-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
-
2
-
-
0025294528
-
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. 1990, 56(6):1919-1925.
-
(1990)
Appl. Environ. Microbiol.
, vol.56
, Issue.6
, 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
-
3
-
-
33847631292
-
Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester
-
Ariesyady H.D., Ito T., Okabe S. Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res. 2007, 41:1554-1568.
-
(2007)
Water Res.
, vol.41
, pp. 1554-1568
-
-
Ariesyady, H.D.1
Ito, T.2
Okabe, S.3
-
4
-
-
34248663784
-
Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge
-
Ariesyady H.D., Ito T., Yoshiguchi K., Okabe S. Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge. Appl. Microbiol. Biotechnol. 2007, 75:673-683.
-
(2007)
Appl. Microbiol. Biotechnol.
, vol.75
, pp. 673-683
-
-
Ariesyady, H.D.1
Ito, T.2
Yoshiguchi, K.3
Okabe, S.4
-
5
-
-
0036667419
-
Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal
-
Björnsson L., Hugenholtz P., Tyson G.W., Blackall L.L. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 2002, 148:2309-2318.
-
(2002)
Microbiology
, vol.148
, pp. 2309-2318
-
-
Björnsson, L.1
Hugenholtz, P.2
Tyson, G.W.3
Blackall, L.L.4
-
6
-
-
0002806157
-
Diversity and taxonomy of methanogens
-
Chapman Hall, New York, J.G. Ferry (Ed.)
-
Boone D.R., Whitman W.B., Rouvuere P. Diversity and taxonomy of methanogens. Methanogenesis 1993, 35-80. Chapman Hall, New York. J.G. Ferry (Ed.).
-
(1993)
Methanogenesis
, pp. 35-80
-
-
Boone, D.R.1
Whitman, W.B.2
Rouvuere, P.3
-
7
-
-
22744444875
-
Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester
-
Chouari R., Le Paslier D., Daegelen P., Ginestet P., Weissenbach J., Sghir A. Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ. Microbiol. 2005, 7(8):1104-1115.
-
(2005)
Environ. Microbiol.
, vol.7
, Issue.8
, pp. 1104-1115
-
-
Chouari, R.1
Le Paslier, D.2
Daegelen, P.3
Ginestet, P.4
Weissenbach, J.5
Sghir, A.6
-
8
-
-
0344172842
-
The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set
-
Daims H., Bruhl A., Amann R., Schleifer K.H., Wagner M. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 1999, 22:434-444.
-
(1999)
Syst. Appl. Microbiol.
, vol.22
, pp. 434-444
-
-
Daims, H.1
Bruhl, A.2
Amann, R.3
Schleifer, K.H.4
Wagner, M.5
-
9
-
-
0034802146
-
Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov
-
Dewhirst F.E., Paster B.J., Tzellas N., Coleman B., Downes J., Spratt D.A., Wade W.G. Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of Olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int. J. Syst. Evol. Microbiol. 2001, 51(Pt 5):1797-1804.
-
(2001)
Int. J. Syst. Evol. Microbiol.
, vol.51
, Issue.PART 5
, pp. 1797-1804
-
-
Dewhirst, F.E.1
Paster, B.J.2
Tzellas, N.3
Coleman, B.4
Downes, J.5
Spratt, D.A.6
Wade, W.G.7
-
10
-
-
0036135188
-
Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes
-
Gich F., Garcia-Gil J., Overmann J. Previously unknown and phylogenetically diverse members of the green nonsulfur bacteria are indigenous to freshwater lakes. Arch. Microbiol. 2001, 177:1-10.
-
(2001)
Arch. Microbiol.
, vol.177
, pp. 1-10
-
-
Gich, F.1
Garcia-Gil, J.2
Overmann, J.3
-
11
-
-
0030872620
-
Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis
-
Godon J.J., Zumstein E., Dabert P., Habouzit F., Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 1997, 63:2802-2813.
-
(1997)
Appl. Environ. Microbiol.
, vol.63
, pp. 2802-2813
-
-
Godon, J.J.1
Zumstein, E.2
Dabert, P.3
Habouzit, F.4
Moletta, R.5
-
12
-
-
2542508293
-
Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval
-
Grosskopf R., Janssen P.H., Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 1998, 64:960-969.
-
(1998)
Appl. Environ. Microbiol.
, vol.64
, pp. 960-969
-
-
Grosskopf, R.1
Janssen, P.H.2
Liesack, W.3
-
13
-
-
58549119451
-
Syntrophic acetate-oxidizing microbes in methanogenic environments
-
Hattori S. Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ. 2008, 23:118-127.
-
(2008)
Microbes Environ.
, vol.23
, pp. 118-127
-
-
Hattori, S.1
-
14
-
-
0036136673
-
Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm by combining microautoradiography and fluorescent in situ hybridization
-
Ito T., Nielsen J.L., Okabe S., Watanabe Y., Nielsen P.H. Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm by combining microautoradiography and fluorescent in situ hybridization. Appl. Environ. Microbiol. 2002, 68:356-364.
