-
1
-
-
0025183708
-
Basic local alignment search tool
-
doi: 10.1016/s0022-2836(05)80360-2
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410. doi: 10.1016/s0022-2836(05)80360-2
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
84882779621
-
Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea."
-
doi: 10.1128/JCM.00845-13
-
Antharam, V. C., Li, E. C., Ishmael, A., Sharma, A., Mai, V., Rand, K. H., et al. (2013). Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea." J. Clin. Microbiol. 51, 2884-2892. doi: 10.1128/JCM.00845-13
-
(2013)
J Clin. Microbiol.
, vol.51
, pp. 2884-2892
-
-
Antharam, V.C.1
Li, E.C.2
Ishmael, A.3
Sharma, A.4
Mai, V.5
Rand, K.H.6
-
3
-
-
66549102207
-
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation
-
doi: 10.1128/IAI.01520-08
-
Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., and Young, V. B. (2009). Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. Immun. 77, 2367-2375. doi: 10.1128/IAI.01520-08
-
(2009)
Infect. Immun.
, vol.77
, pp. 2367-2375
-
-
Antonopoulos, D.A.1
Huse, S.M.2
Morrison, H.G.3
Schmidt, T.M.4
Sogin, M.L.5
Young, V.B.6
-
4
-
-
79953170241
-
Effect of antibiotic treatment on the intestinal metabolome
-
doi: 10.1128/AAC.01664-10
-
Antunes, L. C., Han, J., Ferreira, R. B., Lolic, P., Borchers, C. H., and Finlay, B. B. (2011). Effect of antibiotic treatment on the intestinal metabolome. Antimicrob. Agents Chemother. 55, 1494-1503. doi: 10.1128/AAC.01664-10
-
(2011)
Antimicrob. Agents Chemother.
, vol.55
, pp. 1494-1503
-
-
Antunes, L.C.1
Han, J.2
Ferreira, R.B.3
Lolic, P.4
Borchers, C.H.5
Finlay, B.B.6
-
5
-
-
77951667024
-
Lactobacillus delbrueckii ssp. bulgaricus B-30892 can inhibit cytotoxic effects and adhesion of pathogenic Clostridium difficile to Caco-2 cells
-
doi: 10.1186/1757-4749-1-8
-
Banerjee, P., Merkel, G. J., and Bhunia, A. K. (2009). Lactobacillus delbrueckii ssp. bulgaricus B-30892 can inhibit cytotoxic effects and adhesion of pathogenic Clostridium difficile to Caco-2 cells. Gut Pathog. 1:8. doi: 10.1186/1757-4749-1-8
-
(2009)
Gut Pathog
, vol.1
, pp. 8
-
-
Banerjee, P.1
Merkel, G.J.2
Bhunia, A.K.3
-
6
-
-
0034111016
-
Phylogenetic relationships of butyrate-producing bacteria from the human gut
-
doi: 10.1128/AEM.66.4.1654-1661.2000
-
Barcenilla, A., Pryde, S. E., Martin, J. C., Duncan, S. H., Stewart, C. S., Henderson, C., et al. (2000). Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66, 1654-1661. doi: 10.1128/AEM.66.4.1654-1661.2000
-
(2000)
Appl. Environ. Microbiol.
, vol.66
, pp. 1654-1661
-
-
Barcenilla, A.1
Pryde, S.E.2
Martin, J.C.3
Duncan, S.H.4
Stewart, C.S.5
Henderson, C.6
-
7
-
-
0037204196
-
Clinical practice Antibiotic-associated diarrhea.
-
doi: 10.1056/NEJMcp011603
-
Bartlett, J. G. (2002). Clinical practice. Antibiotic-associated diarrhea. N. Engl. J. Med. 346, 334-339. doi: 10.1056/NEJMcp011603
-
(2002)
N. Engl. J. Med.
, vol.346
, pp. 334-339
-
-
Bartlett, J.G.1
-
8
-
-
84862770598
-
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance
-
doi: 10.1016/j.tim.2012.04.001
-
Britton, R. A., and Young, V. B. (2012). Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Trends Microbiol. 20, 313-319. doi: 10.1016/j.tim.2012.04.001
-
(2012)
Trends Microbiol.
, vol.20
, pp. 313-319
-
-
Britton, R.A.1
Young, V.B.2
-
9
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
doi: 10.1038/nmeth.f.303
-
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-346. doi: 10.1038/nmeth.f.303
-
(2010)
Nat. Methods
, vol.7
, pp. 335-346
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
-
10
-
-
85013721774
-
Nonparametric estimation of the number of classes in a population
-
Chao, A. (1984). Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11, 256-270.
