-
1
-
-
1942443733
-
Diverge and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
-
S.G. Acinas L.A. Marcelino V. Klepac-Ceraj M.F. Polz 2004 Diverge 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
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
S.F. Althschul F. Thomas L. Madden A. Schaffer J. Zhang Z. Zhang W. Miller D. 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
-
-
Althschul, S.F.1
Thomas, F.2
Madden, L.3
Schaffer, A.4
Zhang, J.5
Zhang, Z.6
Miller, W.7
Lipman, D.8
-
3
-
-
10244260491
-
Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium
-
V. Barbe D. Vallenet N. Fonknechten A. Kreimeyer S. Oztas L. Labarre S. Cruveiller C. Robert S. Duprat P. Wincker L.N. Ornston J. Weissenbach P. Marlière G.N. Cohen C. Médigue 2004 Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium Nucleic Acids Res. 32 5766 5779
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5766-5779
-
-
Barbe, V.1
Vallenet, D.2
Fonknechten, N.3
Kreimeyer, A.4
Oztas, S.5
Labarre, L.6
Cruveiller, S.7
Robert, C.8
Duprat, S.9
Wincker, P.10
Ornston, L.N.11
Weissenbach, J.12
Marlière, P.13
Cohen, G.N.14
Médigue, C.15
-
5
-
-
0141891348
-
Genomic analysis of uncultured marine viral communities
-
M. Breitbart P. Salamon B. Andresen J.M. Mahaffy A.M. Segall D. Mead F. Azam F. Rohwer 2003 Genomic analysis of uncultured marine viral communities J. Bacteriol. 185 6220 6223
-
(2003)
J. Bacteriol.
, vol.185
, pp. 6220-6223
-
-
Breitbart, M.1
Salamon, P.2
Andresen, B.3
Mahaffy, J.M.4
Segall, A.M.5
Mead, D.6
Azam, F.7
Rohwer, F.8
-
6
-
-
0035656112
-
Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community
-
A. Buchan E.L. Neidle M.A. Moran 2001 Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community Appl. Environ. Microbiol. 67 5801 5809
-
(2001)
Appl. Environ. Microbiol.
, vol.67
, pp. 5801-5809
-
-
Buchan, A.1
Neidle, E.L.2
Moran, M.A.3
-
8
-
-
0029931803
-
Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium
-
N. Christiansen B.K. Ahring 1996 Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium Int. J. Syst. Bacteriol. 46 442 448
-
(1996)
Int. J. Syst. Bacteriol.
, vol.46
, pp. 442-448
-
-
Christiansen, N.1
Ahring, B.K.2
-
9
-
-
33846072878
-
The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data
-
J.R. Cole B. Chai R.J. Farris Q. Wang A.S. Kulam-Syed-Mohideen D.M. McGarrell A.M. Bandela E. Cardenas G.M. Garrity J.M. Tiedje 2007 The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data Nucleic Acids Res. 35 D169 172
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 169-172
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam-Syed-Mohideen, A.S.5
McGarrell, D.M.6
Bandela, A.M.7
Cardenas, E.8
Garrity, G.M.9
Tiedje, J.M.10
-
11
-
-
0041851187
-
Isolation, characterization and comparison of bacteria from swine feces and manure storage pits
-
M.A. Cotta T.R. Whitehead R.L. Zeltwanger 2003 Isolation, characterization and comparison of bacteria from swine feces and manure storage pits Environ. Microbiol. 5 737 745
-
(2003)
Environ. Microbiol.
, vol.5
, pp. 737-745
-
-
Cotta, M.A.1
Whitehead, T.R.2
Zeltwanger, R.L.3
-
12
-
-
0037388225
-
Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity
-
L.D. Crosby C.S. Criddle 2003 Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity Biotechniques 34 790 794
-
(2003)
Biotechniques
, vol.34
, pp. 790-794
-
-
Crosby, L.D.1
Criddle, C.S.2
-
13
-
-
0035956608
-
Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes
-
K. Daly C.S. Stewart H.J. Flint S.P. Shirazi-Beechey 2001 Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes FEMS Microbiol. Ecol. 38 141 151
-
(2001)
FEMS Microbiol. Ecol.
