-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 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
Lipman, D.J.7
-
2
-
-
0028946084
-
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
-
Amann, R. J., W. Ludwig, and K. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Mol. Biol. Rev. 59, 143-169.
-
(1995)
Microbiol. Mol. Biol. Rev.
, vol.59
, pp. 143-169
-
-
Amann, R.J.1
Ludwig, W.2
Schleifer, K.3
-
3
-
-
29144504177
-
At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies
-
Ashelford, K. E., N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J Weightman. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71, 7724-7736.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 7724-7736
-
-
Ashelford, K.E.1
Chuzhanova, N.A.2
Fry, J.C.3
Jones, A.J.4
Weightman, A.J.5
-
4
-
-
20144364162
-
Higher-level classification of the Archaea: evolution of methanogenesis and methanogens
-
Bapteste, E., C. Brochier, and Y. Boucher. 2005. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1, 353-363.
-
(2005)
Archaea
, vol.1
, pp. 353-363
-
-
Bapteste, E.1
Brochier, C.2
Boucher, Y.3
-
5
-
-
38549164691
-
GenBank
-
Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. 2008. GenBank. Nucleic Acids Res. 36, D25-D30.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
6
-
-
68249149027
-
Dominance of Methanomicrobium phylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis)
-
Chaudhary, P. P. and S. K. Sirohi. 2009. Dominance of Methanomicrobium phylotype in methanogen population present in Murrah buffaloes (Bubalus bubalis). Lett. Appl. Microbiol. 49, 274-277.
-
(2009)
Lett. Appl. Microbiol.
, vol.49
, pp. 274-277
-
-
Chaudhary, P.P.1
Sirohi, S.K.2
-
7
-
-
35948938623
-
Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane
-
Denman, S. E., N. W. Tomkins, and C. S. McSweeney. 2007. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol. Ecol. 62, 313-322.
-
(2007)
FEMS Microbiol. Ecol.
, vol.62
, pp. 313-322
-
-
Denman, S.E.1
Tomkins, N.W.2
McSweeney, C.S.3
-
9
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
10
-
-
0002051540
-
BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
-
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
-
(1999)
Nucleic Acids Symp. Ser.
, vol.41
, pp. 95-98
-
-
Hall, T.A.1
-
11
-
-
0041389955
-
Saponin rich tropical fruits affect fermentation and methanogenesis in faunated and defaunated rumen fluid
-
Hess, H. D., M. Kreuzer, T. E. Díaz, C. E. Lascano, J. E. Carulla, C. R. Soliva, and A. Machmüller. 2003. Saponin rich tropical fruits affect fermentation and methanogenesis in faunated and defaunated rumen fluid. Anim. Feed Sci. Technol. 109, 79-94.
-
(2003)
Anim. Feed Sci. Technol.
, vol.109
, pp. 79-94
-
-
Hess, H.D.1
Kreuzer, M.2
Díaz, T.E.3
Lascano, C.E.4
Carulla, J.E.5
Soliva, C.R.6
Machmüller, A.7
-
12
-
-
58149389302
-
Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow
-
Hook, S. E., K. S. Northwood, A. D. G. Wright, and B. W. McBride. 2009. Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Appl. Environ. Microbiol. 75, 374-380.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 374-380
-
-
Hook, S.E.1
Northwood, K.S.2
Wright, A.D.G.3
McBride, B.W.4
-
13
-
-
11044237974
-
Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa
-
Irbis, C. and K. Ushida. 2004. Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. J. Gen. Appl. Microbiol. 50, 203-212.
-
(2004)
J. Gen. Appl. Microbiol.
, vol.50
, pp. 203-212
-
-
Irbis, C.1
Ushida, K.2
-
15
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
16
-
-
0030860126
-
Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA-targeted oligonucleotide probes
-
Lin, C., L. Raskin, and D. A. Stahl. 1997. Microbial community structure in gastrointestinal tracts of domestic animals: comparative analyses using rRNA-targeted oligonucleotide probes. FEMS Microbiol. Ecol. 22, 281-294.