-
(1984)
Scand. J. Stat.
, vol.11
, pp. 256-270
-
-
Chao, A.1
-
11
-
-
0034387298
-
Estimating the number of shared species in two communities
-
Chao, A., Wen-Han, H., Chen, Y. C., and Kuo, C. Y. (2000). Estimating the number of shared species in two communities. Stat. Sin. 10, 227-246.
-
(2000)
Stat. Sin.
, vol.10
, pp. 227-246
-
-
Chao, A.1
Wen-Han, H.2
Chen, Y.C.3
Kuo, C.Y.4
-
12
-
-
77951026738
-
Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA)
-
doi: 10.1086/651706
-
Cohen, S. H., Gerding, D. N., Johnson, S., Kelly, C. P., Loo, V. G., McDonald, L. C., et al. (2010). Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect. Control Hosp. Epidemiol. 31, 431-455. doi: 10.1086/651706
-
(2010)
Infect. Control Hosp. Epidemiol.
, vol.31
, pp. 431-455
-
-
Cohen, S.H.1
Gerding, D.N.2
Johnson, S.3
Kelly, C.P.4
Loo, V.G.5
McDonald, L.C.6
-
13
-
-
58149200948
-
The Ribosomal database project: improved alignments and new tools for rRNA analysis
-
doi: 10.1093/nar/gkn879
-
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., et al. (2009). The Ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141-5. doi: 10.1093/nar/gkn879
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
-
14
-
-
0028126829
-
The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations
-
doi: 10.1099/00207713-44-4-812
-
Collins, M. D., Lawson, P. A., Willems, A., Cordoba, J. J., Fernandez-Garayzabal, J., Garcia, P., et al. (1994).The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44, 812-826. doi: 10.1099/00207713-44-4-812
-
(1994)
Int. J. Syst. Bacteriol
, vol.44
, pp. 812-826
-
-
Collins, M.D.1
Lawson, P.A.2
Willems, A.3
Cordoba, J.J.4
Fernandez-Garayzabal, J.5
Garcia, P.6
-
15
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
-
doi: 10.1371/journal.pbio.0060280
-
Dethlefsen, L., Huse, S., Sogin, M. L., and Relman, D. A. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:280. doi: 10.1371/journal.pbio.0060280
-
(2008)
PLoS Biol.
, vol.6
, pp. 280
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
16
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
doi: 10.1073/pnas.1000087107
-
Dethlefsen, L., and Relman, D. A. (2010). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl. 1), 4554-4561. doi: 10.1073/pnas.1000087107
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, Issue.1 SUPPL.
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
17
-
-
33845626641
-
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria
-
doi: 10.1128/MMBR.00024-06
-
Deutscher, J., Francke, C., and Postma, P. W. (2006). How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol. Mol. Biol. Rev. 4, 939-1031. doi: 10.1128/MMBR.00024-06
-
(2006)
Microbiol. Mol. Biol. Rev.
, vol.4
, pp. 939-1031
-
-
Deutscher, J.1
Francke, C.2
Postma, P.W.3
-
18
-
-
3242772754
-
The role of the intestinal tract as a reservoir and source for transmission of nosocomial pathogens
-
doi: 10.1086/422002
-
Donskey, C. J. (2004). The role of the intestinal tract as a reservoir and source for transmission of nosocomial pathogens. Clin. Infect. Dis. 39, 219-226. doi: 10.1086/422002
-
(2004)
Clin. Infect. Dis.
, vol.39
, pp. 219-226
-
-
Donskey, C.J.1
-
19
-
-
84858604441
-
Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome
-
doi: 10.1111/j.1758-2229.2012.00327.x
-
Durbán, A., Abellán, J. J., Jiménez-Hernández, N., Salgado, P., Ponce, M., Ponce, J., et al. (2012). Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome. Environ. Microbiol. Rep. 4, 242-247. doi: 10.1111/j.1758-2229.2012.00327.x
-
(2012)
Environ. Microbiol. Rep.
, vol.4
, pp. 242-247
-
-
Durbán, A.1
Abellán, J.J.2
Jiménez-Hernández, N.3
Salgado, P.4
Ponce, M.5
Ponce, J.6
-
20
-
-
0003516147
-
-
Cambridge: Cambridge University Press.
