-
1
-
-
84886795788
-
Microbiota-mediated colonization resistance against intestinal pathogens
-
Buffie, C. G. & Pamer, E. G. Microbiota-mediated colonization resistance against intestinal pathogens. Nature Rev. Immunol. 13, 790-801 (2013).
-
(2013)
Nature Rev. Immunol.
, vol.13
, pp. 790-801
-
-
Buffie, C.G.1
Pamer, E.G.2
-
2
-
-
84857067037
-
Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficileinduced colitis
-
Buffie, C. G. et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficileinduced colitis. Infect. Immun. 80, 62-73 (2012).
-
(2012)
Infect. Immun.
, vol.80
, pp. 62-73
-
-
Buffie, C.G.1
-
3
-
-
67649391053
-
Clostridium difficile infection: New developments in epidemiology and pathogenesis
-
Rupnik, M., Wilcox, M. H. & Gerding, D. N. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nature Rev. Microbiol. 7, 526-536 (2009).
-
(2009)
Nature Rev. Microbiol.
, vol.7
, pp. 526-536
-
-
Rupnik, M.1
Wilcox, M.H.2
Gerding, D.N.3
-
4
-
-
84873019302
-
Duodenal infusion of donor feces for recurrent Clostridium difficile
-
van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368, 407-415 (2013).
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 407-415
-
-
Van Nood, E.1
-
5
-
-
84904554933
-
Insights into secondarymetabolismfroma global analysis of prokaryotic biosynthetic gene clusters
-
Cimermancic, P. et al. Insights into secondarymetabolismfroma global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421 (2014).
-
(2014)
Cell
, vol.158
, pp. 412-421
-
-
Cimermancic, P.1
-
6
-
-
39349107697
-
Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea
-
Chang, J. Y. et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J. Infect. Dis. 197, 435-438 (2008).
-
(2008)
J. Infect. Dis.
, vol.197
, pp. 435-438
-
-
Chang, J.Y.1
-
7
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235 (2005).
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
8
-
-
84865175815
-
Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stemcell transplantation
-
Taur, Y. et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stemcell transplantation. Clin. Infect.Dis. 55, 905-914 (2012).
-
(2012)
Clin. Infect.Dis.
, vol.55
, pp. 905-914
-
-
Taur, Y.1
-
9
-
-
84899733043
-
Early Clostridium difficile infection during allogeneic hematopoietic stem cell transplantation
-
Kinnebrew, M. A. et al. Early Clostridium difficile infection during allogeneic hematopoietic stem cell transplantation. PLoS ONE 9, e90158 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e90158
-
-
Kinnebrew, M.A.1
-
10
-
-
84892708007
-
Ecological modeling from time-series inference: Insight into dynamics and stability of intestinal microbiota
-
Stein, R. R. et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLOS Comput. Biol. 9, e1003388 (2013).
-
(2013)
PLOS Comput. Biol.
, vol.9
, pp. e1003388
-
-
Stein, R.R.1
-
11
-
-
0020554353
-
Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore germination
-
Wilson, K. H. Efficiency of various bile salt preparations for stimulation of Clostridium difficile spore germination. J. Clin. Microbiol. 18, 1017-1019 (1983).
-
(1983)
J. Clin. Microbiol.
, vol.18
, pp. 1017-1019
-
-
Wilson, K.H.1
-
12
-
-
41549142775
-
Bile salts and glycine as cogerminants for Clostridium difficile spores
-
Sorg, J. A.&Sonenshein, A. L. Bile salts and glycine as cogerminants for Clostridium difficile spores. J. Bacteriol. 190, 2505-2512 (2008).
-
(2008)
J. Bacteriol.
, vol.190
, pp. 2505-2512
-
-
Sorg, J.A.1
Sonenshein, A.L.2
-
13
-
-
38849090693
-
Clostridium scindens baiCD and baiH genes encode stereo-specific 7a/7b-hydroxy-3-oxo-D4- cholenoic acid oxidoreductases
-
Kang, D. J., Ridlon, J. M., Moore, D. R., Barnes, S. & Hylemon, P. B. Clostridium scindens baiCD and baiH genes encode stereo-specific 7a/7b-hydroxy-3-oxo-D4- cholenoic acid oxidoreductases. Biochim. Biophys. Acta 1781, 16-25 (2008).
