-
1
-
-
3242884054
-
Fine-scale phylogenetic architecture of a complex bacterial community
-
Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554.
-
(2004)
Nature
, vol.430
, pp. 551-554
-
-
Acinas, S.G.1
Klepac-Ceraj, V.2
Hunt, D.E.3
Pharino, C.4
Ceraj, I.5
Distel, D.L.6
Polz, M.F.7
-
2
-
-
1942443733
-
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
Acinas, S. G., L. A. Marcelino, V. Klepac-Ceraj, and M. F. Polz. 2004. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186:2629-2635.
-
(2004)
J. Bacteriol.
, vol.186
, pp. 2629-2635
-
-
Acinas, S.G.1
Marcelino, L.A.2
Klepac-Ceraj, V.3
Polz, M.F.4
-
4
-
-
0029838624
-
PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases
-
Cline, J., J. C. Braman, and H. H. Hogrefe. 1996. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 24:3546-3551.
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 3546-3551
-
-
Cline, J.1
Braman, J.C.2
Hogrefe, H.H.3
-
5
-
-
13444304367
-
The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis
-
Cole, J. R., B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33:D294-D296.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam, S.A.5
McGarrell, D.M.6
Garrity, G.M.7
Tiedje, J.M.8
-
6
-
-
0034469143
-
Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization
-
Cottrell, M. T., and D. L. Kirchman. 2000. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl. Environ. Microbiol. 66:5116-5122.
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 5116-5122
-
-
Cottrell, T.M.1
Kirchman, D.L.2
-
7
-
-
0032879764
-
Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities
-
Fisher, M. M., and E. W. Triplett. 1999. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol. 65:4630-4636.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 4630-4636
-
-
Fisher, M.M.1
Triplett, E.W.2
-
8
-
-
0033770992
-
Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom
-
González, J. M., R. Simó, R. Massana, J. S. Covert, E. O. Casamayor, C. Pedrós-Alió, and M. A. Moran. 2000. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl. Environ. Microbiol. 66:4237-4246.
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 4237-4246
-
-
González, J.M.1
Simó, R.2
Massana, R.3
Covert, J.S.4
Casamayor, E.O.5
Pedrós-Alió, C.6
Moran, M.A.7
-
9
-
-
0000803388
-
The population frequencies of species and the estimation of population parametres
-
Good, I. J. 1953. The population frequencies of species and the estimation of population parametres. Biometrika 40:237-264.
-
(1953)
Biometrika
, vol.40
, pp. 237-264
-
-
Good, I.J.1
-
10
-
-
0037217221
-
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
-
Hugenholtz, P., and T. Huber. 2003. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Int. J. Syst. Evol. Microbiol. 53:289-293.
-
(2003)
Int. J. Syst. Evol. Microbiol.
, vol.53
, pp. 289-293
-
-
Hugenholtz, P.1
Huber, T.2
-
11
-
-
0035487318
-
Counting the uncountable: Statistical approaches to estimating microbial diversity
-
Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 4399-4406
-
-
Hughes, J.B.1
Hellmann, J.J.2
Ricketts, T.H.3
Bohannan, B.J.M.4
-
12
-
-
0035432220
-
Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR
-
Ishii, K., and M. Fukui. 2001. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl. Environ. Microbiol. 67:3753-3755.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 3753-3755
-
-
Ishii, K.1
Fukui, M.2
-
13
-
-
0242573334
-
Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware estuary
-
Kirchman, D. L., L. Yu, and M. T. Cottrell. 2003. Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware estuary. Appl. Environ. Microbiol. 69:6587-6596.
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 6587-6596
-
-
Kirchman, D.L.1
Yu, L.2
Cottrell, M.T.3
-
14
-
-
0030921309
-
A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations
-
Komatsoulis, G. A., and M. S. Waterman. 1997. A new computational method for detection of chimeric 16S rRNA artifacts generated by PCR amplification from mixed bacterial populations. Appl. Environ. Microbiol. 63:2338-2346.
-
(1997)
Appl. Environ. Microbiol.
, vol.63
, pp. 2338-2346
-
-
Komatsoulis, G.A.1
Waterman, M.S.2
-
15
-
-
0028082207
-
Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms
-
Kopczynski, E. D., M. M. Bateson, and D. M. Ward. 1994. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60:746-748.
-
(1994)
Appl. Environ. Microbiol.