-
Durbin, R., Eddy, S. R., Krogh, A., and Mitchison, G. (1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
-
(1998)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.4
-
21
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
doi: 10.1126/science.1124234
-
Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., et al. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359. doi: 10.1126/science.1124234
-
(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
-
22
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
doi: 10.1038/ismej.2009.72
-
Gómez-Alvarez, V., Teal, T. K., and Schmidt, T. M. (2009). Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3, 1314-1317. doi: 10.1038/ismej.2009.72
-
(2009)
ISME J.
, vol.3
, pp. 1314-1317
-
-
Gómez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
23
-
-
84867705864
-
Infant formula supplemented with polyamines alters the intestinal microbiota in neonatal BALB/cOlaHsd mice
-
doi: 10.1016/j.jnutbio.2011.10.003
-
Gómez-Gallego, C., Collado, M. C., Ilo, T., Jaakkola, U. M., Bernal, M. J., Periago, M. J., et al. (2012). Infant formula supplemented with polyamines alters the intestinal microbiota in neonatal BALB/cOlaHsd mice. J. Nutr. Biochem. 23, 1508-1513. doi: 10.1016/j.jnutbio.2011.10.003
-
(2012)
J. Nutr. Biochem.
, vol.23
, pp. 1508-1513
-
-
Gómez-Gallego, C.1
Collado, M.C.2
Ilo, T.3
Jaakkola, U.M.4
Bernal, M.J.5
Periago, M.J.6
-
24
-
-
79952401369
-
Metatranscriptomic approach to analyze the functional human gut microbiota
-
doi: 10.1371/journal.pone.0017447
-
Gosalbes, M. J., Durbán, A., Pignatelli, M., Abellan, J. J., Jiménez-Hernández, N., Pérez-Cobas, A. E., et al. (2011). Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS ONE 6:17447. doi: 10.1371/journal.pone.0017447
-
(2011)
PLoS ONE
, vol.6
, pp. 17447
-
-
Gosalbes, M.J.1
Durbán, A.2
Pignatelli, M.3
Abellan, J.J.4
Jiménez-Hernández, N.5
Pérez-Cobas, A.E.6
-
25
-
-
0037425743
-
Gut flora in health and disease
-
doi: 10.1016/S0140-6736(03)12489-0
-
Guarner, F., and Malagelada, J. R. (2003). Gut flora in health and disease. Lancet 361, 512-519. doi: 10.1016/S0140-6736(03)12489-0
-
(2003)
Lancet
, vol.361
, pp. 512-519
-
-
Guarner, F.1
Malagelada, J.R.2
-
26
-
-
0037249633
-
The TIGRFAMs database of protein families
-
doi: 10.1093/nar/gkg128
-
Haft, D. H., Selengut, J. D., and White, O. (2003). The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371-373. doi: 10.1093/nar/gkg128
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 371-373
-
-
Haft, D.H.1
Selengut, J.D.2
White, O.3
-
27
-
-
65249119418
-
The human intestinal microbiome: a new frontier of human biology
-
doi: 10.1093/dnares/dsn033
-
Hattori, M., and Taylor, T. D. (2009). The human intestinal microbiome: a new frontier of human biology. DNA Res. 16, 1-12. doi: 10.1093/dnares/dsn033
-
(2009)
DNA Res.
, vol.16
, pp. 1-12
-
-
Hattori, M.1
Taylor, T.D.2
-
28
-
-
64549163185
-
Clostridium difficile associated infection, diarrhea and colitis
-
doi: 10.3748/wjg.15.1554
-
Hookman, P., and Barkin, J. S. (2009). Clostridium difficile associated infection, diarrhea and colitis. World J. Gastroenterol. 15, 1554-1580. doi: 10.3748/wjg.15.1554
-
(2009)
World J. Gastroenterol.
, vol.15
, pp. 1554-1580
-
-
Hookman, P.1
Barkin, J.S.2
-
29
-
-
0036399823
-
How host-microbial interactions shape the nutrient environment of the mammalian intestine
-
doi: 10.1146/annurev.nutr.22.011602.092259
-
Hooper, L. V., Midtvedt, T., and Gordon, J. I. (2002). How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22, 283-307. doi: 10.1146/annurev.nutr.22.011602.092259
-
(2002)
Annu. Rev. Nutr.
, vol.22
, pp. 283-307
-
-
Hooper, L.V.1
Midtvedt, T.2
Gordon, J.I.3
-
30
-
-
0023156767
-
Intestinal bacteria antagonistic to Clostridium difficile in mice
-
doi: 10.1258/002367787780740662
-
Itoh, K., Lee, W. K., Kawamura, H., Mitsuoka, T., and Magaribuchi, T. (1987). Intestinal bacteria antagonistic to Clostridium difficile in mice. Lab. Anim. 21, 20-25. doi: 10.1258/002367787780740662
-
(1987)
Lab. Anim.
