-
1
-
-
70449713952
-
The NIH Human Microbiome Project
-
Peterson, J. et al. The NIH Human Microbiome Project. Genome Res 19, 2317-2323 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
-
2
-
-
77957351250
-
Metagenomics of the intestinal microbiota: Potential applications
-
Ehrlich, S. D. Metagenomics of the intestinal microbiota: potential applications. Gastroenterologie clinique et biologique 34, Supplement 1 S23-S28 (2010).
-
(2010)
Gastroenterologie Clinique et Biologique
, vol.34
, pp. S23-S28
-
-
Ehrlich, S.D.1
-
3
-
-
79960931485
-
Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies
-
Pope, P. B. et al. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333, 646-648 (2011).
-
(2011)
Science
, vol.333
, pp. 646-648
-
-
Pope, P.B.1
-
4
-
-
26844447711
-
Genome-directed isolation of the key nitrogen fxer Leptospirillum ferrodiazotrophum sp. Nov. From an acidophilic microbial community
-
Tyson, G. W. et al. Genome-directed isolation of the key nitrogen fxer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl Environ Microbiol 71, 6319-6324 (2005).
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 6319-6324
-
-
Tyson, G.W.1
-
5
-
-
63149160427
-
Host cell-free growth of the Q fever bacterium Coxiella burnetii
-
Omsland, A. et al. Host cell-free growth of the Q fever bacterium Coxiella burnetii. Proc Natl Acad Sci USA 106, 4430-4434 (2009).
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 4430-4434
-
-
Omsland, A.1
-
6
-
-
84884411052
-
Bacterial colonization factors control specifcity and stability of the gut microbiota
-
Lee, S. M. et al. Bacterial colonization factors control specifcity and stability of the gut microbiota. Nature 501, 426-429 (2013).
-
(2013)
Nature
, vol.501
, pp. 426-429
-
-
Lee, S.M.1
-
7
-
-
84882312793
-
Metabolic niche of a prominent sulfate-reducing human gut bacterium
-
Rey, F. E. et al. Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc Natl Acad Sci USA 110, 13582-13587 (2013).
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 13582-13587
-
-
Rey, F.E.1
-
8
-
-
34447516925
-
Evolution of symbiotic bacteria in the distal human intestine
-
Xu, J. et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5, e156 (2007).
-
(2007)
PLoS Biol
, vol.5
, pp. e156
-
-
Xu, J.1
-
9
-
-
84880468631
-
Mobile genetic elements of the human gastrointestinal tract: Potential for spread of antibiotic resistance genes
-
Broaders, E., Gahan, C. G. & Marchesi, J. R. Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut microbes 4, 271-280 (2013).
-
(2013)
Gut Microbes
, vol.4
, pp. 271-280
-
-
Broaders, E.1
Gahan, C.G.2
Marchesi, J.R.3
-
10
-
-
84880509968
-
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
-
Modi, S. R., Lee, H. H., Spina, C. S. & Collins, J. J. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499, 219-222 (2013).
-
(2013)
Nature
, vol.499
, pp. 219-222
-
-
Modi, S.R.1
Lee, H.H.2
Spina, C.S.3
Collins, J.J.4
-
11
-
-
33644916136
-
Conjugative gene transfer in the gastrointestinal environment
-
Licht, T. R. et al. Conjugative gene transfer in the gastrointestinal environment. Adv. Appl. Microbiol. 58, 77-95 (2006).
-
(2006)
Adv. Appl. Microbiol.
, vol.58
, pp. 77-95
-
-
Licht, T.R.1
-
12
-
-
40449131944
-
Conjugal transfer of the Salmonella enterica virulence plasmid in the mouse intestine
-
Garcia-Quintanilla, M., Ramos-Morales, F. & Casadesus, J. Conjugal transfer of the Salmonella enterica virulence plasmid in the mouse intestine. J. Bacteriol. 190, 1922-1927 (2008).
-
(2008)
J. Bacteriol.
, vol.190
, pp. 1922-1927
-
-
Garcia-Quintanilla, M.1
Ramos-Morales, F.2
Casadesus, J.3
-
13
-
-
84856374839
-
Gut infammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae
-
Stecher, B. et al. Gut infammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc Natl Acad Sci USA 109, 1269-1274 (2012)
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 1269-1274
-
-
Stecher, B.1
-
14
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
15
-
-
70349233883
-
Towards the human intestinal microbiota phylogenetic core
-
Tap, J. et al. Towards the human intestinal microbiota phylogenetic core. Environmental Microbiology 11, 2574-2584 (2009).