, vol.60
, pp. 746-748
-
-
Kopczynski, E.D.1
Bateson, M.M.2
Ward, D.M.3
-
16
-
-
10444268966
-
Reevaluation and reduction of a PCR bias caused by reannealing of templates
-
Kurata, S., T. Kanagawa, Y. Magariyama, K. Takatsu, K. Yamada, T. Yokomaku, and Y. Kamagata. 2004. Reevaluation and reduction of a PCR bias caused by reannealing of templates. Appl. Environ. Microbiol. 70:7545-7549.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 7545-7549
-
-
Kurata, S.1
Kanagawa, T.2
Magariyama, Y.3
Takatsu, K.4
Yamada, K.5
Yokomaku, T.6
Kamagata, Y.7
-
17
-
-
2542523843
-
ARB: A software environment for sequence data
-
Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K.-H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
Strunk, O.2
Westram, R.3
Richter, L.4
Meier, H.5
Yadhukumar6
Buchner, A.7
Lai, T.8
Steppi, S.9
Jobb, G.10
Forster, W.11
Brettske, I.12
Gerber, S.13
Ginhart, A.W.14
Gross, O.15
Grumann, S.16
Hermann, S.17
Jost, R.18
Konig, A.19
Liss, T.20
Lussmann, R.21
May, M.22
Nonhoff, B.23
Reichel, B.24
Strehlow, R.25
Stamatakis, A.26
Stuckmann, N.27
Vilbig, A.28
Lenke, M.29
Ludwig, T.30
Bode, A.31
Schleifer, K.-H.32
more..
-
18
-
-
0037225001
-
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., and M. W. Friedrich. 2003. 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. 69:320-326.
-
(2003)
Appl. Environ Microbiol.
, vol.69
, pp. 320-326
-
-
Lueders, T.1
Friedrich, M.W.2
-
19
-
-
33644855812
-
Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae)
-
in press
-
Luyten, Y. A., J. R. Thompson, Wendy Morrill, M. F. Polz, and D. L. Distel. Extensive variation in intracellular symbiont community composition among members of a single population of the wood-boring bivalve Lyrodus pedicellatus (Bivalvia: Teredinidae). Appl. Environ. Microbiol., in press.
-
Appl. Environ. Microbiol.
-
-
Luyten, Y.A.1
Thompson, J.R.2
Morrill, W.3
Polz, M.F.4
Distel, D.L.5
-
20
-
-
19944408938
-
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment
-
Moran, M. A., A. Buchan, J. M. Gonzalez, J. F. Heidelberg, W. B. Whitman, R. P. Kiene, J. R. Henriksen, G. M. King, R. Belas, C. Fuqua, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J. A. Eisen, E. Rahe, W. M. Sheldon, W. Ye, T. R. Miller, J. Carlton, D. A. Rasko, I. T. Paulsen, Q. Ren, S. C. Daugherty, R. T. Deboy, R. J. Dodson, A. S. Durkin, R. Madupu, W. C. Nelson, S. A Sullivan, M. J. Rosovitz, D. H. Haft, J. Selengut, and N. Ward. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
-
(2004)
Nature
, vol.432
, pp. 910-913
-
-
Moran, M.A.1
Buchan, A.2
Gonzalez, J.M.3
Heidelberg, J.F.4
Whitman, W.B.5
Kiene, R.P.6
Henriksen, J.R.7
King, G.M.8
Belas, R.9
Fuqua, C.10
Brinkac, L.11
Lewis, M.12
Johri, S.13
Weaver, B.14
Pai, G.15
Eisen, J.A.16
Rahe, E.17
Sheldon, W.M.18
Ye, W.19
Miller, T.R.20
Carlton, J.21
Rasko, D.A.22
Paulsen, I.T.23
Ren, Q.24
Daugherty, S.C.25
Deboy, R.T.26
Dodson, R.J.27
Durkin, A.S.28
Madupu, R.29
Nelson, W.C.30
Sullivan, S.A.31
Rosovitz, M.J.32
Haft, D.H.33
Selengut, J.34
Ward, N.35
more..
-
21
-
-
0037180794
-
SAR11 clade dominates ocean surface bacterioplankton communities
-
Morris, R. M., M. S. Rappe, S. A. Connon, K. L. Vergin, W. A. Siebold, C. A. Carlson, and S. J. Giovannoni. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420:806-810.
-
(2002)
Nature
, vol.420
, pp. 806-810
-
-
Morris, R.M.1
Rappe, M.S.2
Connon, S.A.3
Vergin, K.L.4
Siebold, W.A.5
Carlson, C.A.6
Giovannoni, S.J.7
-
22
-
-
0034547801
-
An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics
-
Osborn, A. M., E. R. Moore, and K. N. Timmis. 2000. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2:39-50.
-
(2000)
Environ. Microbiol.
, vol.2
, pp. 39-50
-
-
Osborn, A.M.1
Moore, E.R.2
Timmis, K.N.3
-
23
-
-
0031711754
-
Bias in template-to-product ratios in multitemplate PCR
-
Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 3724-3730
-
-
Polz, M.F.1
Cavanaugh, C.M.2
-
24
-
-
0032845644
-
Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae
-
Polz, M. F., C. Harbison, and C. M. Cavanaugh. 1999. Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae. Appl. Environ. Microbiol. 65:4271-4275.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 4271-4275
-
-
Polz, M.F.1
Harbison, C.2
Cavanaugh, C.M.3
-
25
-
-
0035145056
-
Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning
-
Qiu, X., L. Wu, H. Huang, P. E. McDonel, A. V. Palumbo, J. M. Tiedje, and J. Zhou. 2001. Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67:880-887.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 880-887
-
-
Qiu, X.1
Wu, L.2
Huang, H.3
McDonel, P.E.4
Palumbo, A.V.5
Tiedje, J.M.6
Zhou, J.7
-
26
-
-
0028915470
-
Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences
-
Robison-Cox, J. F., M. M. Bateson, and D. M. Ward. 1995. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl. Environ. Microbiol. 61:1240-1245.