-
(2008)
Biochim. Biophys. Acta
, vol.1781
, pp. 16-25
-
-
Kang, D.J.1
Ridlon, J.M.2
Moore, D.R.3
Barnes, S.4
Hylemon, P.B.5
-
14
-
-
33244467651
-
Bile salt biotransformations by human intestinal bacteria
-
Ridlon, J. M., Kang, D. J. & Hylemon, P. B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 47, 241-259 (2006).
-
(2006)
J. Lipid Res.
, vol.47
, pp. 241-259
-
-
Ridlon, J.M.1
Kang, D.J.2
Hylemon, P.B.3
-
15
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol. 31, 814-821 (2013).
-
(2013)
Nature Biotechnol.
, vol.31
, pp. 814-821
-
-
Langille, M.G.1
-
16
-
-
84855850294
-
Bile acid sequestrants: More than simple resins
-
Out, C., Groen, A. K. & Brufau, G. Bile acid sequestrants: more than simple resins. Curr. Opin. Lipidol. 23, 43-55 (2012).
-
(2012)
Curr. Opin. Lipidol.
, vol.23
, pp. 43-55
-
-
Out, C.1
Groen, A.K.2
Brufau, G.3
-
17
-
-
0028126829
-
The phylogeny of the genus Clostridium: Proposal of five new genera and eleven new species combinations
-
Collins, M. D. et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812-826 (1994).
-
(1994)
Int. J. Syst. Bacteriol.
, vol.44
, pp. 812-826
-
-
Collins, M.D.1
-
18
-
-
84885176098
-
A genomic update on clostridial phylogeny: Gramnegative spore formers and other misplaced clostridia
-
Yutin, N. & Galperin, M. Y. A genomic update on clostridial phylogeny: Gramnegative spore formers and other misplaced clostridia. Environ. Microbiol. 15, 2631-2641 (2013).
-
(2013)
Environ. Microbiol.
, vol.15
, pp. 2631-2641
-
-
Yutin, N.1
Galperin, M.Y.2
-
19
-
-
0034034841
-
Assignment of Eubacterium sp VPI 12708 and related strains with high bile acid 7a-dehydroxylating activity to Clostridium scindens and proposal of Clostridiumhylemonae sp nov, isolated from human faeces
-
Kitahara, M., Takamine, F., Imamura, T. & Benno, Y. Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7a-dehydroxylating activity to Clostridium scindens and proposal of Clostridiumhylemonae sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 50, 971-978 (2000).
-
(2000)
Int. J. Syst. Evol. Microbiol.
, vol.50
, pp. 971-978
-
-
Kitahara, M.1
Takamine, F.2
Imamura, T.3
Benno, Y.4
-
20
-
-
0034010274
-
Identification and characterization of a bile acid 7a-dehydroxylation operon in Clostridium sp strain TO-931, a highly active 7a-dehydroxylating strain isolated from human feces
-
Wells, E. & Hylemon, B. Identification and characterization of a bile acid 7a-dehydroxylation operon in Clostridium sp. strain TO-931, a highly active 7a-dehydroxylating strain isolated from human feces. Appl. Environ. Microbiol. 66, 1107-1113 (2000).
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 1107-1113
-
-
Wells, E.1
Hylemon, B.2
-
21
-
-
84894105226
-
Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection
-
Weingarden, A. R. et al. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am. J. Physiol. Gastrointest. Liver Physiol. 306, G310-G319 (2014).
-
(2014)
Am. J. Physiol. Gastrointest. Liver Physiol.
, vol.306
, pp. G310-G319
-
-
Weingarden, A.R.1
-
22
-
-
11844262660
-
Bile acids as carcinogens in human gastrointestinal cancers
-
Bernstein, H., Bernstein, C., Payne, C. M., Dvorakova, K. & Garewal, H. Bile acids as carcinogens in human gastrointestinal cancers. Mutat. Res. 589, 47-65 (2005).
-
(2005)
Mutat. Res.
, vol.589
, pp. 47-65
-
-
Bernstein, H.1
Bernstein, C.2
Payne, C.M.3
Dvorakova, K.4
Garewal, H.5
-
23
-
-
84885573828
-
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
-
Ng, K. M. et al. Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96-99 (2013).
-
(2013)
Nature
, vol.502
, pp. 96-99
-
-
Ng, K.M.1
-
24
-
-
84867605854
-
Critical role for MyD88-mediated neutrophil recruitment during Clostridium difficile colitis
-
Jarchum, I., Liu, M., Shi, C., Equinda, M. & Pamer, E. G. Critical role for MyD88-mediated neutrophil recruitment during Clostridium difficile colitis. Infect. Immun. 80, 2989-2996 (2012).