-
(2009)
Environmental Microbiology
, vol.11
, pp. 2574-2584
-
-
Tap, J.1
-
16
-
-
79951811014
-
Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach
-
Sekelja, M., Berget, I., Naes, T. & Rudi, K. Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach. ISME J 5, 519-531 (2011).
-
(2011)
ISME J
, vol.5
, pp. 519-531
-
-
Sekelja, M.1
Berget, I.2
Naes, T.3
Rudi, K.4
-
17
-
-
64549143788
-
An improved Escherichia coli donor strain for diparental mating
-
Toma, S. & Schobert, M. An improved Escherichia coli donor strain for diparental mating. FEMS Microbiol Lett 294, 127-132 (2009).
-
(2009)
FEMS Microbiol Lett
, vol.294
, pp. 127-132
-
-
Toma, S.1
Schobert, M.2
-
18
-
-
0021027842
-
A broad host range mobilization system for in vivo genetic engineering: Transposon mutagenesis in Gram negative bacteria
-
Simon, R., Priefer, U. & Puhler, A. A broad host range mobilization system for in vivo genetic engineering: Transposon mutagenesis in Gram negative bacteria. Nat Biotech 1, 784 (1983).
-
(1983)
Nat Biotech
, vol.1
, pp. 784
-
-
Simon, R.1
Priefer, U.2
Puhler, A.3
-
19
-
-
0023158055
-
Tn1545: A conjugative shuttle transposon
-
Courvalin, P. & Carlier, C. Tn1545: a conjugative shuttle transposon. Mol. Gen. Genet. 206, 259-264 (1987).
-
(1987)
Mol. Gen. Genet.
, vol.206
, pp. 259-264
-
-
Courvalin, P.1
Carlier, C.2
-
20
-
-
84864384245
-
The "most wanted" taxa from the human microbiome for whole genome sequencing
-
Fodor, A. A. et al. The "most wanted" taxa from the human microbiome for whole genome sequencing. PLoS ONE 7, e41294 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e41294
-
-
Fodor, A.A.1
-
21
-
-
0028051630
-
Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli
-
Tauch, A., Kirchner, O., Wehmeier, L., Kalinowski, J. & Pühler, A. Corynebacterium glutamicum DNA is subjected to methylation-restriction in Escherichia coli. FEMS Microbiology Letters 123, 343-347 (1994).
-
(1994)
FEMS Microbiology Letters
, vol.123
, pp. 343-347
-
-
Tauch, A.1
Kirchner, O.2
Wehmeier, L.3
Kalinowski, J.4
Pühler, A.5
-
22
-
-
0025295967
-
Diferential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants
-
Grant, S. G., Jessee, J., Bloom, F. R. & Hanahan, D. Diferential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc Natl Acad Sci USA 87, 4645-4649 (1990).
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4645-4649
-
-
Grant, S.G.1
Jessee, J.2
Bloom, F.R.3
Hanahan, D.4
-
23
-
-
84907323900
-
Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria
-
Rettedal, E. A., Gumpert, H. & Sommer, M. O. A. Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria. Nat Commun 5, (2014).
-
(2014)
Nat Commun
, vol.5
-
-
Rettedal, E.A.1
Gumpert, H.2
Sommer, M.O.A.3
-
24
-
-
84869113067
-
Microbial culturomics: Paradigm shif in the human gut microbiome study
-
Lagier, J. C. et al. Microbial culturomics: paradigm shif in the human gut microbiome study. Clin Microbiol Infect 18, 1185-1193 (2012).
-
(2012)
Clin Microbiol Infect
, vol.18
, pp. 1185-1193
-
-
Lagier, J.C.1
-
25
-
-
23944475626
-
Mechanisms of, and barriers to, horizontal gene transfer between bacteria
-
Tomas, C. M. & Nielsen, K. M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Micro 3, 711-721 (2005).
-
(2005)
Nat Rev Micro
, vol.3
, pp. 711-721
-
-
Tomas, C.M.1
Nielsen, K.M.2
-
26
-
-
80052679931
-
In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota
-
Kim, B. S., Kim, J. N. & Cerniglia, C. E. In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota. J Biomed Biotechnol 2011, 838040 (2011).
-
(2011)
J Biomed Biotechnol
, vol.2011
, pp. 838040
-
-
Kim, B.S.1
Kim, J.N.2
Cerniglia, C.E.3
-
27
-
-
0030958150
-
Genetic diversity through the looking glass: Effect of enrichment bias
-
Dunbar, J., White, S. & Forney, L. Genetic diversity through the looking glass: Effect of enrichment bias. Applied and Environmental Microbiology 63, 1326-1331 (1997).
