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Volumn 61, Issue 3, 2005, Pages 305-319

Novel phylogenetic assignment database for terminal-restriction fragment length polymorphism analysis of human colonic microbiota

Author keywords

16S rRNA gene clone library; Database; Human colonic microbiota; T RFLP

Indexed keywords

RESTRICTION ENDONUCLEASE;

EID: 17644367543     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2004.12.009     Document Type: Article
Times cited : (62)

References (37)
  • 1
    • 0034038056 scopus 로고    scopus 로고
    • Isolation PCR-quality DNA from human feces with soil DNA kit
    • B.G. Clement, and C.L. Kitts Isolation PCR-quality DNA from human feces with soil DNA kit BioTechniques 28 2000 640 646
    • (2000) BioTechniques , vol.28 , pp. 640-646
    • Clement, B.G.1    Kitts, C.L.2
  • 2
    • 0033941482 scopus 로고    scopus 로고
    • Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis
    • J. Dunbar, L.O. Ticknor, and C.R. Kuske Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis Appl. Environ. Microbiol. 66 2000 2943 2950
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 2943-2950
    • Dunbar, J.1    Ticknor, L.O.2    Kuske, C.R.3
  • 3
    • 0035163587 scopus 로고    scopus 로고
    • Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities
    • J. Dunbar, L.O. Ticknor, and C.R. Kuske Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities Appl. Environ. Microbiol. 67 2001 190 197
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 190-197
    • Dunbar, J.1    Ticknor, L.O.2    Kuske, C.R.3
  • 4
    • 0036739483 scopus 로고    scopus 로고
    • Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces
    • S.H. Duncan, G.L. Hold, A. Barcenilla, C.S. Stewart, and H.J. Flint Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces Int. J. Syst. Evol. Microbiol. 52 2002 1615 1620
    • (2002) Int. J. Syst. Evol. Microbiol. , vol.52 , pp. 1615-1620
    • Duncan, S.H.1    Hold, G.L.2    Barcenilla, A.3    Stewart, C.S.4    Flint, H.J.5
  • 5
    • 0038221194 scopus 로고    scopus 로고
    • Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure
    • M. Egert, and M.W. Friedrich Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure Appl. Environ. Microbiol. 69 2003 2555 2562
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 2555-2562
    • Egert, M.1    Friedrich, M.W.2
  • 7
    • 0031692488 scopus 로고    scopus 로고
    • Variation of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes
    • A.H. Franks, H.J.M. Harmsen, G.C. Raangs, G.J. Jansen, F. Schut, and G.W. Welling Variation of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes Appl. Environ. Microbiol. 64 1998 3336 3345
    • (1998) Appl. Environ. Microbiol. , vol.64 , pp. 3336-3345
    • Franks, A.H.1    Harmsen, H.J.M.2    Raangs, G.C.3    Jansen, G.J.4    Schut, F.5    Welling, G.W.6
  • 8
    • 0035488974 scopus 로고    scopus 로고
    • Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus
    • M.W. Friedrich, D. Schmitt-Wagner, T. Lueders, and A. Brune Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus Appl. Environ. Microbiol. 67 2001 4880 4890
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 4880-4890
    • Friedrich, M.W.1    Schmitt-Wagner, D.2    Lueders, T.3    Brune, A.4
  • 9
    • 0037133369 scopus 로고    scopus 로고
    • Diversity and phylogenetic analysis of bacteria in mucosa of chicken ceca and comparison with bacteria in the cecal lumen
    • J. Gong, R.J. Forster, H. Yu, J.R. Chambers, P.M. Sabour, R. Wheatcroft, and S. Chen Diversity and phylogenetic analysis of bacteria in mucosa of chicken ceca and comparison with bacteria in the cecal lumen FEMS Microbiol. Lett. 208 2002 1 7