, vol.21
, pp. 20-25
-
-
Itoh, K.1
Lee, W.K.2
Kawamura, H.3
Mitsuoka, T.4
Magaribuchi, T.5
-
31
-
-
78049494788
-
Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome
-
doi: 10.1371/journal.pone.0009836
-
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., and Engstrand, L. (2010). Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE 5:9836. doi: 10.1371/journal.pone.0009836
-
(2010)
PLoS ONE
, vol.5
, pp. 9836
-
-
Jakobsson, H.E.1
Jernberg, C.2
Andersson, A.F.3
Sjölund-Karlsson, M.4
Jansson, J.K.5
Engstrand, L.6
-
32
-
-
78049522796
-
Long-term impacts of antibiotic exposure on the human intestinal microbiota
-
doi: 10.1099/mic.0.040618-0
-
Jernberg, C., Löfmark, S., Edlund, C., and Jansson, J. K. (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156, 3216-3223. doi: 10.1099/mic.0.040618-0
-
(2010)
Microbiology
, vol.156
, pp. 3216-3223
-
-
Jernberg, C.1
Löfmark, S.2
Edlund, C.3
Jansson, J.K.4
-
33
-
-
0141651685
-
Abnormal growth of polyamine-deficient Escherichia coli mutant is partially caused by oxidative stress-induced damage
-
doi: 10.1016/j.abb.2003.08.003
-
Jung, I. L., Oh, T. J., and Kim, I. G. (2003). Abnormal growth of polyamine-deficient Escherichia coli mutant is partially caused by oxidative stress-induced damage. Arch. Biochem. Biophys. 418, 125-132. doi: 10.1016/j.abb.2003.08.003
-
(2003)
Arch. Biochem. Biophys.
, vol.418
, pp. 125-132
-
-
Jung, I.L.1
Oh, T.J.2
Kim, I.G.3
-
34
-
-
78649622569
-
Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray
-
doi: 10.1002/ibd.21319
-
Kang, S., Denman, S. E., Morrison, M., Yu, Z., Dore, J., Leclerc, M., et al. (2010). Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm. Bowel Dis. 16, 2034-2042. doi: 10.1002/ibd.21319
-
(2010)
Inflamm. Bowel Dis.
, vol.16
, pp. 2034-2042
-
-
Kang, S.1
Denman, S.E.2
Morrison, M.3
Yu, Z.4
Dore, J.5
Leclerc, M.6
-
35
-
-
70349993601
-
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
-
doi: 10.1093/bioinformatics/btp508
-
Kristiansson, E., Hugenholtz, P., and Dalevi, D. (2009). ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinformatics 25, 2737-2738. doi: 10.1093/bioinformatics/btp508
-
(2009)
Bioinformatics
, vol.25
, pp. 2737-2738
-
-
Kristiansson, E.1
Hugenholtz, P.2
Dalevi, D.3
-
36
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
doi: 10.1093/dnares/dsm018
-
Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., et al. (2007). Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169-181. doi: 10.1093/dnares/dsm018
-
(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
-
37
-
-
84868158515
-
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice
-
doi: 10.1371/journal.ppat.1002995
-
Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., et al. (2012). Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog. 8:1002995. doi: 10.1371/journal.ppat.1002995
-
(2012)
PLoS Pathog.
, vol.8
, pp. 1002995
-
-
Lawley, T.D.1
Clare, S.2
Walker, A.W.3
Stares, M.D.4
Connor, T.R.5
Raisen, C.6
-
38
-
-
69949088176
-
Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host
-
doi: 10.1111/j.1462-2920.2009.01941.x
-
Leser, T. D., and Mølbak, L. (2009). Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ. Microbiol. 11, 2194-2206. doi: 10.1111/j.1462-2920.2009.01941.x
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 2194-2206
-
-
Leser, T.D.1
Mølbak, L.2
-
39
-
-
84867161176
-
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
-
doi: 10.1101/gr.138198.112
-
Lozupone, C., Faust, K., Raes, J., Faith, J. J., Frank, D. N., Zaneveld, J., et al. (2012). Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 22, 1974-1984. doi: 10.1101/gr.138198.112
-
(2012)
Genome Res.