, vol.38
, pp. 141-151
-
-
Daly, K.1
Stewart, C.S.2
Flint, H.J.3
Shirazi-Beechey, S.P.4
-
14
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
P.B. Eckburg E.M. Bik C.N. Bernstein E. Purdom L. Dethlefsen M. Sargent S.R. Gill K.E. Nelson D.A. Relman 2005 Diversity of the human intestinal microbial flora Science 308 1635 1638
-
(2005)
Science
, vol.308
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
16
-
-
0038180530
-
Phenotypic description and antimicrobial susceptibilities of Aerococcus sanguinicola isolates from human clinical samples
-
R. Facklam M. Lovgren P.L. Shewmaker G. Tyrrell 2003 Phenotypic description and antimicrobial susceptibilities of Aerococcus sanguinicola isolates from human clinical samples J. Clin. Microbiol. 41 2587 2592
-
(2003)
J. Clin. Microbiol.
, vol.41
, pp. 2587-2592
-
-
Facklam, R.1
Lovgren, M.2
Shewmaker, P.L.3
Tyrrell, G.4
-
17
-
-
26844541486
-
Effects of orally administered tetracycline on the intestinal community structure of chickens and on tet determinant carriage by commensal bacteria and Campylobacter jejuni
-
A.S. Fairchild J.L. Smith U. Idris J. Lu S. Sanchez L.B. Purvis C. Hofacre M.D. Lee 2005 Effects of orally administered tetracycline on the intestinal community structure of chickens and on tet determinant carriage by commensal bacteria and Campylobacter jejuni Appl. Environ. Microbiol. 71 5865 5872
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 5865-5872
-
-
Fairchild, A.S.1
Smith, J.L.2
Idris, U.3
Lu, J.4
Sanchez, S.5
Purvis, L.B.6
Hofacre, C.7
Lee, M.D.8
-
18
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
S.R. Gill M. Pop R.T. Deboy P.B. Eckburg P.J. Turnbaugh B.S. Samuel J.I. Gordon D.A. Relman C.M. Fraser-Liggett K.E. Nelson 2006 Metagenomic analysis of the human distal gut microbiome Science 312 1355 1359
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
Deboy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
19
-
-
33845678685
-
16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: From crops to ceca
-
J. Gong W. Si R.J. Forster R. Huang H. Yu Y. Yin C. Yang Y. Han 2007 16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: from crops to ceca FEMS Microbiol. Ecol. 59 147 157
-
(2007)
FEMS Microbiol. Ecol.
, vol.59
, pp. 147-157
-
-
Gong, J.1
Si, W.2
Forster, R.J.3
Huang, R.4
Yu, H.5
Yin, Y.6
Yang, C.7
Han, Y.8
-
20
-
-
5044240973
-
Bellerophon: A program to detect chimeric sequences in multiple sequence alignments
-
T. Huber G. Faulkner P. Hugenholtz 2004 Bellerophon: a program to detect chimeric sequences in multiple sequence alignments Bioinformatics 20 2317 2319
-
(2004)
Bioinformatics
, vol.20
, pp. 2317-2319
-
-
Huber, T.1
Faulkner, G.2
Hugenholtz, P.3
-
21
-
-
0032478603
-
Biochemical and molecular characterization of 1-hydroxy-2-naphthoate dioxygenase from Nocardioides sp. KP7
-
T. Iwabuchi S. Harayama 1998 Biochemical and molecular characterization of 1-hydroxy-2-naphthoate dioxygenase from Nocardioides sp. KP7 J. Biol. Chem. 273 8332 8336
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 8332-8336
-
-
Iwabuchi, T.1
Harayama, S.2
-
22
-
-
33644952722
-
Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes
-
P.H. Janssen 2006 Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes Appl. Environ. Microbiol. 72 1719 1728
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 1719-1728
-
-
Janssen, P.H.1
-
23
-
-
0035197202
-
Implication of multiple antimicrobial-resistant enterococci associated with the poultry environment
-
S.W. Joseph J.R. Hayes L.L. English L.E. Carr D.D. Wagner 2001 Implication of multiple antimicrobial-resistant enterococci associated with the poultry environment Food Addit. Contam. 18 1118 1123
-
(2001)
Food Addit. Contam.
