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Volumn 59, Issue 4, 2010, Pages 776-786

PCR-Denaturing gradient gel electrophoresis of complex microbial communities: A two-step approach to address the effect of gel-to-gel variation and allow valid comparisons across a large dataset

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

EID: 77953323855     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-009-9613-x     Document Type: Article
Times cited : (28)

References (46)
  • 2
    • 0036266631 scopus 로고    scopus 로고
    • Multicenter comparison of three different analytical systems for evaluation of DNA banding patterns from Cryptococcus neoformans
    • Cardinali G, Martini A, Preziosi R, Bistoni F, Baldelli F (2002) Multicenter comparison of three different analytical systems for evaluation of DNA banding patterns from Cryptococcus neoformans. J Clin Microbiol 40: 2095-2100.
    • (2002) J Clin Microbiol , vol.40 , pp. 2095-2100
    • Cardinali, G.1    Martini, A.2    Preziosi, R.3    Bistoni, F.4    Baldelli, F.5
  • 3
    • 0038506977 scopus 로고    scopus 로고
    • Optimization of computer software settings improves accuracy of pulsed-field gel electrophoresis macrorestriction fragment pattern analysis
    • Duck WM, Steward CD, Banerjee SN, McGowan JE, Tenover FC (2003) Optimization of computer software settings improves accuracy of pulsed-field gel electrophoresis macrorestriction fragment pattern analysis. J Clin Microbiol 41: 3035-3042.
    • (2003) J Clin Microbiol , vol.41 , pp. 3035-3042
    • Duck, W.M.1    Steward, C.D.2    Banerjee, S.N.3    McGowan, J.E.4    Tenover, F.C.5
  • 4
    • 33751419313 scopus 로고    scopus 로고
    • DNA fingerprinting of microbial communities
    • A. M. Osborn and C. J. Smith (Eds.), Abingdon: Taylor & Francis
    • Felske A, Osborn AM (2005) DNA fingerprinting of microbial communities. In: Osborn AM, Smith CJ (eds) Molecular microbial ecology. Taylor & Francis, Abingdon.
    • (2005) Molecular Microbial Ecology
    • Felske, A.1    Osborn, A.M.2
  • 5
    • 0033133556 scopus 로고    scopus 로고
    • Distribution of microbial assemblages in the Central Arctic Ocean Basin studied by PCR/DGGE: Analysis of a large data set
    • Ferrari VC, Hollibaugh JT (1999) Distribution of microbial assemblages in the Central Arctic Ocean Basin studied by PCR/DGGE: analysis of a large data set. Hydrobiologia 401: 55-68.
    • (1999) Hydrobiologia , vol.401 , pp. 55-68
    • Ferrari, V.C.1    Hollibaugh, J.T.2
  • 6
    • 0030063913 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community
    • Ferris MJ, Muyzer G, Ward DM (1996) Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community. Appl Environ Microbiol 62: 340-346.
    • (1996) Appl Environ Microbiol , vol.62 , pp. 340-346
    • Ferris, M.J.1    Muyzer, G.2    Ward, D.M.3
  • 7
    • 2942525588 scopus 로고    scopus 로고
    • Molecular microbial ecology: Land of the one-eyed king
    • Forney LJ, Zhou X, Brown CJ (2004) Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 7: 210-220.
    • (2004) Curr Opin Microbiol , vol.7 , pp. 210-220
    • Forney, L.J.1    Zhou, X.2    Brown, C.J.3
  • 9
    • 0031978085 scopus 로고    scopus 로고
    • Computerized analysis of restriction fragment length polymorphism patterns: Comparative evaluation of two commercial software packages
    • Gerner-Smidt P, Graves LM, Hunter S, Swaminathan B (1998) Computerized analysis of restriction fragment length polymorphism patterns: comparative evaluation of two commercial software packages. J Clin Microbiol 36: 1318-1323.
    • (1998) J Clin Microbiol , vol.36 , pp. 1318-1323
    • Gerner-Smidt, P.1    Graves, L.M.2    Hunter, S.3    Swaminathan, B.4
  • 10
    • 0037338334 scopus 로고    scopus 로고
    • Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils
    • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69: 1800-1809.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1800-1809
    • Girvan, M.S.1    Bullimore, J.2    Pretty, J.N.3    Osborn, A.M.4    Ball, A.S.5
  • 11
    • 42149108601 scopus 로고    scopus 로고
    • Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens
    • Gong J, Yu H, Liu T, Gill JJ, Chambers JR, Wheatcroft R, Sabour PM (2008) Effects of zinc bacitracin, bird age and access to range on bacterial microbiota in the ileum and caeca of broiler chickens. J Appl Microbiol 104: 1372-1382.