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 356-364
-
-
Ito, T.1
Nielsen, J.L.2
Okabe, S.3
Watanabe, Y.4
Nielsen, P.H.5
-
15
-
-
81855185536
-
Identification of a novel acetate-utilizing bacterium belonging to synergistes group 4 in anaerobic digester sludge
-
Ito T., Yoshiguchi K., Ariesyady H.D., Okabe S. Identification of a novel acetate-utilizing bacterium belonging to synergistes group 4 in anaerobic digester sludge. ISME J. 2011, 5:1837-1849.
-
(2011)
ISME J.
, vol.5
, pp. 1837-1849
-
-
Ito, T.1
Yoshiguchi, K.2
Ariesyady, H.D.3
Okabe, S.4
-
16
-
-
1642418320
-
Eco-physiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms
-
Kindaichi T., Ito T., Okabe S. Eco-physiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms. Appl. Environ. Microbiol. 2004, 70:1641-1650.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 1641-1650
-
-
Kindaichi, T.1
Ito, T.2
Okabe, S.3
-
17
-
-
4644327755
-
Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants
-
Kong Y., Nielsen J.L., Nielsen P.H. Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants. Appl. Environ. Microbiol. 2004, 70(9):5383-5390.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, Issue.9
, pp. 5383-5390
-
-
Kong, Y.1
Nielsen, J.L.2
Nielsen, P.H.3
-
18
-
-
3242810318
-
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
-
Kumar S., Tamura K., Nei M. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform. 2004, 5:150-163.
-
(2004)
Brief Bioinform.
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
19
-
-
0001857117
-
16S/23S rRNA sequencing
-
John Wiley and Sons, Chichester, England, E. Stackebrandt, M. Goodfellow (Eds.)
-
Lane D.J. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. John Wiley and Sons, Chichester, England. E. Stackebrandt, M. Goodfellow (Eds.).
-
(1991)
Nucleic Acid Techniques in Bacterial Systematics
, pp. 115-175
-
-
Lane, D.J.1
-
20
-
-
0032986790
-
Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology
-
Lee N., Nielsen P.H., Andreasen K.H., Juretschko S., Nielsen J.L., Schleifer K.H., et al. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. Appl. Environ. Microbiol. 1999, 65:1289-1297.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 1289-1297
-
-
Lee, N.1
Nielsen, P.H.2
Andreasen, K.H.3
Juretschko, S.4
Nielsen, J.L.5
Schleifer, K.H.6
-
21
-
-
0032900278
-
Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen
-
Liu Y., Balkwill D.L., Aldrich H.C., Drake G.R., Boone D.R. Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov. sp. nov. and Syntrophobacter wolinii. Int. J. Syst. Bacteriol. 1999, 49:545-556.
-
(1999)
nov. sp. nov. and Syntrophobacter wolinii. Int. J. Syst. Bacteriol.
, vol.49
, pp. 545-556
-
-
Liu, Y.1
Balkwill, D.L.2
Aldrich, H.C.3
Drake, G.R.4
Boone, D.R.5
-
22
-
-
0842266326
-
Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients
-
Lueders T., Manefield M., Friedrich M.W. Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients. Environ. Microbiol. 2004, 6:73-78.
-
(2004)
Environ. Microbiol.
, vol.6
, pp. 73-78
-
-
Lueders, T.1
Manefield, M.2
Friedrich, M.W.3
-
23
-
-
0036452120
-
Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function
-
Manefield M., Whiteley A.S., Ostle N., Ineson P., Bailey M.J. Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function. Rapid Commun. Mass Spectrom. 2002, 16:2179-2183.
-
(2002)
Rapid Commun. Mass Spectrom.
, vol.16
, pp. 2179-2183
-
-
Manefield, M.1
Whiteley, A.S.2
Ostle, N.3
Ineson, P.4
Bailey, M.J.5
-
24
-
-
0038122918
-
Identification of Propionibacterium acnes by polymerase chain reaction for amplification of 16S ribosomal RNA and lipase genes
-
Nakamura M., Kametani I., Higaki S., Yamagishi T. Identification of Propionibacterium acnes by polymerase chain reaction for amplification of 16S ribosomal RNA and lipase genes. Anaerobe 2003, 9(1):5-10.
-
(2003)
Anaerobe
, vol.9
, Issue.1
, pp. 5-10
-
-
Nakamura, M.1
Kametani, I.2
Higaki, S.3
Yamagishi, T.4
-
25
-
-
0034551726
-
Studies on the in situ physiology of Thiothrix spp. present in activated sludge
-
Nielsen P.H., De Muro M.A., Nielsen J.L. Studies on the in situ physiology of Thiothrix spp. present in activated sludge. Environ. Microbiol. 2000, 2:389-398.