, vol.18
, pp. 1118-1123
-
-
Joseph, S.W.1
Hayes, J.R.2
English, L.L.3
Carr, L.E.4
Wagner, D.D.5
-
24
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
K. Kurokawa T. Itoh T. Kuwahara K. Oshima H. Toh A. Toyoda H. Takami H. Morita V.K. Sharma T.P. Srivastava T.D. Taylor H. Noguchi H. Mori Y. Ogura D.S. Ehrlich K. Itoh T. Takagi Y. Sakaki T. Hayashi M. Hattori 2007 Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes DNA Res. 14 169 181
-
(2007)
DNA Res.
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
Taylor, T.D.11
Noguchi, H.12
Mori, H.13
Ogura, Y.14
Ehrlich, D.S.15
Itoh, K.16
Takagi, T.17
Sakaki, Y.18
Hayashi, T.19
Hattori, M.20
more..
-
28
-
-
34547501670
-
Identification of chicken-specific fecal microbial sequences using a metagenomic approach
-
J. Lu J.W. S. Domingo O.C. Shanks 2007 Identification of chicken-specific fecal microbial sequences using a metagenomic approach Water Res. 41 3561 3574
-
(2007)
Water Res.
, vol.41
, pp. 3561-3574
-
-
Lu, J.1
Domingo, J.W.S.2
Shanks, O.C.3
-
29
-
-
0034488341
-
How quantitative is quantitative PCR with respect to cell counts?
-
W. Ludwig K.H. Schleifer 2000 How quantitative is quantitative PCR with respect to cell counts? Syst. Appl. Microbiol. 23 556 562
-
(2000)
Syst. Appl. Microbiol.
, vol.23
, pp. 556-562
-
-
Ludwig, W.1
Schleifer, K.H.2
-
30
-
-
0037009845
-
A reverse transcription-PCR assay to detect viable Mycoplasma synoviae in poultry environmental samples
-
C. Marois C. Savoye M. Kobisch I. Kempf 2002 A reverse transcription-PCR assay to detect viable Mycoplasma synoviae in poultry environmental samples Vet. Microbiol. 89 17 28
-
(2002)
Vet. Microbiol.
, vol.89
, pp. 17-28
-
-
Marois, C.1
Savoye, C.2
Kobisch, M.3
Kempf, I.4
-
31
-
-
0033985050
-
Assigning genomic sequences to CATH
-
F.M.G. Pearl D. Lee J.E. Bray I. Sillitoe A.E. Todd A.P. Harrison J.M. Thornton C.A. Orengo 2000 Assigning genomic sequences to CATH Nucleic Acids Res. 28 277 282
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 277-282
-
-
Pearl, F.M.G.1
Lee, D.2
Bray, J.E.3
Sillitoe, I.4
Todd, A.E.5
Harrison, A.P.6
Thornton, J.M.7
Orengo, C.A.8
-
32
-
-
0033125574
-
Aspects of enzymology and biochemical properties of Brevibacterium linens relevant to cheese ripening: A review
-
F.P. Rattray P.F. Fox 1999 Aspects of enzymology and biochemical properties of Brevibacterium linens relevant to cheese ripening: a review J. Dairy Sci. 82 891 909
-
(1999)