-
(1995)
Appl. Environ. Microbiol.
, vol.61
, pp. 1240-1245
-
-
Robison-Cox, J.F.1
Bateson, M.M.2
Ward, D.M.3
-
27
-
-
85045498207
-
Modeling of heteroduplex formation during PCR from mixtures of DNA templates
-
Ruano, G., and K. K. Kidd. 1992. Modeling of heteroduplex formation during PCR from mixtures of DNA templates. PCR Methods Appl. 2:112-116.
-
(1992)
PCR Methods Appl
, vol.2
, pp. 112-116
-
-
Ruano, G.1
Kidd, K.K.2
-
28
-
-
0842285837
-
A newly discovered Roseobacter cluster in temperate and polar oceans
-
Selje, N., M. Simon, and T. Brinkhoff. 2004. A newly discovered Roseobacter cluster in temperate and polar oceans. Nature 427:445-448.
-
(2004)
Nature
, vol.427
, pp. 445-448
-
-
Selje, N.1
Simon, M.2
Brinkhoff, T.3
-
29
-
-
0035163597
-
Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences
-
Speksnijder, A. G. C. L., G. A. Kowalchuk, S. De Jong, E. Kline, J. R. Stephen, and H. J. Laanbroek. 2001. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences. Appl. Environ. Microbiol. 67:469-472.
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 469-472
-
-
Speksnijder, A.G.C.L.1
Kowalchuk, G.A.2
De Jong, S.3
Kline, E.4
Stephen, J.R.5
Laanbroek, H.J.6
-
30
-
-
0031790538
-
Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity
-
Suzuki, M., M. S. Rappé, and S. J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:4522-4529.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 4522-4529
-
-
Suzuki, M.1
Rappé, M.S.2
Giovannoni, S.J.3
-
31
-
-
0030067991
-
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
-
Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
-
(1996)
Appl. Environ. Microbiol.
, vol.62
, pp. 625-630
-
-
Suzuki, M.T.1
Giovannoni, S.J.2
-
32
-
-
0036566806
-
Heteroduplexes in mixed-template amplifications: Formation, consequence and elimination by 'reconditioning PCR'
-
Thompson, J. R., L. A. Marcelino, and M. F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res. 30:2083-2088.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2083-2088
-
-
Thompson, J.R.1
Marcelino, L.A.2
Polz, M.F.3
-
33
-
-
14544287770
-
Genotypic diversity within a natural coastal bacterioplankton population
-
Thompson, J. R., S. Pacocha, C. Pharino, V. Klepac-Ceraj, D. E. Hunt, J. Benoit, R. Sarma-Rupavtarm, D. L. Distel, and M. F. Polz. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313.
-
(2005)
Science
, vol.307
, pp. 1311-1313
-
-
Thompson, J.R.1
Pacocha, S.2
Pharino, C.3
Klepac-Ceraj, V.4
Hunt, D.E.5
Benoit, J.6
Sarma-Rupavtarm, R.7
Distel, D.L.8
Polz, M.F.9
-
34
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
Venter, C. J., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. H. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, P. C., Y.-H. Rogers, and H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, C.J.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
Eisen, J.A.6
Wu, D.7
Paulsen, I.8
Nelson, K.E.9
Nelson, W.10
Fouts, D.E.11
Levy, S.12
Knap, A.H.13
Lomas, M.W.14
Nealson, K.H.15
White, O.16
Peterson, J.17
Hoffman, J.18
Parsons, R.19
Baden-Tillson, H.20
C., P.21
Rogers, Y.-H.22
Smith, H.O.23
more..
-
35
-
-
0345195995
-
Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
-
Von Wintzingerode, F., U. B. Gobel, and E. Stackebrandt. 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
-
36
-
-
12044254346
-
Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift
-
Wagner, A., N. Blackstone, P. Cartwright, M. Dick, B. Misof, P. Snow, G. P. Wagner, J. Bartels, M. Murtha, and J. Pendleton. 1994. Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43:250-261.
-
(1994)
Syst. Biol.
, vol.43
, pp. 250-261
-
-
Wagner, A.1
Blackstone, N.2
Cartwright, P.3
Dick, M.4
Misof, B.5
Snow, P.6
Wagner, G.P.7
Bartels, J.8
Murtha, M.9
Pendleton, J.10
-
37
-
-
0029972052
-
The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species
-
Wang, G. C., and Y. Wang. 1996. The frequency of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from different bacterial species. Microbiology 142:1107-1114.
-
(1996)
Microbiology
, vol.142
, pp. 1107-1114
-
-
Wang, G.C.1
Wang, Y.2
-
38
-
-
0030844080
-
Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes
-
Wang, G. C., and Y. Wang. 1997. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol. 63:4645-4650.
-
(1997)
Appl. Environ. Microbiol.
, vol.63
, pp. 4645-4650
-
-
Wang, G.C.1
Wang, Y.2
|