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Volumn 92, Issue 3, 2013, Pages 256-263

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis

Author keywords

DGGE artifact; Microbial diversity; Multitemplate PCR; Preferential amplification

Indexed keywords

AMPLICON; ANALYTIC METHOD; ARTICLE; ARTIFACT; BACTERIUM ISOLATE; COMMUNITY STRUCTURE; DENATURING GRADIENT GEL ELECTROPHORESIS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA GENE; SEQUENCE ANALYSIS;

EID: 84873734899     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.12.021     Document Type: Article
Times cited : (69)

References (32)
  • 1
    • 67650131351 scopus 로고    scopus 로고
    • Quantitative improvement of 16S rDNA DGGE analysis of soil bacterial community using real-time PCR
    • Ahn J.K., Kim Y., Kim T., Song H., Kang C., Ka J. Quantitative improvement of 16S rDNA DGGE analysis of soil bacterial community using real-time PCR. J. Microbiol. Methods 2009, 78:216-222.
    • (2009) J. Microbiol. Methods , vol.78 , pp. 216-222
    • Ahn, J.K.1    Kim, Y.2    Kim, T.3    Song, H.4    Kang, C.5    Ka, J.6
  • 3
    • 0141564890 scopus 로고    scopus 로고
    • Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system
    • Bodour A.A., Wang J., Brusseau M.L., Maier R.M. Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environ. Microbiol. 2003, 5:888-895.
    • (2003) Environ. Microbiol. , vol.5 , pp. 888-895
    • Bodour, A.A.1    Wang, J.2    Brusseau, M.L.3    Maier, R.M.4
  • 4
    • 0035511958 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages
    • Cocolin L., Manzano M., Cantoni C., Comi G. Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages. Appl. Environ. Microbiol. 2001, 67:5113-5121.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 5113-5121
    • Cocolin, L.1    Manzano, M.2    Cantoni, C.3    Comi, G.4
  • 5
    • 78149468119 scopus 로고    scopus 로고
    • Growth of quailbush in acidic, metalliferous desert mine tailings: effect of Azospirillum brasilense Sp6 on biomass production and rhizosphere community structure
    • de Bashan L.E., Hernandez J., Nelson K.N., Bashan Y., Maier R.M. Growth of quailbush in acidic, metalliferous desert mine tailings: effect of Azospirillum brasilense Sp6 on biomass production and rhizosphere community structure. Microb. Ecol. 2010, 60:915-927.
    • (2010) Microb. Ecol. , vol.60 , pp. 915-927
    • de Bashan, L.E.1    Hernandez, J.2    Nelson, K.N.3    Bashan, Y.4    Maier, R.M.5
  • 7
    • 0030613348 scopus 로고    scopus 로고
    • Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis
    • Ferris M.J., Ward D.M. Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 1997, 63:1375-1381.
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 1375-1381
    • Ferris, M.J.1    Ward, D.M.2
  • 8
    • 0030063913 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community
    • Ferris M.J., Muyzer G., Ward D.M. Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl. Environ. Microbiol. 1996, 62:340-346.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 340-346
    • Ferris, M.J.1    Muyzer, G.2    Ward, D.M.3
  • 9
    • 67650092738 scopus 로고    scopus 로고
    • Optimization of plant growth-promoting bacteria-assisted stabilization of mine tailings
    • Grandlic C.J., Palmer M.W., Maier R.M. Optimization of plant growth-promoting bacteria-assisted stabilization of mine tailings. Soil Biol. Biochem. 2009, 41:1734-1740.
    • (2009) Soil Biol. Biochem. , vol.41 , pp. 1734-1740
    • Grandlic, C.J.1    Palmer, M.W.2    Maier, R.M.3
  • 10
    • 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. 1998, 26:141-149.
    • (1998) FEMS Microbiol. Ecol. , vol.26 , pp. 141-149
    • Hansen, M.C.1    Tolker-Nielsen, T.2    Givskov, M.3    Molin, S.4
  • 11
    • 33947194423 scopus 로고    scopus 로고
    • Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage
    • Hong H., Pruden A., Reardon K.F. Comparison of CE-SSCP and DGGE for monitoring a complex microbial community remediating mine drainage. J. Microbiol. Methods 2007, 69:52-64.
    • (2007) J. Microbiol. Methods , vol.69 , pp. 52-64
    • Hong, H.1    Pruden, A.2    Reardon, K.F.3
  • 12
    • 1842457611 scopus 로고    scopus 로고
    • A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis
    • Janse I., Bok J., Zwart G. A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis. J. Microbiol. Methods 2004, 57:279-281.
    • (2004) J. Microbiol. Methods , vol.57 , pp. 279-281
    • Janse, I.1    Bok, J.2    Zwart, G.3
  • 13
    • 0344629203 scopus 로고    scopus 로고
    • Bias and artifacts in multitemplate polymerase chain reactions (PCR)
    • Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 2003, 96:317-323.
    • (2003) J. Biosci. Bioeng. , vol.96 , pp. 317-323
    • Kanagawa, T.1
  • 14
  • 17
    • 0037225001 scopus 로고    scopus 로고
    • Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts
    • Lueders T., Friedrich M.W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl. Environ. Microbiol. 2003, 69:320-326.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 320-326
    • Lueders, T.1    Friedrich, M.W.2
  • 19
    • 33947378663 scopus 로고    scopus 로고
    • Soil microbial community analysis using denaturing gradient gel electrophoresis
    • Nakatsu C.H. Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci. Soc. Am. J. 2007, 71:562-571.
    • (2007) Soil Sci. Soc. Am. J. , vol.71 , pp. 562-571
    • Nakatsu, C.H.1
  • 20
    • 0029796310 scopus 로고    scopus 로고
    • Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
    • Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R.I., Ludwig W., Backhaus H. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 1996, 178:5636-5643.
    • (1996) J. Bacteriol. , vol.178 , pp. 5636-5643
    • Nübel, U.1    Engelen, B.2    Felske, A.3    Snaidr, J.4    Wieshuber, A.5    Amann, R.I.6    Ludwig, W.7    Backhaus, H.8
  • 21
    • 77950805647 scopus 로고    scopus 로고
    • Nested PCR bias: a case study of Pseudomonas spp. in soil microcosms
    • Park J., Crowley D.E. Nested PCR bias: a case study of Pseudomonas spp. in soil microcosms. J. Environ. Monit. 2010, 12:985-988.
    • (2010) J. Environ. Monit. , vol.12 , pp. 985-988
    • Park, J.1    Crowley, D.E.2
  • 22
    • 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. 1998, 64:3724-3730.
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3724-3730
    • Polz, M.F.1    Cavanaugh, C.M.2
  • 25
    • 0036208363 scopus 로고    scopus 로고
    • Molecular method to assess the diversity of Burkholderia species in environmental samples
    • Salles J.F., de Souza F.A., van Elsas J.D. Molecular method to assess the diversity of Burkholderia species in environmental samples. Appl. Environ. Microbiol. 2002, 68:1595-1603.
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 1595-1603
    • Salles, J.F.1    de Souza, F.A.2    van Elsas, J.D.3
  • 26
    • 0035146181 scopus 로고    scopus 로고
    • Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis
    • Satokari R.M., Vaughan E.E., Akkermans A.D.L., Saarela M., de Vos W.M. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 2001, 67:504-513.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 504-513
    • Satokari, R.M.1    Vaughan, E.E.2    Akkermans, A.D.L.3    Saarela, M.4    de Vos, W.M.5
  • 27
    • 0034857157 scopus 로고    scopus 로고
    • A single band does not always represent single bacterial strains in denaturing gel electrophoresis analysis
    • Sekiguchi H., Tomioka N., Nakahara T., Uchiyama H. A single band does not always represent single bacterial strains in denaturing gel electrophoresis analysis. Biotechnol. Lett. 2001, 23:1205-1208.
    • (2001) Biotechnol. Lett. , vol.23 , pp. 1205-1208
    • Sekiguchi, H.1    Tomioka, N.2    Nakahara, T.3    Uchiyama, H.4
  • 28
    • 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. 1996, 62:625-630.
    • (1996) Appl. Environ. Microbiol. , vol.62 , pp. 625-630
    • Suzuki, M.T.1    Giovannoni, S.J.2
  • 29
    • 84866035224 scopus 로고    scopus 로고
    • A positive control for detecting heteroduplexes in DGGE for microbial community fingerprinting
    • Syvyk A., Nalian A., Hume M., Martynova-vanKley A. A positive control for detecting heteroduplexes in DGGE for microbial community fingerprinting. Tex. J. Sci. 2008, 60:33-44.
    • (2008) Tex. J. Sci. , vol.60 , pp. 33-44
    • Syvyk, A.1    Nalian, A.2    Hume, M.3    Martynova-vanKley, A.4
  • 30
    • 1542356381 scopus 로고    scopus 로고
    • Standardized determination of real-time PCR efficiency from a single reaction set-up
    • Tichopad A., Dilger M., Schwarz G., Pfaffl M.W. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res. 2003, 31:6688. 10:1093/nar/gkg885.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6688
    • Tichopad, A.1    Dilger, M.2    Schwarz, G.3    Pfaffl, M.W.4
  • 32
    • 0033987792 scopus 로고    scopus 로고
    • Rhizosphere microbial community structure in relation to root location and plant iron nutritional status
    • Yang C.H., Crowley D.E. Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl. Environ. Microbiol. 2000, 66:345-351.
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 345-351
    • Yang, C.H.1    Crowley, D.E.2


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