    • (2008) J Appl Microbiol , vol.104 , pp. 1372-1382
    • Gong, J.1    Yu, H.2    Liu, T.3    Gill, J.J.4    Chambers, J.R.5    Wheatcroft, R.6    Sabour, P.M.7
  • 13
    • 0037445311 scopus 로고    scopus 로고
    • Effect of fermentable carbohydrates on piglet faecal bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA
    • Konstantinov SR, Zhu WY, Williams BA, Tamminga S, de Vos WM, Akkermans ADL (2003) Effect of fermentable carbohydrates on piglet faecal bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA. FEMS Microbiol Ecol 43: 225-235.
    • (2003) FEMS Microbiol Ecol , vol.43 , pp. 225-235
    • Konstantinov, S.R.1    Zhu, W.Y.2    Williams, B.A.3    Tamminga, S.4    de Vos, W.M.5    Akkermans, A.D.L.6
  • 14
    • 0030901922 scopus 로고    scopus 로고
    • Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments
    • Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM, Woldendorp JW (1997) Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol 63: 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
  • 15
    • 1842457702 scopus 로고    scopus 로고
    • Significance test for comparing complex microbial community fingerprints using pairwise similarity measures
    • Kropf S, Heuer H, Gruning M, Smalla K (2004) Significance test for comparing complex microbial community fingerprints using pairwise similarity measures. J Microbiol Methods 57: 187-195.
    • (2004) J Microbiol Methods , vol.57 , pp. 187-195
    • Kropf, S.1    Heuer, H.2    Gruning, M.3    Smalla, K.4
  • 18
    • 0030661563 scopus 로고    scopus 로고
    • Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
    • Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63: 4516-4522.
    • (1997) Appl Environ Microbiol , vol.63 , pp. 4516-4522
    • Liu, W.T.1    Marsh, T.L.2    Cheng, H.3    Forney, L.J.4
  • 20
    • 53049095376 scopus 로고    scopus 로고
    • Bacterial population dynamics and faecal short-chain fatty acid (SCFA) concentrations in healthy humans
    • McOrist AL, Abell GCJ, Cooke C, Nyland K (2008) Bacterial population dynamics and faecal short-chain fatty acid (SCFA) concentrations in healthy humans. Brit J Nutr 100: 138-146.
    • (2008) Brit J Nutr , vol.100 , pp. 138-146
    • McOrist, A.L.1    Abell, G.C.J.2    Cooke, C.3    Nyland, K.4
  • 21
    • 0035197594 scopus 로고    scopus 로고
    • Comparison of SmaI-defined genotypes of Campylobacter jejuni examined by KpnI: A population-based study
    • Michaud S, Menard S, Gaudreau C, Arbeit RD (2001) Comparison of SmaI-defined genotypes of Campylobacter jejuni examined by KpnI: a population-based study. J Med Microbiol 50: 1075-1081.
    • (2001) J Med Microbiol , vol.50 , pp. 1075-1081
    • Michaud, S.1    Menard, S.2    Gaudreau, C.3    Arbeit, R.D.4
  • 22
    • 0032812081 scopus 로고    scopus 로고
    • Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis
    • Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65: 3518-3525.
    • (1999) Appl Environ Microbiol , vol.65 , pp. 3518-3525
    • Moeseneder, M.M.1    Arrieta, J.M.2    Muyzer, G.3    Winter, C.4    Herndl, G.J.5
  • 23
    • 26044446676 scopus 로고    scopus 로고
    • A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles
    • Mouser PJ, Rizzo DM, Roling WFM, van Breukelen BM (2005) A multivariate statistical approach to spatial representation of groundwater contamination using hydrochemistry and microbial community profiles. Environ Sci Technol 39: 7551-7559.
    • (2005) Environ Sci Technol , vol.39 , pp. 7551-7559
    • Mouser, P.J.1    Rizzo, D.M.2    Roling, W.F.M.3    van Breukelen, B.M.4
  • 24
    • 0027460328 scopus 로고
    • Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
    • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
    • (1993) Appl Environ Microbiol , vol.59 , pp. 695-700
    • Muyzer, G.1    de Waal, E.C.2    Uitterlinden, A.G.3
  • 25
    • 33947378663 scopus 로고    scopus 로고
    • Soil microbial community analysis using denaturing gradient gel electrophoresis
    • Nakatsu CH (2007) Soil microbial community analysis using denaturing gradient gel electrophoresis. Soil Sci Soc Am J 71: 562-571.