    • (2002) FEMS Microbiol. Lett. , vol.208 , pp. 1-7
    • Gong, J.1    Forster, R.J.2    Yu, H.3    Chambers, J.R.4    Sabour, P.M.5    Wheatcroft, R.6    Chen, S.7
  • 10
    • 0036024611 scopus 로고    scopus 로고
    • Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods
    • H. Hayashi, M. Sakamoto, and Y. Benno Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods Microbiol. Immunol. 46 2002 535 548
    • (2002) Microbiol. Immunol. , vol.46 , pp. 535-548
    • Hayashi, H.1    Sakamoto, M.2    Benno, Y.3
  • 11
    • 0036917143 scopus 로고    scopus 로고
    • Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation
    • H. Hayashi, M. Sakamoto, and Y. Benno Fecal microbial diversity in a strict vegetarian as determined by molecular analysis and cultivation Microbiol. Immunol. 46 2002 819 831
    • (2002) Microbiol. Immunol. , vol.46 , pp. 819-831
    • Hayashi, H.1    Sakamoto, M.2    Benno, Y.3
  • 12
    • 0042471955 scopus 로고    scopus 로고
    • Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP
    • H. Hayashi, M. Sakamoto, M. Kitahara, and Y. Benno Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP Microbiol. Immunol. 47 2003 557 570
    • (2003) Microbiol. Immunol. , vol.47 , pp. 557-570
    • Hayashi, H.1    Sakamoto, M.2    Kitahara, M.3    Benno, Y.4
  • 13
    • 0036139245 scopus 로고    scopus 로고
    • Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA
    • H.G.H.J. Heilig, E.G. Zoetendal, E.E. Vaughan, P. Marteau, A.D.L. Akkermans, and W.M. de Vos Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA Appl. Environ. Microbiol. 68 2002 114 123
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 114-123
    • Heilig, H.G.H.J.1    Zoetendal, E.G.2    Vaughan, E.E.3    Marteau, P.4    Akkermans, A.D.L.5    De Vos, W.M.6
  • 14
    • 0029115109 scopus 로고
    • Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens
    • A. Hiraishi, Y. Kamagata, and K. Nakamura Polymerase chain reaction amplification and restriction fragment length polymorphism analysis of 16S rRNA genes from methanogens J. Ferment. Bioeng. 79 1995 523 529
    • (1995) J. Ferment. Bioeng. , vol.79 , pp. 523-529
    • Hiraishi, A.1    Kamagata, Y.2    Nakamura, K.3
  • 15
    • 0036185771 scopus 로고    scopus 로고
    • Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis
    • G.L. Hold, S.E. Pryde, V.J. Russell, E. Furrie, and H.J. Flint Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis FEMS Microbiol. Ecol. 39 2002 33 39
    • (2002) FEMS Microbiol. Ecol. , vol.39 , pp. 33-39
    • Hold, G.L.1    Pryde, S.E.2    Russell, V.J.3    Furrie, E.4    Flint, H.J.5
  • 16
    • 0033865965 scopus 로고    scopus 로고
    • Catenibacterium mitsuikai gen. nov., sp. nov., a Gram-positive anaerobic bacterium isolated from human faeces
    • A. Kageyama, and Y. Benno Catenibacterium mitsuikai gen. nov., sp. nov., a Gram-positive anaerobic bacterium isolated from human faeces Int. J. Syst. Evol. Microbiol. 50 2000 1595 1599
    • (2000) Int. J. Syst. Evol. Microbiol. , vol.50 , pp. 1595-1599
    • Kageyama, A.1    Benno, Y.2
  • 17
    • 0032899737 scopus 로고    scopus 로고
    • Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsellaas Collinsella aerofaciens gen. nov., comb. nov.
    • A. Kageyama, Y. Benno, and T. Nakase Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsellaas Collinsella aerofaciens gen. nov., comb. nov. Int. J. Syst. Bacteriol. 2 1999 557 565
    • (1999) Int. J. Syst. Bacteriol. , vol.2 , pp. 557-565
    • Kageyama, A.1    Benno, Y.2    Nakase, T.3
  • 18
    • 0032726894 scopus 로고    scopus 로고
    • Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov.
    • A. Kageyama, Y. Benno, and T. Nakase Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov. Int. J. Syst. Bacteriol. 49 1999 1725 1732