-
(2012)
Infect. Immun.
, vol.80
, pp. 2989-2996
-
-
Jarchum, I.1
Liu, M.2
Shi, C.3
Equinda, M.4
Pamer, E.G.5
-
25
-
-
79953300500
-
Toll-like receptor 5 stimulation protects mice fromacute Clostridiumdifficile colitis
-
Jarchum, I., Liu, M., Lipuma, L. & Pamer, E. G. Toll-like receptor 5 stimulation protects mice fromacute Clostridiumdifficile colitis. Infect.Immun. 79, 1498-1503 (2011).
-
(2011)
Infect.Immun.
, vol.79
, pp. 1498-1503
-
-
Jarchum, I.1
Liu, M.2
Lipuma, L.3
Pamer, E.G.4
-
26
-
-
77952679997
-
Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile
-
Rea, M. C. et al. Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. Proc. Natl Acad. Sci. USA 107, 9352-9357 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 9352-9357
-
-
Rea, M.C.1
-
27
-
-
57249086250
-
A mouse model of Clostridium difficile-associated disease
-
Chen, X. et al. A mouse model of Clostridium difficile-associated disease. Gastroenterology 135, 1984-1992 (2008).
-
(2008)
Gastroenterology
, vol.135
, pp. 1984-1992
-
-
Chen, X.1
-
28
-
-
77649282955
-
Metabolism of bile salts in mice influences spore germination in Clostridium difficile
-
Giel, J. L., Sorg, J. A., Sonenshein, A. L. & Zhu, J. Metabolism of bile salts in mice influences spore germination in Clostridium difficile. PLoS ONE 5, e8740 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e8740
-
-
Giel, J.L.1
Sorg, J.A.2
Sonenshein, A.L.3
Zhu, J.4
-
29
-
-
78649895980
-
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans
-
Ubeda, C. et al. Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J. Clin. Invest. 120, 4332-4341 (2010).
-
(2010)
J. Clin. Invest.
, vol.120
, pp. 4332-4341
-
-
Ubeda, C.1
-
30
-
-
0037403187
-
Development and application of a polymerase chain reaction assay for the detection and enumeration of bile acid 7a-dehydroxylating bacteria in human feces
-
Wells, J. E., Williams, K. B., Whitehead, T. R., Heuman, D. M. & Hylemon, P. B. Development and application of a polymerase chain reaction assay for the detection and enumeration of bile acid 7a-dehydroxylating bacteria in human feces. Clin. Chim. Acta 331, 127-134 (2003).
-
(2003)
Clin. Chim. Acta
, vol.331
, pp. 127-134
-
-
Wells, J.E.1
Williams, K.B.2
Whitehead, T.R.3
Heuman, D.M.4
Hylemon, P.B.5
-
31
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624 (2012).
-
(2012)
ISME J.
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
-
32
-
-
84874672692
-
Intestinal microbiota containing Barnesiella cures vancomycin-resistant Enterococcus faecium colonization
-
Ubeda, C. et al. Intestinal microbiota containing Barnesiella cures vancomycin-resistant Enterococcus faecium colonization. Infect. Immun. 81, 965-973 (2013).
-
(2013)
Infect. Immun.
, vol.81
, pp. 965-973
-
-
Ubeda, C.1
-
33
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
34
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
35
-
-
33750983947
-
Clearcut: A fast implementation of relaxed neighbor joining
-
Sheneman, L., Evans, J. & Foster, J. A. Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22, 2823-2824 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 2823-2824
-
-
Sheneman, L.1
Evans, J.2
Foster, J.A.3
-
36
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335-336 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
37
-
-
84876533617
-
Building phylogenetic trees from molecular data with MEGA
-
Hall, B. G. Building phylogenetic trees from molecular data with MEGA. Mol. Biol. Evol. 30, 1229-1235 (2013).
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1229-1235
-
-
Hall, B.G.1
-
38
-
-
84862276328
-
Function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium Structure
-
Human Microbiome Project Consortium Structure. Function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
39
-
-
84855167751
-
RAPSearch2: A fast and memory-efficient protein similarity search tool for next-generation sequencing data
-
Zhao, Y., Tang, H. & Ye, Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28, 125-126 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
Tang, H.2
Ye, Y.3
|