-
(1997)
FEMS Microbiol. Ecol.
, vol.22
, pp. 281-294
-
-
Lin, C.1
Raskin, L.2
Stahl, D.A.3
-
17
-
-
0029062828
-
Formation of complexes between polyvinyl pyrrolidones or polyethylene glycols and tannins, and their implication in gas production and true digestibility in in vitro techniques
-
Makkar, H. P. S., M. Blümmel, and K. Becker. 1995. Formation of complexes between polyvinyl pyrrolidones or polyethylene glycols and tannins, and their implication in gas production and true digestibility in in vitro techniques. Br. J. Nutr. 73, 897-913.
-
(1995)
Br. J. Nutr.
, vol.73
, pp. 897-913
-
-
Makkar, H.P.S.1
Blümmel, M.2
Becker, K.3
-
18
-
-
0002383758
-
Estimation of the energetic feed value obtained by chemical analysis and in vitro gas production using rumen fluid
-
Menke, K. H. and H. Steingass. 1988. Estimation of the energetic feed value obtained by chemical analysis and in vitro gas production using rumen fluid. Anim. Res. Dev. 28, 7-55.
-
(1988)
Anim. Res. Dev.
, vol.28
, pp. 7-55
-
-
Menke, K.H.1
Steingass, H.2
-
19
-
-
76849092210
-
Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle
-
Pei, C. X., S. Y. Mao, Y. F. Cheng, and W. Y. Zhu. 2009. Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle. Animal 4, 20-29.
-
(2009)
Animal
, vol.4
, pp. 20-29
-
-
Pei, C.X.1
Mao, S.Y.2
Cheng, Y.F.3
Zhu, W.Y.4
-
20
-
-
3843051445
-
Assessment of ciliates in the sheep rumen by DGGE
-
Regensbogenova, M., P. Pristas, P. Javorsky, S. Y. Moon-van Der Staay, G. W. M. van Der Staay, J. H. P. Hackstein, C. J. Newbold, and N. R. McEwan. 2004. Assessment of ciliates in the sheep rumen by DGGE. Lett. Appl. Microbiol. 39, 144-147.
-
(2004)
Lett. Appl. Microbiol.
, vol.39
, pp. 144-147
-
-
Regensbogenova, M.1
Pristas, P.2
Javorsky, P.3
Moon-van der staay, S.Y.4
van der Staay, G.W.M.5
Hackstein, J.H.P.6
Newbold, C.J.7
Mcewan, N.R.8
-
21
-
-
0034727087
-
The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum
-
Ruepp, A., W. Graml, M. L. Santos-Martinez, K. K. Koretke, C. Volker, H. W. Mewes, D. Frishman, S. Stocker, A. N. Lupas, and W. Baumeister. 2000. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508-513.
-
(2000)
Nature
, vol.407
, pp. 508-513
-
-
Ruepp, A.1
Graml, W.2
Santos-Martinez, M.L.3
Koretke, K.K.4
Volker, C.5
Mewes, H.W.6
Frishman, D.7
Stocker, S.8
Lupas, A.N.9
Baumeister, W.10
-
22
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
24
-
-
0032080814
-
Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system
-
Sharp, R., C. J. Ziemer, M. D. Stern, and D. A. Stahl. 1998. Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system. FEMS Microbiol. Ecol. 26, 71-78.
-
(1998)
FEMS Microbiol. Ecol.
, vol.26
, pp. 71-78
-
-
Sharp, R.1
Ziemer, C.J.2
Stern, M.D.3
Stahl, D.A.4
-
25
-
-
8844267653
-
Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence
-
Shin, E. C., B. R. Choi, W. J. Lim, S. Y. Hong, C. L. An, K. M. Cho, Y. K. Kim, and H. D. Yun. 2004. Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe 10, 313-319.