-
(1997)
Applied and Environmental Microbiology
, vol.63
, pp. 1326-1331
-
-
Dunbar, J.1
White, S.2
Forney, L.3
-
28
-
-
78650155416
-
Highlighting new phylogenetic specifcities of Crohn's disease microbiota
-
Mondot, S. et al. Highlighting new phylogenetic specifcities of Crohn's disease microbiota. Infammatory Bowel Diseases 17, 185-192 (2011).
-
(2011)
Infammatory Bowel Diseases
, vol.17
, pp. 185-192
-
-
Mondot, S.1
-
29
-
-
55949124035
-
Faecalibacterium prausnitzii is an anti-infammatory commensal bacterium identifed by gut microbiota analysis of Crohn disease patients
-
Sokol, H. et al. Faecalibacterium prausnitzii is an anti-infammatory commensal bacterium identifed by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 105, 16731-16736 (2008).
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
-
30
-
-
84881477044
-
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota
-
Atarashi, K. et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500, 232-236 (2013).
-
(2013)
Nature
, vol.500
, pp. 232-236
-
-
Atarashi, K.1
-
31
-
-
77949389510
-
Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982 with description of Flavonifractor plautii gen. Nov. Comb. Nov. and reassignment of Bacteroides capillosus to Pseudofavonifractor capillosus gen. Nov. Comb. Nov
-
Carlier, J.-P., Bedora-Faure, M., K'ouas, G., Alauzet, C. & Mory, F. Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudofavonifractor capillosus gen. nov., comb. nov. International Journal of Systematic and Evolutionary Microbiology 60, 585-590 (2010).
-
(2010)
International Journal of Systematic and Evolutionary Microbiology
, vol.60
, pp. 585-590
-
-
Carlier, J.-P.1
Bedora-Faure, M.2
K'Ouas, G.3
Alauzet, C.4
Mory, F.5
-
32
-
-
0025766077
-
Clostridium orbiscindens sp. Nov., a human intestinal bacterium capable of cleaving the favonoid C-ring
-
Winter, J., Popof, M. R., Grimont, P. & Bokkenheuser, V. D. Clostridium orbiscindens sp. nov., a human intestinal bacterium capable of cleaving the favonoid C-ring. Int J Syst Bacteriol 41, 355-357 (1991).
-
(1991)
Int J Syst Bacteriol
, vol.41
, pp. 355-357
-
-
Winter, J.1
Popof, M.R.2
Grimont, P.3
Bokkenheuser, V.D.4
-
33
-
-
79955062464
-
Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon
-
Aguirre de Carcer, D. et al. Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon. ISME J 5, 801-809 (2011).
-
(2011)
ISME J
, vol.5
, pp. 801-809
-
-
Aguirre De Carcer, D.1
-
34
-
-
84863472497
-
A crypt-specifc core microbiota resides in the mouse colon
-
Pedron, T. et al. A crypt-specifc core microbiota resides in the mouse colon. MBio 3, (2012).
-
(2012)
MBio
, vol.3
-
-
Pedron, T.1
-
35
-
-
77952208123
-
Indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis
-
Obata, T. et al. Indigenous opportunistic bacteria inhabit mammalian gut-associated lymphoid tissues and share a mucosal antibody-mediated symbiosis. Proc Natl Acad Sci USA 107, 7419-7424 (2010).
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 7419-7424
-
-
Obata, T.1
-
36
-
-
84900423596
-
CD4CD8aa lymphocytes, a novel human regulatory T cell subset induced by colonic bacteria and defcient in patients with infammatory bowel disease
-
Sarrabayrouse, G. et al. CD4CD8aa lymphocytes, a novel human regulatory T cell subset induced by colonic bacteria and defcient in patients with infammatory bowel disease. PLoS Biol 12, e1001833 (2014).
-
(2014)
PLoS Biol
, vol.12
, pp. e1001833
-
-
Sarrabayrouse, G.1
-
37
-
-
84908406670
-
Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models
-
Woting, A., Pfeifer, N., Loh, G., Klaus, S. & Blaut, M. Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models. MBio 5, e01530-01514 (2014).
-
(2014)
MBio
, vol.5
, pp. e01530-01514
-
-
Woting, A.1
Pfeifer, N.2
Loh, G.3
Klaus, S.4
Blaut, M.5
-
38
-
-
72049109957
-
Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367
-
Tolonen, A. C., Chilaka, A. C. & Church, G. M. Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Molecular Microbiology 74, 1300-1313 (2009).
-
(2009)
Molecular Microbiology
, vol.74
, pp. 1300-1313
-
-
Tolonen, A.C.1
Chilaka, A.C.2
Church, G.M.3
-
39
-
-
67649205495
-
A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species
-
Aakvik, T. et al. A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett 296, 149-158 (2009).
