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Volumn 40, Issue 2, 2000, Pages 111-123

Competitive PCR-DGGE analysis of bacterial mixturesan internal standard and an appraisal of template enumeration accuracy

Author keywords

16S rDNA; Competition; Culture independent enumeration; DGGE

Indexed keywords

RNA 16S;

EID: 0343416244     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(99)00126-8     Document Type: Article
Times cited : (60)

References (39)
  • 1
    • 0025294528 scopus 로고
    • Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations
    • Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1990;1919-1925.
    • (1990) Appl. Environ. Microbiol. , vol.56 , pp. 1919-1925
    • Amann, R.I.1    Binder, B.J.2    Olson, R.J.3    Chisholm, S.W.4    Devereux, R.5    Stahl, D.A.6
  • 2
    • 0024095388 scopus 로고
    • Reductive dissolution of iron-oxides by Pseudomonas sp. 200
    • Arnold R.G., DiChristina T.J., Hoffmann M.R. Reductive dissolution of iron-oxides by Pseudomonas sp. 200. Biotechnol. Bioeng. 32:1988;01081-01096.
    • (1988) Biotechnol. Bioeng. , vol.32 , pp. 01081-01096
    • Arnold, R.G.1    Dichristina, T.J.2    Hoffmann, M.R.3
  • 4
    • 2642590009 scopus 로고    scopus 로고
    • Higher sensitivity of denaturing gradient gel electrophoresis than sequencing in the detection of mutations in DNA from tumor samples
    • Carcia-Delgado M., Gonzalez-Navarro C.J., Napal M.C Baldonado C., Vizmanos J.L., Gullon A. Higher sensitivity of denaturing gradient gel electrophoresis than sequencing in the detection of mutations in DNA from tumor samples. Biotechniques. 24:1998;72-76.
    • (1998) Biotechniques , vol.24 , pp. 72-76
    • Carcia-Delgado, M.1    Gonzalez-Navarro, C.J.2    Napal M.c Baldonado, C.3    Vizmanos, J.L.4    Gullon, A.5
  • 5
    • 0031149569 scopus 로고    scopus 로고
    • Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries
    • Chandler D.P., Fredrickson J.K., Brockman F.J. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6:1997;475-482.
    • (1997) Mol. Ecol. , vol.6 , pp. 475-482
    • Chandler, D.P.1    Fredrickson, J.K.2    Brockman, F.J.3
  • 6
    • 0032432372 scopus 로고    scopus 로고
    • Redefining relativity: Quantitative PCR at low template concentrations for industrial and environmental microbiology
    • Chandler D.P. Redefining relativity: quantitative PCR at low template concentrations for industrial and environmental microbiology. J. Ind. Microbiol. Biotechnol. 21:1998;128-140.
    • (1998) J. Ind. Microbiol. Biotechnol. , vol.21 , pp. 128-140
    • Chandler, D.P.1
  • 9
    • 0031791939 scopus 로고    scopus 로고
    • Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns
    • Duineveld B.M., Rosado A.S., van Elsas J.D., van Veen J.A. Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl. Environ. Microbiol. 64:1998;4950-4957.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4950-4957
    • Duineveld, B.M.1    Rosado, A.S.2    Van Elsas, J.D.3    Van Veen, J.A.4
  • 10
    • 0029032318 scopus 로고
    • Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species
    • Farrelly V., Rainey F.A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:1995;2798-2801.
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 2798-2801
    • Farrelly, V.1    Rainey, F.A.2    Stackebrandt, E.3
  • 11
    • 0031732597 scopus 로고    scopus 로고
    • Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints
    • Felske A., Akkermans A.D., De Vos W.M. Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl. Environ. Microbiol. 64:1998;4581-4587.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4581-4587
    • Felske, A.1    Akkermans, A.D.2    De Vos, W.M.3
  • 12
    • 0033135928 scopus 로고    scopus 로고
    • Reviewing the DA001-files: A 16S rRNA chase on suspect #X99967, a Bacillus and Dutch underground activist
    • Felske A. Reviewing the DA001-files: a 16S rRNA chase on suspect #X99967, a Bacillus and Dutch underground activist. J. Microbiol. Methods. 36:1999;77-93.
    • (1999) J. Microbiol. Methods , vol.36 , pp. 77-93
    • Felske, A.1
  • 13
    • 0031662785 scopus 로고    scopus 로고
    • Two intracellular symbiotic bacteria from the mulberry psyllid Anomoneura mori (Insecta Homoptera)
    • Fukatsu T., Nikoh N. Two intracellular symbiotic bacteria from the mulberry psyllid Anomoneura mori (Insecta Homoptera). Appl. Environ. Microbiol. 64:1998;3599-3606.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3599-3606