-
(2004)
Anaerobe
, vol.10
, pp. 313-319
-
-
Shin, E.C.1
Choi, B.R.2
Lim, W.J.3
Hong, S.Y.4
An, C.L.5
Cho, K.M.6
Kim, Y.K.7
Yun, H.D.8
-
26
-
-
0032976011
-
Phylogenetic diversity of symbiotic methanogens living in the hindgut of the lower termite Reticulitermes speratus analyzed by PCR and in situ hybridization
-
Shinzato, N., T. Matsumoto, I. Yamaoka, T. Oshima, and A. Yamagishi. 1999. Phylogenetic diversity of symbiotic methanogens living in the hindgut of the lower termite Reticulitermes speratus analyzed by PCR and in situ hybridization. Appl. Environ. Microbiol. 65, 837-840.
-
(1999)
Appl. Environ. Microbiol.
, vol.65
, pp. 837-840
-
-
Shinzato, N.1
Matsumoto, T.2
Yamaoka, I.3
Oshima, T.4
Yamagishi, A.5
-
27
-
-
4544357886
-
16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs
-
Skillman, L. C., P. N. Evans, G. E. Naylor, B. Morvan, G. N. Jarvis, and K. N. Joblin. 2004. 16S ribosomal DNA-directed PCR primers for ruminal methanogens and identification of methanogens colonising young lambs. Anaerobe 10, 277-285.
-
(2004)
Anaerobe
, vol.10
, pp. 277-285
-
-
Skillman, L.C.1
Evans, P.N.2
Naylor, G.E.3
Morvan, B.4
Jarvis, G.N.5
Joblin, K.N.6
-
28
-
-
0035849668
-
Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens
-
Tajima, K., T. Nagamine, H. Matsui, M. Nakamura, and R. I. Aminov. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol. Lett. 200, 67-72.
-
(2001)
FEMS Microbiol. Lett.
, vol.200
, pp. 67-72
-
-
Tajima, K.1
Nagamine, T.2
Matsui, H.3
Nakamura, M.4
Aminov, R.I.5
-
29
-
-
34547781750
-
MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
-
Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 1596-1599
-
-
Tamura, K.1
Dudley, J.2
Nei, M.3
Kumar, S.4
-
30
-
-
27544484487
-
Methane production from in vitro rumen incubations with Lotus pedunculatus and Medicago sativa, and effects of extractable condensed tannin fractions on methanogenesis
-
Tavendale, M. H., L. P. Meagher, D. Pacheco, N. Walker, G. T. Attwood, and S. Sivakumaran. 2005. Methane production from in vitro rumen incubations with Lotus pedunculatus and Medicago sativa, and effects of extractable condensed tannin fractions on methanogenesis. Anim. Feed Sci. Technol. 123, 403-419.
-
(2005)
Anim. Feed Sci. Technol.
, vol.123
, pp. 403-419
-
-
Tavendale, M.H.1
Meagher, L.P.2
Pacheco, D.3
Walker, N.4
Attwood, G.T.5
Sivakumaran, S.6
-
31
-
-
84925364141
-
Determination of extractable and bound condensed tannin concentrations in forage plants, protein concentrate meals and cereal grains
-
Terrill, T. H., A. M. Rowan, G. B. Douglas, and T. N. Barry. 1992. Determination of extractable and bound condensed tannin concentrations in forage plants, protein concentrate meals and cereal grains. J. Sci. Food Agric. 58, 321-329.
-
(1992)
J. Sci. Food Agric.
, vol.58
, pp. 321-329
-
-
Terrill, T.H.1
Rowan, A.M.2
Douglas, G.B.3
Barry, T.N.4
-
32
-
-
0000616298
-
Condensed tannin concentration in Sericea lespedeza as influenced by preservation method
-
Terrill, T. H., W. R. Windham, J. J. Evans, and C. S. Hoveland. 1990. Condensed tannin concentration in Sericea lespedeza as influenced by preservation method. Crop Sci. 30, 219-224.
-
(1990)
Crop Sci.
