고    scopus 로고
    • Highperformance single cell genetic analysis using microfluidic emulsion generator arrays
    • Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA (2010). Highperformance single cell genetic analysis using microfluidic emulsion generator arrays. Anal Chem 82: 3183-3190.
    • (2010) Anal Chem , vol.82 , pp. 3183-3190
    • Zeng, Y.1    Novak, R.2    Shuga, J.3    Smith, M.T.4    Mathies, R.A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.