    • (2007) Soil Sci Soc Am J , vol.71 , pp. 562-571
    • Nakatsu, C.H.1
  • 26
    • 23744493882 scopus 로고    scopus 로고
    • Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis
    • Neufeld JD, Mohn WW (2005) Fluorophore-labeled primers improve the sensitivity, versatility, and normalization of denaturing gradient gel electrophoresis. Appl Environ Microbiol 71: 4893-4896.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 4893-4896
    • Neufeld, J.D.1    Mohn, W.W.2
  • 27
    • 45849118694 scopus 로고    scopus 로고
    • Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra
    • Nielsen DS, Snitkjaer P, van den Berg F (2008) Investigating the fermentation of cocoa by correlating denaturing gradient gel electrophoresis profiles and near infrared spectra. Int J Food Microbiol 125: 133-140.
    • (2008) Int J Food Microbiol , vol.125 , pp. 133-140
    • Nielsen, D.S.1    Snitkjaer, P.2    van den Berg, F.3
  • 28
    • 34547579868 scopus 로고    scopus 로고
    • Genotypic microbial community profiling: A critical technical review
    • Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54: 276-289.
    • (2007) Microb Ecol , vol.54 , pp. 276-289
    • Nocker, A.1    Burr, M.2    Camper, A.K.3
  • 29
    • 0029796310 scopus 로고    scopus 로고
    • Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
    • Nubel U, Engelen B, Felske A, Snaidr J, Wieshuber A, Amann RI, Ludwig W, Backhaus H (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178: 5636-5643.
    • (1996) J Bacteriol , vol.178 , pp. 5636-5643
    • Nubel, U.1    Engelen, B.2    Felske, A.3    Snaidr, J.4    Wieshuber, A.5    Amann, R.I.6    Ludwig, W.7    Backhaus, H.8
  • 30
    • 32044431649 scopus 로고    scopus 로고
    • Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques
    • Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71: 6784-6792.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 6784-6792
    • Nunan, N.1    Daniell, T.J.2    Singh, B.K.3    Papert, A.4    McNicol, J.W.5    Prosser, J.I.6
  • 31
    • 0242507740 scopus 로고    scopus 로고
    • Scaling up: The next challenge in environmental microbiology
    • Paerl HW, Steppe TF (2003) Scaling up: the next challenge in environmental microbiology. Environ Microbiol 5: 1025-1038.
    • (2003) Environ Microbiol , vol.5 , pp. 1025-1038
    • Paerl, H.W.1    Steppe, T.F.2
  • 32
    • 0038107873 scopus 로고    scopus 로고
    • Microbial community variation in pristine and polluted nearshore Antarctic sediments
    • Powell SM, Bowman JP, Snape I, Stark JS (2003) Microbial community variation in pristine and polluted nearshore Antarctic sediments. FEMS Microbiol Ecol 45: 135-145.
    • (2003) FEMS Microbiol Ecol , vol.45 , pp. 135-145
    • Powell, S.M.1    Bowman, J.P.2    Snape, I.3    Stark, J.S.4
  • 33
    • 42649102004 scopus 로고    scopus 로고
    • Effects of dietary inulin on the intestinal short chain fatty acids and microbial ecology in broiler chickens as revealed by denaturing gradient gel electrophoresis
    • Rehman H, Hellweg P, Taras D, Zentek J (2008) Effects of dietary inulin on the intestinal short chain fatty acids and microbial ecology in broiler chickens as revealed by denaturing gradient gel electrophoresis. Poult Sci 87: 783-789.
    • (2008) Poult Sci , vol.87 , pp. 783-789
    • Rehman, H.1    Hellweg, P.2    Taras, D.3    Zentek, J.4
  • 34
    • 0035382473 scopus 로고    scopus 로고
    • Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns
    • Rementeria A, Gallego L, Quindos G, Garaizar J (2001) Comparative evaluation of three commercial software packages for analysis of DNA polymorphism patterns. Clin Microbiol Infect 7: 331-336.
