-
1
-
-
84938244327
-
Human microbiota. Small molecules from the human microbiota
-
Donia, M. S., and Fischbach, M. A. (2015) Human microbiota. Small molecules from the human microbiota. Science 349, 1254766
-
(2015)
Science
, vol.349
, pp. 1254766
-
-
Donia, M.S.1
Fischbach, M.A.2
-
2
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M. G., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G., and Huttenhower, C. (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 814-821
-
-
Langille, M.G.1
Zaneveld, J.2
Caporaso, J.G.3
McDonald, D.4
Knights, D.5
Reyes, J.A.6
Clemente, J.C.7
Burkepile, D.E.8
Vega Thurber, R.L.9
Knight, R.10
Beiko, R.G.11
Huttenhower, C.12
-
3
-
-
84979608055
-
An introduction to the analysis of shotgun metagenomic data
-
Sharpton, T. J. (2014) An introduction to the analysis of shotgun metagenomic data. Front. Plant Sci. 5, 209
-
(2014)
Front. Plant Sci.
, vol.5
, pp. 209
-
-
Sharpton, T.J.1
-
4
-
-
84864037467
-
Metabolic reconstruction for metagenomic data and its application to the human microbiome
-
Abubucker, S., Segata, N., Goll, J., Schubert, A. M., Izard, J., Cantarel, B. L., Rodriguez-Mueller, B., Zucker, J., Thiagarajan, M., Henrissat, B., White, O., Kelley, S. T., Methe, B., Schloss, P. D., Gevers, D., et al. (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002358
-
-
Abubucker, S.1
Segata, N.2
Goll, J.3
Schubert, A.M.4
Izard, J.5
Cantarel, B.L.6
Rodriguez-Mueller, B.7
Zucker, J.8
Thiagarajan, M.9
Henrissat, B.10
White, O.11
Kelley, S.T.12
Methe, B.13
Schloss, P.D.14
Gevers, D.15
-
5
-
-
53549118607
-
The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E. M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J., and Edwards, R. A. (2008) The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes.BMC Bioinformatics 9, 386
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
Paarmann, D.2
D'Souza, M.3
Olson, R.4
Glass, E.M.5
Kubal, M.6
Paczian, T.7
Rodriguez, A.8
Stevens, R.9
Wilke, A.10
Wilkening, J.11
Edwards, R.A.12
-
6
-
-
77957761759
-
METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics
-
Goll, J., Rusch, D. B., Tanenbaum, D. M., Thiagarajan, M., Li, K., Methe, B. A., and Yooseph, S. (2010) METAREP: JCVI metagenomics reports-an open source tool for high-performance comparative metagenomics. Bioinformatics 26, 2631-2632
-
(2010)
Bioinformatics
, vol.26
, pp. 2631-2632
-
-
Goll, J.1
Rusch, D.B.2
Tanenbaum, D.M.3
Thiagarajan, M.4
Li, K.5
Methe, B.A.6
Yooseph, S.7
-
7
-
-
85091137006
-
The Khmer software package: Enabling efficient nucleotide sequence analysis
-
Crusoe, M. R., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A., Constantinides, B., Edvenson, G., Fay, S., Fenton, J., Fenzl, T., Fish, J., Garcia-Gutierrez, L., Garland, P., et al. (2015) The khmer software package: enabling efficient nucleotide sequence analysis. F1000Res. 4, 900
-
(2015)
F1000Res.
, vol.4
, pp. 900
-
-
Crusoe, M.R.1
Alameldin, H.F.2
Awad, S.3
Boucher, E.4
Caldwell, A.5
Cartwright, R.6
Charbonneau, A.7
Constantinides, B.8
Edvenson, G.9
Fay, S.10
Fenton, J.11
Fenzl, T.12
Fish, J.13
Garcia-Gutierrez, L.14
Garland, P.15
-
8
-
-
84946889766
-
Anvi'o: An advanced analysis and visualization platform for 'omics data
-
Eren, A. M., Esen, O.C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., and Delmont, T. O. (2015) Anvi'o: an advanced analysis and visualization platform for 'omics data. PeerJ. 3, e1319
-
(2015)
PeerJ.