    • Fukatsu, T.1    Nikoh, N.2
  • 14
    • 0031842162 scopus 로고    scopus 로고
    • Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region
    • Hansen M.C., Tolker-Nielsen T., Givskov M., Molin S. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26:1998;141-149.
    • (1998) FEMS Microbiol. Ecol. , vol.26 , pp. 141-149
    • Hansen, M.C.1    Tolker-Nielsen, T.2    Givskov, M.3    Molin, S.4
  • 15
    • 0030739128 scopus 로고    scopus 로고
    • Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients
    • Heuer H., Krsek M., Baker P., Smalla K., Wellington E.M. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl. Environ. Microbiol. 63:1997;3233-3241.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 3233-3241
    • Heuer, H.1    Krsek, M.2    Baker, P.3    Smalla, K.4    Wellington, E.M.5
  • 16
    • 0030901922 scopus 로고    scopus 로고
    • Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes using denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S rDNA fragments
    • Kowalchuk G.A., Stephen J.R., De Boer W., Prosser J.I., Embley T.M., Woldendorp J.W. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes using denaturing gradient gel electrophoresis and sequencing of PCR amplified 16S rDNA fragments. Appl. Environ. Microbiol. 63:1997;1489-1497.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 1489-1497
    • Kowalchuk, G.A.1    Stephen, J.R.2    De Boer, W.3    Prosser, J.I.4    Embley, T.M.5    Woldendorp, J.W.6
  • 17
    • 0030754258 scopus 로고    scopus 로고
    • Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18s rDNA
    • Kowalchuk G.A., Gerards S., Woldendorp J.W. Detection and characterization of fungal infections of Ammophila arenaria (marram grass) roots by denaturing gradient gel electrophoresis of specifically amplified 18s rDNA. Appl. Environ. Microbiol. 63:1997;3858-3865.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 3858-3865
    • Kowalchuk, G.A.1    Gerards, S.2    Woldendorp, J.W.3
  • 19
    • 0023504650 scopus 로고
    • Adsorption of DNA to sand and variable degradation rates of adsorbed DNA
    • Lorenz M.G., Wackernagel W. Adsorption of DNA to sand and variable degradation rates of adsorbed DNA. Appl. Environ. Microbiol. 53:1987;2948-2952.
    • (1987) Appl. Environ. Microbiol. , vol.53 , pp. 2948-2952
    • Lorenz, M.G.1    Wackernagel, W.2
  • 21
    • 0031745941 scopus 로고    scopus 로고
    • Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA
    • (Published erratum appears in: Appl. Environ. Microbiol. 1998. 64, 2333).
    • Marchesi J.R., Sato T., Weightman A.J., Martin T.A., Fry J.C., Hiom S.J., Dymock D., Wade W.G. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64:1998;795-799. (Published erratum appears in: Appl. Environ. Microbiol. 1998. 64, 2333).
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 795-799
    • Marchesi, J.R.1    Sato, T.2    Weightman, A.J.3    Martin, T.A.4    Fry, J.C.5    Hiom, S.J.6    Dymock, D.7    Wade, W.G.8
  • 24
    • 0027460328 scopus 로고
    • Profiling of microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA
    • Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:1993;695-700.
    • (1993) Appl. Environ. Microbiol. , vol.59 , pp. 695-700
    • Muyzer, G.1    De Waal, E.C.2    Uitterlinden, A.G.3
  • 25
    • 0031959006 scopus 로고    scopus 로고
    • Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
    • Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek. 73:1998;127-141.
    • (1998) Antonie Van Leeuwenhoek , vol.73 , pp. 127-141
    • Muyzer, G.1    Smalla, K.2
  • 26
    • 0031435214 scopus 로고    scopus 로고
    • Differentiation and quantification of the cereal eyespot fungi Tapesia yallundae and Tapesia acuformis using a PCR assay
    • Nicholson P., Rezanoor H.N., Simpson D.R., Joyce D. Differentiation and quantification of the cereal eyespot fungi Tapesia yallundae and Tapesia acuformis using a PCR assay. Plant Pathol. 46:1997;842-856.
    • (1997) Plant Pathol. , vol.46 , pp. 842-856
    • Nicholson, P.1    Rezanoor, H.N.2    Simpson, D.R.3    Joyce, D.4
  • 27
    • 0019503845 scopus 로고
    • Genetic mapping of chromosomal determinants for the production of exopolysaccharide alginate in a Pseudomonas aeruginosa cystic fibrosis isolate