, vol.22
, pp. 1974-1984
-
-
Lozupone, C.1
Faust, K.2
Raes, J.3
Faith, J.J.4
Frank, D.N.5
Zaneveld, J.6
-
40
-
-
0028080726
-
Effect of fiber source on short-chain fatty acid production and on the growth and toxin production by Clostridium difficile
-
doi: 10.3109/00365529409094863
-
May, T., Mackie, R. I., Fahey, G. C. Jr., Cremin, J. C., and Garleb, K. A. (1994). Effect of fiber source on short-chain fatty acid production and on the growth and toxin production by Clostridium difficile. Scand. J. Gastroenterol. 29, 916-922. doi: 10.3109/00365529409094863
-
(1994)
Scand. J. Gastroenterol.
, vol.29
, pp. 916-922
-
-
May, T.1
Mackie, R.I.2
Fahey Jr., G.C.3
Cremin, J.C.4
Garleb, K.A.5
-
41
-
-
0347950950
-
Prevention of fatal Clostridium difficile-associated disease during continuous administration of clindamycin in hamsters
-
doi: 10.1086/379836
-
Merrigan, M. M., Sambol, S. P., Johnson, S., and Gerding, D. N. (2003). Prevention of fatal Clostridium difficile-associated disease during continuous administration of clindamycin in hamsters. J. Infect. Dis. 188, 1922-1927. doi: 10.1086/379836
-
(2003)
J. Infect. Dis.
, vol.188
, pp. 1922-1927
-
-
Merrigan, M.M.1
Sambol, S.P.2
Johnson, S.3
Gerding, D.N.4
-
42
-
-
67650388772
-
Intestinal microbiota and its functions
-
doi: 10.1016/S1594-5804(09)60016-4
-
Montalto, M., D'Onofrio, F., Gallo, A., Cazzato, A., and Gasbarrini, G. (2009). Intestinal microbiota and its functions. Dig. Liver Dis. Suppl 3, 30-34 doi: 10.1016/S1594-5804(09)60016-4
-
(2009)
Dig. Liver Dis
, Issue.3 SUPPL.
, pp. 30-34
-
-
Montalto, M.1
D'Onofrio, F.2
Gallo, A.3
Cazzato, A.4
Gasbarrini, G.5
-
43
-
-
84866549438
-
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
-
doi: 10.1186/gb-2012-13-9-r79
-
Morgan, X. C., Tickle, T. L., Sokol, H., Gevers, D., Devaney, K. L., Ward, D. V., et al. (2012). Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13:79. doi: 10.1186/gb-2012-13-9-r79
-
(2012)
Genome Biol.
, vol.13
, pp. 79
-
-
Morgan, X.C.1
Tickle, T.L.2
Sokol, H.3
Gevers, D.4
Devaney, K.L.5
Ward, D.V.6
-
44
-
-
3042571551
-
Inhibition of Clostridium difficile strains by intestinal Lactobacillus species
-
doi: 10.1099/jmm.0.45595-0
-
Naaber, P., Smidt, I., Stsepetova, J., Brilene, T., Annuk, H., and Mikelsaar, M. J. (2004). Inhibition of Clostridium difficile strains by intestinal Lactobacillus species. Med. Microbiol. 53, 551-554. doi: 10.1099/jmm.0.45595-0
-
(2004)
Med. Microbiol.
, vol.53
, pp. 551-554
-
-
Naaber, P.1
Smidt, I.2
Stsepetova, J.3
Brilene, T.4
Annuk, H.5
Mikelsaar, M.J.6
-
45
-
-
84885573828
-
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
-
doi: 10.1038/nature12503
-
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., et al. (2013). Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96-99. doi: 10.1038/nature12503
-
(2013)
Nature
, vol.502
, pp. 96-99
-
-
Ng, K.M.1
Ferreyra, J.A.2
Higginbottom, S.K.3
Lynch, J.B.4
Kashyap, P.C.5
Gopinath, S.6
-
46
-
-
70349255569
-
-
R package version 1.17-9. Available online at:
-
Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., O'Hara, R. B., Minchin, P. R., et al. (2011). Vegan: Community Ecology Package. R package version 1.17-9. Available online at: http://CRAN.R-project.org/package=vegan
-
(2011)
Vegan: Community Ecology Package
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
O'Hara, R.B.5
Minchin, P.R.6
-
47
-
-
84894268743
-
Differential effects of antibiotic therapy on the structure and function of human gut microbiota
-
doi: 10.1371/journal.pone.0080201
-
Pérez-Cobas, A. E., Artacho, A., Knecht, H., Friedrichs, A., Ott, S. J., Moya, A., et al. (2013b). Differential effects of antibiotic therapy on the structure and function of human gut microbiota. PLoS ONE 8:80201. doi: 10.1371/journal.pone.0080201
-
(2013)
PLoS ONE
, vol.8
, pp. 80201
-
-
Pérez-Cobas, A.E.1
Artacho, A.2
Knecht, H.3
Friedrichs, A.4
Ott, S.J.5
Moya, A.6
-
48
-
-
84885641936
-
Gut microbiota disturbance during antibiotic therapy: a multi-omic approach
-
doi: 10.1136/gutjnl-2012-303184
-
Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H., Artacho, A., Eismann, K., et al. (2013a). Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62, 1591-1601. doi: 10.1136/gutjnl-2012-303184
-
(2013)
Gut
, vol.62
, pp. 1591-1601
-
-
Pérez-Cobas, A.E.1
Gosalbes, M.J.2
Friedrichs, A.3
Knecht, H.4
Artacho, A.5
Eismann, K.6
-
49
-
-
0037126667
-
The microbiology of butyrate formation in the human colon
-
doi: 10.1016/S0378-1097(02)01106-0
-
Pryde, S. E., Duncan, S. H., Hold, G. L., Stewart, C. S., and Flint, H. J. (2002). The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217, 133-139. doi: 10.1016/S0378-1097(02)01106-0
-
(2002)
FEMS Microbiol. Lett.