, vol.30
, pp. 219-224
-
-
Terrill, T.H.1
Windham, W.R.2
Evans, J.J.3
Hoveland, C.S.4
-
33
-
-
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., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
34
-
-
79959699455
-
-
US-EPA, Washington, D. C.: United States Environmental Protection Agency EPA 430-R-06-003
-
US-EPA. 2006. Washington, D. C.: United States Environmental Protection Agency EPA 430-R-06-003.
-
(2006)
-
-
-
36
-
-
3142580313
-
Phylogenetic analysis of methanogens from the bovine rumen
-
Whitford, M. F., R. M. Teather, and R. J. Forster. 2001. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol. 1, 5.
-
(2001)
BMC Microbiol.
, vol.1
, pp. 5
-
-
Whitford, M.F.1
Teather, R.M.2
Forster, R.J.3
-
37
-
-
0001814282
-
Early indications that methane emissions from ruminants
-
Woodward, S. I., G. C. Waghorn, M. J. Ulyatt, and K. R. Lassey. 2001. Early indications that methane emissions from ruminants. Proc. N. Z. Soc. Anim. Prod. 61, 23-26.
-
(2001)
Proc. N.Z. Soc. Anim. Prod.
, vol.61
, pp. 23-26
-
-
Woodward, S.I.1
Waghorn, G.C.2
Ulyatt, M.J.3
Lassey, K.R.4
-
38
-
-
34447511716
-
Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada
-
Wright, A. D. G., C. H. Auckland, and D. H. Lynn. 2007. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl. Environ. Microbiol. 73, 4206-4210.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 4206-4210
-
-
Wright, A.D.G.1
Auckland, C.H.2
Lynn, D.H.3
-
39
-
-
46149087251
-
Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela
-
Wright, A. D. G., X. Ma, and N. E. Obispo. 2008. Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microb. Ecol. 56, 390-394.
-
(2008)
Microb. Ecol.
, vol.56
, pp. 390-394
-
-
Wright, A.D.G.1
Ma, X.2
Obispo, N.E.3
-
40
-
-
0141643392
-
Improved strategy for presumptive identification of methanogens using 16S riboprinting
-
Wright, A. D. G. and C. L. Pimm. 2003. Improved strategy for presumptive identification of methanogens using 16S riboprinting. J. Microbiol. Methods 55, 337-349.
-
(2003)
J. Microbiol. Methods
, vol.55
, pp. 337-349
-
-
Wright, A.D.G.1
Pimm, C.L.2
-
41
-
-
33744800527
-
Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea
-
Wright, A. D. G., A. F. Toovey, and C. L. Pimm. 2006. Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea. Anaerobe 12, 134-139.
-
(2006)
Anaerobe
, vol.12
, pp. 134-139
-
-
Wright, A.D.G.1
Toovey, A.F.2
Pimm, C.L.3
-
42
-
-
1642408693
-
Molecular diversity of rumen methanogens from sheep in Western Australia
-
Wright, A. D. G., A. J. Williams, B. Winder, C. Christophersen, S. Rodgers, and K. Smith. 2004. Molecular diversity of rumen methanogens from sheep in Western Australia. Appl. Environ. Microbiol. 70, 1263-1270.
-
(2004)
Appl. Environ. Microbiol.
, vol.70
, pp. 1263-1270
-
-
Wright, A.D.G.1
Williams, A.J.2
Winder, B.3
Christophersen, C.4
Rodgers, S.5
Smith, K.6
-
43
-
-
0034251959
-
Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization
-
Yanagita, K., Y. Kamagata, M. Kawaharasaki, T. Suzuki, Y. Nakamura, and H. Minato. 2000. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci. Biotechnol. Biochem. 64, 1737-1742.
-
(2000)
Biosci. Biotechnol. Biochem.
, vol.64
, pp. 1737-1742
-
-
Yanagita, K.1
Kamagata, Y.2
Kawaharasaki, M.3
Suzuki, T.4
Nakamura, Y.5
Minato, H.6
|