    • Ohman D.E., Chakrabarty A.M. Genetic mapping of chromosomal determinants for the production of exopolysaccharide alginate in a Pseudomonas aeruginosa cystic fibrosis isolate. Infect. Immun. 33:1981;124-148.
    • (1981) Infect. Immun. , vol.33 , pp. 124-148
    • Ohman, D.E.1    Chakrabarty, A.M.2
  • 28
    • 0031711754 scopus 로고    scopus 로고
    • Bias in template-to-product ratios in multitemplate PCR
    • Polz M.F., Cavanaugh C.M. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:1998;3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 29
    • 85045497403 scopus 로고
    • Rapid quantitation by PCR of endomycorrhizal fungi
    • Simon L., Levesque R.C., Lalonde M. Rapid quantitation by PCR of endomycorrhizal fungi. PCR Methods Appl. 2:1992;76-80.
    • (1992) PCR Methods Appl. , vol.2 , pp. 76-80
    • Simon, L.1    Levesque, R.C.2    Lalonde, M.3
  • 30
    • 0001548496 scopus 로고
    • A comparison of direct and plate counting techniques for the quantitative estimation of soil microorganisms
    • Skinner F.A., Jones P.C.T., Mollison J.E. A comparison of direct and plate counting techniques for the quantitative estimation of soil microorganisms. J. Gen. Microbiol. 6:1952;261-271.
    • (1952) J. Gen. Microbiol. , vol.6 , pp. 261-271
    • Skinner, F.A.1    Jones, P.C.T.2    Mollison, J.E.3
  • 31
    • 0000023099 scopus 로고
    • Attachment of a 4-base pair G+C rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes
    • Sheffield V.C., Cox D.R., Lerman L.S., Myers R.M. Attachment of a 4-base pair G+C rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA. 86:1989;232-236.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 232-236
    • Sheffield, V.C.1    Cox, D.R.2    Lerman, L.S.3    Myers, R.M.4
  • 32
    • 0033108163 scopus 로고    scopus 로고
    • Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge
    • Snaidr J., Fuchs B., Wallner G., Wagner M., Schleifer K.-H., Amann R. Phylogeny and in situ identification of a morphologically conspicuous bacterium, Candidatus Magnospira bakii, present at very low frequency in activated sludge. Environ. Microbiol. 1:1999;125-135.
    • (1999) Environ. Microbiol. , vol.1 , pp. 125-135
    • Snaidr, J.1    Fuchs, B.2    Wallner, G.3    Wagner, M.4    Schleifer, K.-H.5    Amann, R.6
  • 33
    • 0031904158 scopus 로고    scopus 로고
    • Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing
    • Stephen J.R., Kowalchuk G.A., Bruns M.-A.V., McCaig A.E., Phillips C.J., Embley T.M., Prosser J.I. Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ. Microbiol. 64:1998;2958-2965.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 2958-2965
    • Stephen, J.R.1    Kowalchuk, G.A.2    Bruns, M.-A.V.3    McCaig, A.E.4    Phillips, C.J.5    Embley, T.M.6    Prosser, J.I.7
  • 35
    • 0030067991 scopus 로고    scopus 로고
    • Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
    • Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:1996;625-630.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 36
    • 0032219204 scopus 로고    scopus 로고
    • Novel techniques for analysing microbial diversity in natural and perturbed environments
    • Torsvik V., Daae F.L., Sandaa R.A., Ovreas L. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64:1998;53-62.
    • (1998) J. Biotechnol. , vol.64 , pp. 53-62
    • Torsvik, V.1    Daae, F.L.2    Sandaa, R.A.3    Ovreas, L.4
  • 38
    • 0031734089 scopus 로고    scopus 로고
    • Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge
    • Watanabe K., Teramoto M., Futamata H., Harayama S. Molecular detection, isolation, and physiological characterization of functionally dominant phenol-degrading bacteria in activated sludge. Appl. Environ. Microbiol. 64:1998;4396-4402.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 4396-4402
    • Watanabe, K.1    Teramoto, M.2    Futamata, H.3    Harayama, S.4
  • 39
    • 0003128545 scopus 로고
    • Clostridium
    • A.L. Sonenshein, J.A. Hoch, & R. Losick. Washington, DC: American Society for Microbiology
    • Young C.C., Cole S.T. Clostridium. Sonenshein A.L., Hoch J.A., Losick R. Bacillus subtilis and Other Gram-positive Organisms. 1993;35-52 American Society for Microbiology, Washington, DC.
    • (1993) Bacillus Subtilis and Other Gram-positive Organisms , pp. 35-52
    • Young, C.C.1    Cole, S.T.2


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