, vol.217
, pp. 133-139
-
-
Pryde, S.E.1
Duncan, S.H.2
Hold, G.L.3
Stewart, C.S.4
Flint, H.J.5
-
51
-
-
79952773376
-
Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon
-
doi: 10.1073/pnas.1001224107
-
Rea, M. C., Dobson, A., O'Sullivan, O., Crispie, F., Fouhy, F., Cotter, P. D., et al. (2011). Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl. 1), 4639-4644. doi: 10.1073/pnas.1001224107
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, Issue.SUPPL. 1
, pp. 4639-4644
-
-
Rea, M.C.1
Dobson, A.2
O'Sullivan, O.3
Crispie, F.4
Fouhy, F.5
Cotter, P.D.6
-
52
-
-
84867615958
-
Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae
-
doi: 10.1128/IAI.00647-12
-
Reeves, A. E., Koenigsknecht, M. J., Bergin, I. L., and Young, V. B. (2012). Suppression of Clostridium difficile in the gastrointestinal tracts of germfree mice inoculated with a murine isolate from the family Lachnospiraceae. Infect. Immun. 80, 3786-3794. doi: 10.1128/IAI.00647-12
-
(2012)
Infect. Immun.
, vol.80
, pp. 3786-3794
-
-
Reeves, A.E.1
Koenigsknecht, M.J.2
Bergin, I.L.3
Young, V.B.4
-
53
-
-
80051717743
-
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection
-
doi: 10.4161/gmic.2.3.16333
-
Reeves, A. E., Theriot, C. M., Bergin, I. L., Huffnagle, G. B., Schloss, P. D., and Young, V. B. (2011). The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection. Gut Microbes 2, 145-158. doi: 10.4161/gmic.2.3.16333
-
(2011)
Gut Microbes
, vol.2
, pp. 145-158
-
-
Reeves, A.E.1
Theriot, C.M.2
Bergin, I.L.3
Huffnagle, G.B.4
Schloss, P.D.5
Young, V.B.6
-
54
-
-
84864756231
-
The human microbiome: ecosystem resilience and health
-
doi: 10.1111/j.1753-4887.2012.00489.x
-
Relman, D. A. (2012). The human microbiome: ecosystem resilience and health. Nutr. Rev. 70(Suppl), 2-9. doi: 10.1111/j.1753-4887.2012.00489.x
-
(2012)
Nutr. Rev.
, vol.70
, Issue.SUPPL.
, pp. 2-9
-
-
Relman, D.A.1
-
55
-
-
33845276869
-
Short-chain fatty acids: ready for prime time?
-
doi: 10.1177/0115426506021004351
-
Roy, C. C., Kien, C. L., Bouthillier, L., and Levy, E. (2006). Short-chain fatty acids: ready for prime time? Nutr. Clin. Pract. 21, 351-366. doi: 10.1177/0115426506021004351
-
(2006)
Nutr. Clin. Pract.