    • (2001) Clin Microbiol Infect , vol.7 , pp. 331-336
    • Rementeria, A.1    Gallego, L.2    Quindos, G.3    Garaizar, J.4
  • 36
    • 3242799110 scopus 로고    scopus 로고
    • Multivariate analyses of Burkholderia species in soil: Effect of crop and land use history
    • Salles JF, van Veen JA, van Elsas JD (2004) Multivariate analyses of Burkholderia species in soil: effect of crop and land use history. Appl Environ Microbiol 70: 4012-4020.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 4012-4020
    • Salles, J.F.1    van Veen, J.A.2    van Elsas, J.D.3
  • 37
    • 34648816563 scopus 로고    scopus 로고
    • Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities
    • Sanchez O, Gasol JM, Massana R, Mas J, Pedros-Alio C (2007) Comparison of different denaturing gradient gel electrophoresis primer sets for the study of marine bacterioplankton communities. Appl Environ Microbiol 73: 5962-5967.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5962-5967
    • Sanchez, O.1    Gasol, J.M.2    Massana, R.3    Mas, J.4    Pedros-Alio, C.5
  • 38
    • 0033754245 scopus 로고    scopus 로고
    • Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53
    • Simpson JM, McCracken VJ, Gaskins HR, Mackie RI (2000) Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl Environ Microbiol 66: 4705-4714.
    • (2000) Appl Environ Microbiol , vol.66 , pp. 4705-4714
    • Simpson, J.M.1    McCracken, V.J.2    Gaskins, H.R.3    Mackie, R.I.4
  • 39
    • 34247866371 scopus 로고    scopus 로고
    • Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: Do the different methods provide similar results?
    • Smalla K, Oros-Sichler M, Milling A, Heuer H, Baumgarte S, Becker R, Neuber G, Kropf S, Ulrich A, Tebbe CC (2007) Bacterial diversity of soils assessed by DGGE, T-RFLP and SSCP fingerprints of PCR-amplified 16S rRNA gene fragments: do the different methods provide similar results? J Microbiol Methods 69: 470-479.
    • (2007) J Microbiol Methods , vol.69 , pp. 470-479
    • Smalla, K.1    Oros-Sichler, M.2    Milling, A.3    Heuer, H.4    Baumgarte, S.5    Becker, R.6    Neuber, G.7    Kropf, S.8    Ulrich, A.9    Tebbe, C.C.10
  • 40
    • 62549083826 scopus 로고    scopus 로고
    • DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost
    • Szekely A, Sipos R, Berta B, Vajna B, Hajdu C, Marialigeti K (2009) DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost. Microb Ecol 57: 522-533.
    • (2009) Microb Ecol , vol.57 , pp. 522-533
    • Szekely, A.1    Sipos, R.2    Berta, B.3    Vajna, B.4    Hajdu, C.5    Marialigeti, K.6
  • 42
    • 46749145764 scopus 로고    scopus 로고
    • The immediate environment during postnatal development has long-term impact on gut community structure in pigs
    • Thompson CL, Wang B, Holmes AJ (2008) The immediate environment during postnatal development has long-term impact on gut community structure in pigs. ISME J 2: 739-748.
    • (2008) ISME J , vol.2 , pp. 739-748
    • Thompson, C.L.1    Wang, B.2    Holmes, A.J.3
  • 43
    • 0036781558 scopus 로고    scopus 로고
    • Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth
    • van der Wielen PWJJ, Keuzenkamp DA, Lipman LJA, van Knapen F, Biesterveld S (2002) Spatial and temporal variation of the intestinal bacterial community in commercially raised broiler chickens during growth. Microb Ecol 44: 286-293.
    • (2002) Microb Ecol , vol.44 , pp. 286-293
    • van der Wielen, P.W.J.J.1    Keuzenkamp, D.A.2    Lipman, L.J.A.3    van Knapen, F.4    Biesterveld, S.5
  • 44
    • 0345195995 scopus 로고    scopus 로고
    • Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
    • von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
    • (1997) FEMS Microbiol Rev , vol.21 , pp. 213-229
    • von Wintzingerode, F.1    Gobel, U.B.2    Stackebrandt, E.3
  • 46
    • 0031684010 scopus 로고    scopus 로고
    • Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria
    • Zoetendal EG, Akkermans ADL, De Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64: 3854-3859.
    • (1998) Appl Environ Microbiol , vol.64 , pp. 3854-3859
    • Zoetendal, E.G.1    Akkermans, A.D.L.2    de Vos, W.M.3


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