-
(2009)
FEMS Microbiol Lett
, vol.296
, pp. 149-158
-
-
Aakvik, T.1
-
40
-
-
79952709427
-
Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries
-
Kakirde, K. S. et al. Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries. Gene 475, 57-62 (2011).
-
(2011)
Gene
, vol.475
, pp. 57-62
-
-
Kakirde, K.S.1
-
41
-
-
19744383226
-
Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation
-
Clarke, P., Ó Cuív, P. & O'Connell, M. Novel mobilizable prokaryotic two-hybrid system vectors for high-throughput protein interaction mapping in Escherichia coli by bacterial conjugation. Nucleic Acids Res 33, e18 (2005).
-
(2005)
Nucleic Acids Res
, vol.33
, pp. e18
-
-
Clarke, P.1
Cuív, Ó.P.2
O'Connell, M.3
-
43
-
-
37649001610
-
-
(eds Harinder, P.S., Makkar & Christopher, S. McSweeney) Springer
-
McSweeney, C. S., Denman, S. E. & Mackie, R. I. in Methods in gut microbial ecology for ruminants (eds Harinder, P.S., Makkar & Christopher, S. McSweeney) 23-37 (Springer, 2005).
-
(2005)
Methods in Gut Microbial Ecology for Ruminants
, pp. 23-37
-
-
McSweeney, C.S.1
Denman, S.E.2
Mackie, R.I.3
-
44
-
-
0034111016
-
Phylogenetic relationships of butyrate-producing bacteria from the human gut
-
Barcenilla, A. et al. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Applied and Environmental Microbiology 66, 1654-1661 (2000).
-
(2000)
Applied and Environmental Microbiology
, vol.66
, pp. 1654-1661
-
-
Barcenilla, A.1
-
45
-
-
0015138341
-
Anaerobic roll tube media for nonselective enumeration and isolation of bacteria in human feces
-
Eller, C., Crabill, M. R. & Bryant, M. P. Anaerobic roll tube media for nonselective enumeration and isolation of bacteria in human feces. Applied microbiology 22, 522-529 (1971).
-
(1971)
Applied Microbiology
, vol.22
, pp. 522-529
-
-
Eller, C.1
Crabill, M.R.2
Bryant, M.P.3
-
46
-
-
0041527233
-
Development of a sensitive gene expression reporter system and an inducible promoter-repressor system for Clostridium acetobutylicum
-
Girbal, L. et al. Development of a sensitive gene expression reporter system and an inducible promoter-repressor system for Clostridium acetobutylicum. Appl Environ Microbiol 69, 4985-4988 (2003).
-
(2003)
Appl Environ Microbiol
, vol.69
, pp. 4985-4988
-
-
Girbal, L.1
-
47
-
-
0025195680
-
Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria
-
De Lorenzo, V., Herrero, M., Jakubzik, U. & Timmis, K. N. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J Bacteriol 172, 6568-6572 (1990).
-
(1990)
J Bacteriol
, vol.172
, pp. 6568-6572
-
-
De Lorenzo, V.1
Herrero, M.2
Jakubzik, U.3
Timmis, K.N.4
-
48
-
-
2442510059
-
Improved extraction of PCR-quality community DNA from digesta and fecal samples
-
Yu, Z. & Morrison, M. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808-812 (2004).
-
(2004)
Biotechniques
, vol.36
, pp. 808-812
-
-
Yu, Z.1
Morrison, M.2
-
50
-
-
79951509848
-
The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue
-
Ó. Cuív, P. et al. The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue. Microb Ecol 61, 353-362 (2011).
-
(2011)
Microb Ecol
, vol.61
, pp. 353-362
-
-
Cuív, P.Ó.1
-
51
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Cole, J. R. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37, 141-145 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 141-145
-
-
Cole, J.R.1
-
52
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7, 335-336 (2010).
-
(2010)
Nat Meth
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
53
-
-
0018800089
-
A rapid alkaline extraction procedure for screening recombinant plasmid DNA
-
Birnboim, H. C. & Doly, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7, 1513-1523 (1979).
-
(1979)
Nucleic Acids Res
, vol.7
, pp. 1513-1523
-
-
Birnboim, H.C.1
Doly, J.2
-
54
-
-
2542523843
-
ARB: A sofware environment for sequence data
-
Ludwig, W. et al. ARB: a sofware environment for sequence data. Nucleic Acids Res 32, 1363-1371 (2004).
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1363-1371
-
-
Ludwig, W.1
|