, vol.21
, pp. 351-366
-
-
Roy, C.C.1
Kien, C.L.2
Bouthillier, L.3
Levy, E.4
-
56
-
-
0037115014
-
Colonization for the prevention of Clostridium difficile disease in hamsters
-
doi: 10.1086/345676
-
Sambol, S. P., Merrigan, M. M., Tang, J. K., Johnson, S., and Gerding, D. N. (2002). Colonization for the prevention of Clostridium difficile disease in hamsters. J. Infect. Dis. 186, 1781-1789. doi: 10.1086/345676
-
(2002)
J. Infect. Dis.
, vol.186
, pp. 1781-1789
-
-
Sambol, S.P.1
Merrigan, M.M.2
Tang, J.K.3
Johnson, S.4
Gerding, D.N.5
-
57
-
-
77955124773
-
Learning Bayesian Networks with the bnlearn R Package
-
Available online at:
-
Scutari, M. (2010). Learning Bayesian Networks with the bnlearn R Package. J. Stat. Softw. 35, 1-22. Available online at: http://www.jstatsoft.org/v35/i03/
-
(2010)
J. Stat. Softw
, vol.35
, pp. 1-22
-
-
Scutari, M.1
-
58
-
-
77955647582
-
Gut microbiota in health and disease
-
doi: 10.1152/physrev.00045.2009
-
Sekirov, I., Russell, S. L., Antunes, L. C., and Finlay, B. B. (2010). Gut microbiota in health and disease. Physiol. Rev. 90, 859-904. doi: 10.1152/physrev.00045.2009
-
(2010)
Physiol. Rev.
, vol.90
, pp. 859-904
-
-
Sekirov, I.1
Russell, S.L.2
Antunes, L.C.3
Finlay, B.B.4
-
59
-
-
84871633923
-
The colonic microbiota in health and disease
-
doi: 10.1097/MOG.0b013e32835a3493
-
Shanahan, F. (2013). The colonic microbiota in health and disease. Curr. Opin. Gastroenterol. 29, 49-54. doi: 10.1097/MOG.0b013e32835a3493
-
(2013)
Curr. Opin. Gastroenterol.
, vol.29
, pp. 49-54
-
-
Shanahan, F.1
-
60
-
-
84856043672
-
A mathematical theory of communication
-
doi: 10.1002/j.1538-7305.1948.tb01338.x
-
Shannon, C. E. (1948). A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423. doi: 10.1002/j.1538-7305.1948.tb01338.x
-
(1948)
Bell Syst. Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
61
-
-
79960598587
-
Insights into the Rrf2 repressor family-the structure of CymR, the global cysteine regulator of Bacillus subtilis
-
doi: 10.1111/j.1742-4658.2011.08195.x
-
Shepard, W., Soutourina, O., Courtois, E., England, P., Haouz, A., and Martin-Verstraete, I. (2011). Insights into the Rrf2 repressor family-the structure of CymR, the global cysteine regulator of Bacillus subtilis. FEBS J. 278, 2689-2701. doi: 10.1111/j.1742-4658.2011.08195.x
-
(2011)
FEBS J.
, vol.278
, pp. 2689-2701
-
-
Shepard, W.1
Soutourina, O.2
Courtois, E.3
England, P.4
Haouz, A.5
Martin-Verstraete, I.6
-
62
-
-
79551687271
-
Mechanisms controlling pathogen colonization of the gut
-
doi: 10.1016/j.mib.2010.10.003
-
Stecher, B., and Hardt, W. D. (2011). Mechanisms controlling pathogen colonization of the gut. Curr. Opin. Microbiol. 14, 82-91. doi: 10.1016/j.mib.2010.10.003
-
(2011)
Curr. Opin. Microbiol.
, vol.14
, pp. 82-91
-
-
Stecher, B.1
Hardt, W.D.2
-
63
-
-
33745612095
-
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
-
doi: 10.1093/bioinformatics/btl117
-
Suzuki, R., and Shimodaira, H. (2006). Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540-1542. doi: 10.1093/bioinformatics/btl117
-
(2006)
Bioinformatics
, vol.22
, pp. 1540-1542
-
-
Suzuki, R.1
Shimodaira, H.2
-
64
-
-
70349233883
-
Towards the human intestinal microbiota phylogenetic core
-
doi: 10.1111/j.1462-2920.2009.01982.x
-
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J. P., et al. (2009). Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11, 2574-2584. doi: 10.1111/j.1462-2920.2009.01982.x
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 2574-2584
-
-
Tap, J.1
Mondot, S.2
Levenez, F.3
Pelletier, E.4
Caron, C.5
Furet, J.P.6
-
65
-
-
84892894991
-
Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection
-
doi: 10.1038/ncomms4114
-
Theriot, C. M., Koenigsknecht, M. J., Carlson, P. E. Jr., Hatton, G. E., Nelson, A. M., Li, B., et al. (2014). Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat. Commun. 5, 3114. doi: 10.1038/ncomms4114
-
(2014)
Nat. Commun.