    • (1999) Int. J. Syst. Bacteriol. , vol.49 , pp. 1725-1732
    • Kageyama, A.1    Benno, Y.2    Nakase, T.3
  • 19
    • 0242657463 scopus 로고    scopus 로고
    • Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities
    • A.D. Kent, D.J. Smith, B.J. Benson, and E.W. Triplett Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities Appl. Environ. Microbiol. 69 2003 6768 6776
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 6768-6776
    • Kent, A.D.1    Smith, D.J.2    Benson, B.J.3    Triplett, E.W.4
  • 20
    • 0035040382 scopus 로고    scopus 로고
    • Terminal restriction fragment patterns: A tool for comparing microbial communities and assessing community dynamics
    • C.L. Kitts Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics Curr. Issues Intest. Microbiol. 2 2001 17 25
    • (2001) Curr. Issues Intest. Microbiol. , vol.2 , pp. 17-25
    • Kitts, C.L.1
  • 21
    • 0001857117 scopus 로고
    • 16S/23S rRNA sequencing
    • E. Stackebrandt M. Goodfellow Wiley Chichester
    • D.J. Lane 16S/23S rRNA sequencing E. Stackebrandt M. Goodfellow Nucleic acid techniques in bacterial systematics 1991 Wiley Chichester 115 175
    • (1991) Nucleic Acid Techniques in Bacterial Systematics , pp. 115-175
    • Lane, D.J.1
  • 22
    • 0029162158 scopus 로고
    • Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and application in fecal samples
    • P.S. Langendijik, F. Schut, G.J. Jansen, G.C. Raangs, G.R. Kamphuis, M.H.F. Wilkinson, and G.W. Welling Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and application in fecal samples Appl. Environ. Microbiol. 61 1995 3069 3075
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 3069-3075
    • Langendijik, P.S.1    Schut, F.2    Jansen, G.J.3    Raangs, G.C.4    Kamphuis, G.R.5    Wilkinson, M.H.F.6    Welling, G.W.7
  • 23
    • 0030661563 scopus 로고    scopus 로고
    • Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA
    • W.-T. Liu, T.L. Marsh, H. Cheng, and L. Forney Characterization of microbial diversity by determining terminal restriction fragment length polymorphism of genes encoding 16S rRNA Appl. Environ. Microbiol. 63 1997 4516 4522
    • (1997) Appl. Environ. Microbiol. , vol.63 , pp. 4516-4522
    • Liu, W.-T.1    Marsh, T.L.2    Cheng, H.3    Forney, L.4
  • 24
    • 0343503030 scopus 로고    scopus 로고
    • Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores
    • H. Ludemann, I. Arth, and W. Liesack Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores Appl. Environ. Microbiol. 66 2000 754 762
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 754-762
    • Ludemann, H.1    Arth, I.2    Liesack, W.3
  • 25
    • 0033933786 scopus 로고    scopus 로고
    • Archaeal population dynamics during sequential reduction processes in rice field soil
    • T. Lueders, and M. Friedrich Archaeal population dynamics during sequential reduction processes in rice field soil Appl. Environ. Microbiol. 66 2000 2732 2742
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 2732-2742
    • Lueders, T.1    Friedrich, M.2
  • 26
    • 0031860407 scopus 로고    scopus 로고
    • Beginning a molecular analysis of the eukaryal community in activated sludge
    • T.L. Marsh, W.T. Liu, L.J. Forney, and H. Cheng Beginning a molecular analysis of the eukaryal community in activated sludge Water Sci. Technol. 37 1998 455 460
    • (1998) Water Sci. Technol. , vol.37 , pp. 455-460
    • Marsh, T.L.1    Liu, W.T.2    Forney, L.J.3    Cheng, H.4
  • 27
    • 0033868092 scopus 로고    scopus 로고
    • Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis
    • T.L. Marsh, P. P. Saxman, J. Cole, and J. Tiedje Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis Appl. Environ. Microbiol. 66 2000 3616 3620