J. Dairy Sci.
, vol.82
, pp. 891-909
-
-
Rattray, F.P.1
Fox, P.F.2
-
33
-
-
18844481269
-
Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms
-
M.R. Rondon P.R. August A.D. Bettermann S.F. Brady T.H. Grossman M.R. Liles K.A. Loiacono B.A. Lynch I.A. MacNeil C. Minor C.L. Tiong M. Gilman M.S. Osburne J. Clardy J. Handelsman R.M. Goodman 2000 Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl. Environ. Microbiol. 66 2541 2547
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 2541-2547
-
-
Rondon, M.R.1
August, P.R.2
Bettermann, A.D.3
Brady, S.F.4
Grossman, T.H.5
Liles, M.R.6
Loiacono, K.A.7
Lynch, B.A.8
MacNeil, I.A.9
Minor, C.10
Tiong, C.L.11
Gilman, M.12
Osburne, M.S.13
Clardy, J.14
Handelsman, J.15
Goodman, R.M.16
-
35
-
-
0036154232
-
Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic Myxobacterium
-
R.A. Sanford J.R. Cole J.M. Tiedje 2002 Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic Myxobacterium Appl. Environ. Microbiol. 68 893 900
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 893-900
-
-
Sanford, R.A.1
Cole, J.R.2
Tiedje, J.M.3
-
36
-
-
2142687116
-
Metagenome survey of biofilms in drinking-water networks
-
C. Schmeisser C. Stöckigt C. Raasch J. Wingender K.N. Timmis D.F. Wenderoth H.C. Flemming H. Liesegang R.A. Schmitz K.-E. Jaeger W.R. Streit 2003 Metagenome survey of biofilms in drinking-water networks Appl. Environ. Microbiol. 69 7298 7309
-
(2003)
Appl. Environ. Microbiol.
, vol.69
, pp. 7298-7309
-
-
Schmeisser, C.1
Stöckigt, C.2
Raasch, C.3
Wingender, J.4
Timmis, K.N.5
Wenderoth, D.F.6
Flemming, H.C.7
Liesegang, H.8
Schmitz, R.A.9
Jaeger, K.-E.10
Streit, W.R.11
-
37
-
-
33947211934
-
Succession in the intestinal microbiota of preadolescent turkeys
-
A.J. Scupham 2007 Succession in the intestinal microbiota of preadolescent turkeys FEMS Microbiol. Ecol. 60 136 147
-
(2007)
FEMS Microbiol. Ecol.
, vol.60
, pp. 136-147
-
-
Scupham, A.J.1
-
38
-
-
34250210542
-
Examination of the microbial ecology of the avian intestine in vivo using bromouridine
-
A.J. Scupham 2007 Examination of the microbial ecology of the avian intestine in vivo using bromouridine Environ. Microbiol. 9 1801 1809
-
(2007)
Environ. Microbiol.
, vol.9
, pp. 1801-1809
-
-
Scupham, A.J.1
-
40
-
-
0032755259
-
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 J. Doré 1999 Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut Appl. Environ. Microbiol. 65 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
Doré, J.7
-
41
-
-
0033760479
-
Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays
-
M.T. Suzuki L.T. Taylor E.F. DeLong 2000 Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays Appl. Environ. Microbiol. 66 4605 4614
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 4605-4614
-
-
Suzuki, M.T.1
Taylor, L.T.2
Delong, E.F.3
-
42
-
-
0030660581
-
A genomic perspective on protein families
-
R.L. Tatusov E.V. Koonin D.J. Lipman 1997 A genomic perspective on protein families Science 278 631 637
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
43
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
S.G. Tringe C. Von Mering A. Kobayashi A.A. Salamov K. Chen H.W. Chang M. Podar J.M. Short E.J. Mathur J.C. Detter P. Bork P. Hugenholtz E.M. Rubin 2005 Comparative metagenomics of microbial communities Science 308 554 557
-
(2005)
Science
, vol.308
, pp. 554-557
-
-
Tringe, S.G.1
Von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
44
-
-
0036211846
-
Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20
-
Y. Zhong F. Chen S.W. Wilhelm L. Poorvin R.E. Hodson 2002 Phylogenetic diversity of marine cyanophage isolates and natural virus communities as revealed by sequences of viral capsid assembly protein gene g20 Appl. Environ. Microbiol. 68 1576 1584
-
(2002)
Appl. Environ. Microbiol.
, vol.68
, pp. 1576-1584
-
-
Zhong, Y.1
Chen, F.2
Wilhelm, S.W.3
Poorvin, L.4
Hodson, R.E.5
|