-
(2000)
Environ. Microbiol.
, vol.2
, pp. 389-398
-
-
Nielsen, P.H.1
De Muro, M.A.2
Nielsen, J.L.3
-
26
-
-
0032746992
-
Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms
-
Okabe S., Itoh T., Satoh H., Watanabe Y. Analyses of spatial distributions of sulfate-reducing bacteria and their activity in aerobic wastewater biofilms. Appl. Environ. Microbiol. 1999, 65:5107-5116.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 5107-5116
-
-
Okabe, S.1
Itoh, T.2
Satoh, H.3
Watanabe, Y.4
-
27
-
-
33746591373
-
MAR-FISH-an ecophysiological approach to link phylogenetic affiliation and in situ metabolic activity of microorganisms at a single-cell resolution
-
Okabe S., Kindaichi T., Ito T. MAR-FISH-an ecophysiological approach to link phylogenetic affiliation and in situ metabolic activity of microorganisms at a single-cell resolution. Microbes Environ. 2004, 19:83-98.
-
(2004)
Microbes Environ.
, vol.19
, pp. 83-98
-
-
Okabe, S.1
Kindaichi, T.2
Ito, T.3
-
28
-
-
22144472619
-
14C-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms
-
14C-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms. Appl. Environ. Microbiol. 2005, 71:3987-3994.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 3987-3994
-
-
Okabe, S.1
Kindaichi, T.2
Ito, T.3
-
29
-
-
78650042374
-
A great leap forward in microbial ecology
-
Okabe S., Oshiki M., Kamagata Y., Yamaguchi N., Toyofuku M., Yawata Y., Tashiro Y., Nomura N., Ohta H., Ohkuma M., Hiraishi A., Minamisawa K. A great leap forward in microbial ecology. Microbes Environ. 2010, 25:230-240.
-
(2010)
Microbes Environ.
, vol.25
, pp. 230-240
-
-
Okabe, S.1
Oshiki, M.2
Kamagata, Y.3
Yamaguchi, N.4
Toyofuku, M.5
Yawata, Y.6
Tashiro, Y.7
Nomura, N.8
Ohta, H.9
Ohkuma, M.10
Hiraishi, A.11
Minamisawa, K.12
-
30
-
-
0028165830
-
Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens
-
Raskin L., Stromley J.M., Rittmann B.E., Stahl D.A. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 1994, 60:1232-1240.
-
(1994)
Appl. Environ. Microbiol.
, vol.60
, pp. 1232-1240
-
-
Raskin, L.1
Stromley, J.M.2
Rittmann, B.E.3
Stahl, D.A.4
-
31
-
-
67549099704
-
Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge
-
Rivière D., Desvignes V., Pelletier E., Chaussonnerie S., Guermazi S., Weissenbach J., et al. Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J. 2009, 3:700-714.
-
(2009)
ISME J.
, vol.3
, pp. 700-714
-
-
Rivière, D.1
Desvignes, V.2
Pelletier, E.3
Chaussonnerie, S.4
Guermazi, S.5
Weissenbach, J.6
-
32
-
-
0028172253
-
In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides
-
Roller C., Wagner M., Amann R., Ludwig W., Schleifer K.H. In situ probing of gram-positive bacteria with high DNA G + C content using 23S rRNA-targeted oligonucleotides. Microbiology 1994, 140:2849-2858.
-
(1994)
Microbiology
, vol.140
, pp. 2849-2858
-
-
Roller, C.1
Wagner, M.2
Amann, R.3
Ludwig, W.4
Schleifer, K.H.5
-
33
-
-
0030871461
-
Energetics of syntrophic cooperation in methanogenic degradation
-
Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol. Mol. Biol. Rev. 1997, 61:262-280.
-
(1997)
Microbiol. Mol. Biol. Rev.
, vol.61
, pp. 262-280
-
-
Schink, B.1
-
34
-
-
77956173523
-
Qualitative and quantitative assessment of microbial community in batch anaerobic digestion of secondary sludge
-
Shin S.G., Lee S., Lee C., Hwang K., Hwang S. Qualitative and quantitative assessment of microbial community in batch anaerobic digestion of secondary sludge. Bioresour. Technol. 2010, 101:9461-9470.
-
(2010)
Bioresour. Technol.
, vol.101
, pp. 9461-9470
-
-
Shin, S.G.1
Lee, S.2
Lee, C.3
Hwang, K.4
Hwang, S.5
-
35
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
36
-
-
0343570513
-
16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides
-
Weller R., Glöckner F.O., Amann R. 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Syst. Appl. Microbiol. 2000, 23:107-114.
-
(2000)
Syst. Appl. Microbiol.
, vol.23
, pp. 107-114
-
-
Weller, R.1
Glöckner, F.O.2
Amann, R.3
|