    • (2000) Appl. Environ. Microbiol. , vol.66 , pp. 3616-3620
    • Marsh, T.L.1    Saxman P, P.2    Cole, J.3    Tiedje, J.4
  • 28
    • 0034987688 scopus 로고    scopus 로고
    • Molecular ecological analysis of dietary and antibiotic-induce alterations of the mouse intestinal microbiota
    • V.J. McCracken, J.M. Simson, R.I. Mackie, and H.R. Gaskins Molecular ecological analysis of dietary and antibiotic-induce alterations of the mouse intestinal microbiota J. Nutr. 131 2001 1862 1870
    • (2001) J. Nutr. , vol.131 , pp. 1862-1870
    • McCracken, V.J.1    Simson, J.M.2    MacKie, R.I.3    Gaskins, H.R.4
  • 30
    • 0016167941 scopus 로고
    • Human fecal flora: The normal flora of 20 Japanese-Hawaiians
    • W.E.C. Moore, and L.V. Holdman Human fecal flora: the normal flora of 20 Japanese-Hawaiians Appl. Microbiol. 27 1974 961 979
    • (1974) Appl. Microbiol. , vol.27 , pp. 961-979
    • Moore, W.E.C.1    Holdman, L.V.2
  • 31
    • 0347297590 scopus 로고    scopus 로고
    • Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces
    • K. Nagashima, T. Hisada, M. Sato, and J. Mochizuki Application of new primer-enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces Appl. Environ. Microbiol. 69 2003 1251 1262
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 1251-1262
    • Nagashima, K.1    Hisada, T.2    Sato, M.3    Mochizuki, J.4
  • 32
    • 0023989064 scopus 로고
    • Improvement tools for biological sequence comparison
    • E.W. Pearson, and D.J. Lipman Improvement tools for biological sequence comparison Proc. Natl. Acad. Sci. U. S. A. 85 1988 2444 2448
    • (1988) Proc. Natl. Acad. Sci. U. S. A. , vol.85 , pp. 2444-2448
    • Pearson, E.W.1    Lipman, D.J.2
  • 33
    • 0037281247 scopus 로고    scopus 로고
    • Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities
    • M. Sakamoto, H. Hayashi, and Y. Benno Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities Microbiol. Immunol. 47 2003 133 142
    • (2003) Microbiol. Immunol. , vol.47 , pp. 133-142
    • Sakamoto, M.1    Hayashi, H.2    Benno, Y.3
  • 34
    • 0037239111 scopus 로고    scopus 로고
    • Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis
    • M. Sakamoto, Y. Takeuchi, M. Umeda, I. Ishikawa, and Y. Benno Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis J. Med. Microbiol. 52 2003 79 89
    • (2003) J. Med. Microbiol. , vol.52 , pp. 79-89
    • Sakamoto, M.1    Takeuchi, Y.2    Umeda, M.3    Ishikawa, I.4    Benno, Y.5
  • 35
    • 0032925262 scopus 로고    scopus 로고
    • Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota
    • J.M. Simpson, V.J. McCracken, B.A. White, H.R. Gaskins, and R.I. Mackie Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota J. Microbiol. Methods 36 1999 167 179
    • (1999) J. Microbiol. Methods , vol.36 , pp. 167-179
    • Simpson, J.M.1    McCracken, V.J.2    White, B.A.3    Gaskins, H.R.4    MacKie, R.I.5
  • 36
    • 0032755259 scopus 로고    scopus 로고
    • Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut
    • A. Suau, R. Bonnet, M. Sutren, J.J. Godon, G.R. Gibson, M.D. Collins, and J. Dore Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut Appl. Environ. Microbiol. 65 1999 4799 4807
    • (1999) Appl. Environ. Microbiol. , vol.65 , pp. 4799-4807
    • Suau, A.1    Bonnet, R.2    Sutren, M.3    Godon, J.J.4    Gibson, G.R.5    Collins, M.D.6    Dore, J.7
  • 37
    • 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
    • E.G. Zoetendal, A.D.L. Akkermans, and W.M. de Vos 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 1998 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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