, vol.5
, pp. 3114
-
-
Theriot, C.M.1
Koenigsknecht, M.J.2
Carlson Jr., P.E.3
Hatton, G.E.4
Nelson, A.M.5
Li, B.6
-
66
-
-
78649895980
-
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans
-
doi: 10.1172/JCI43918
-
Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., et al. (2010). 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. doi: 10.1172/JCI43918
-
(2010)
J. Clin. Invest.
, vol.120
, pp. 4332-4341
-
-
Ubeda, C.1
Taur, Y.2
Jenq, R.R.3
Equinda, M.J.4
Son, T.5
Samstein, M.6
-
67
-
-
49649087440
-
Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
-
doi: 10.1371/journal.pone.0002527
-
Urich, T., Lanzén, A., Qi, J., Huson, D. H., Schleper, C., and Schuster, S. C. (2008). Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3:2527. doi: 10.1371/journal.pone.0002527
-
(2008)
PLoS ONE
, vol.3
, pp. 2527
-
-
Urich, T.1
Lanzén, A.2
Qi, J.3
Huson, D.H.4
Schleper, C.5
Schuster, S.C.6
-
68
-
-
84898829359
-
Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection
-
doi: 10.1186/2049-2618-1-18
-
Vincent, C., Stephens, D. A., Loo, V. G., Edens, T. J., Behr, M. A., Dewar, K., et al. (2013). Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection. Microbiome 1:18. doi: 10.1186/2049-2618-1-18
-
(2013)
Microbiome
, vol.1
, pp. 18
-
-
Vincent, C.1
Stephens, D.A.2
Loo, V.G.3
Edens, T.J.4
Behr, M.A.5
Dewar, K.6
-
70
-
-
79952768866
-
Shifting the balance: antibiotic effects on host-microbiota mutualism
-
doi: 10.1038/nrmicro2536
-
Willing, B. P., Russell, S. L., and Finlay, B. B. (2011). Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat. Rev. Microbiol. 9, 233-243. doi: 10.1038/nrmicro2536
-
(2011)
Nat. Rev. Microbiol.
, vol.9
, pp. 233-243
-
-
Willing, B.P.1
Russell, S.L.2
Finlay, B.B.3
-
71
-
-
71549143840
-
Disulfides as redox switches: from molecular mechanisms to functional significance
-
doi: 10.1089/ARS.2009.2510
-
Wouters, M. A., Fan, S. W., and Haworth, N. L. (2010). Disulfides as redox switches: from molecular mechanisms to functional significance. Antioxid. Redox. Signal. 12, 53-91. doi: 10.1089/ARS.2009.2510
-
(2010)
Antioxid. Redox. Signal.
, vol.12
, pp. 53-91
-
-
Wouters, M.A.1
Fan, S.W.2
Haworth, N.L.3
-
72
-
-
80052606131
-
WebMGA: a customizable web server for fast metagenomic sequence analysis
-
doi: 10.1186/1471-2164-12-444.
-
Wu, S., Zhu, Z., Fu, L., Niu, B., and Li, W. (2011). WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics 12:444. doi: 10.1186/1471-2164-12-444.
-
(2011)
BMC Genomics
, vol.12
, pp. 444
-
-
Wu, S.1
Zhu, Z.2
Fu, L.3
Niu, B.4
Li, W.5
-
73
-
-
84882664672
-
Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22
-
doi: 10.1016/j.immuni.2013.08.003
-
Zelante, T., Iannitti, R. G., Cunha, C., De Luca, A., Giovannini, G., Pieraccini, G., et al. (2013).Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39, 372-385. doi: 10.1016/j.immuni.2013.08.003
-
(2013)
Immunity
, vol.39
, pp. 372-385
-
-
Zelante, T.1
Iannitti, R.G.2
Cunha, C.3
De Luca, A.4
Giovannini, G.5
Pieraccini, G.6
-
74
-
-
54349126970
-
High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota
-
doi: 10.1136/gut.2007.133603
-
Zoetendal, E. G., Rajilic-Stojanovic, M., and de Vos, W. M. (2008). High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57, 1605-1615. doi: 10.1136/gut.2007.133603
-
(2008)
Gut
, vol.57
, pp. 1605-1615
-
-
Zoetendal, E.G.1
Rajilic-Stojanovic, M.2
de Vos, W.M.3
|