, vol.3
, pp. e1319
-
-
Eren, A.M.1
Esen, O.C.2
Quince, C.3
Vineis, J.H.4
Morrison, H.G.5
Sogin, M.L.6
Delmont, T.O.7
-
9
-
-
84964803999
-
Use of metatranscriptomics in microbiome research
-
Bashiardes, S., Zilberman-Schapira, G., and Elinav, E. (2016) Use of metatranscriptomics in microbiome research. Bioinform. Biol. Insights 10, 19-25
-
(2016)
Bioinform. Biol. Insights
, vol.10
, pp. 19-25
-
-
Bashiardes, S.1
Zilberman-Schapira, G.2
Elinav, E.3
-
10
-
-
0016778734
-
Gnotobiotic animals in research: Their uses and limitations
-
Coates, M. E. (1975) Gnotobiotic animals in research: their uses and limitations. Lab. Anim. 9, 275-282
-
(1975)
Lab. Anim.
, vol.9
, pp. 275-282
-
-
Coates, M.E.1
-
11
-
-
84945289175
-
Use of germ-free animal models in microbiota-related research
-
Al-Asmakh, M., and Zadjali, F. (2015) Use of germ-free animal models in microbiota-related research. J. Microbiol. Biotechnol. 25, 1583-1588
-
(2015)
J. Microbiol. Biotechnol.
, vol.25
, pp. 1583-1588
-
-
Al-Asmakh, M.1
Zadjali, F.2
-
12
-
-
84941801496
-
Maintaining and monitoring the defined microbiota status of gnotobiotic rodents
-
Nicklas, W., Keubler, L., and Bleich, A. (2015) Maintaining and monitoring the defined microbiota status of gnotobiotic rodents. ILAR J. 56, 241-249
-
(2015)
ILAR J.
, vol.56
, pp. 241-249
-
-
Nicklas, W.1
Keubler, L.2
Bleich, A.3
-
13
-
-
34249036137
-
A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model
-
Martin, F.-P., Dumas, M.-E., Wang, Y., Legido-Quigley, C., Yap, I. K., Tang, H., Zirah, S., Murphy, G. M., Cloarec, O., Lindon, J. C., Sprenger, N., Fay, L. B., Kochhar, S., van Bladeren, P., Holmes, E., and Nicholson, J. K. (2007) A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3, 112
-
(2007)
Mol. Syst. Biol.
, vol.3
, pp. 112
-
-
Martin, F.-P.1
Dumas, M.-E.2
Wang, Y.3
Legido-Quigley, C.4
Yap, I.K.5
Tang, H.6
Zirah, S.7
Murphy, G.M.8
Cloarec, O.9
Lindon, J.C.10
Sprenger, N.11
Fay, L.B.12
Kochhar, S.13
Van Bladeren, P.14
Holmes, E.15
Nicholson, J.K.16
-
14
-
-
62649151803
-
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
-
Wikoff, W. R., Anfora, A. T., Liu, J., Schultz, P. G., Lesley, S. A., Peters, E. C., and Siuzdak, G. (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. U.S.A. 106, 3698-3703
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 3698-3703
-
-
Wikoff, W.R.1
Anfora, A.T.2
Liu, J.3
Schultz, P.G.4
Lesley, S.A.5
Peters, E.C.6
Siuzdak, G.7
-
15
-
-
53949089441
-
Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes
-
Claus, S. P., Tsang, T. M., Wang, Y., Cloarec, O., Skordi, E., Martin, F.-P., Rezzi, S., Ross, A., Kochhar, S., Holmes, E., and Nicholson, J. K. (2008) Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol. Syst. Biol. 4, 219
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 219
-
-
Claus, S.P.1
Tsang, T.M.2
Wang, Y.3
Cloarec, O.4
Skordi, E.5
Martin, F.-P.6
Rezzi, S.7
Ross, A.8
Kochhar, S.9
Holmes, E.10
Nicholson, J.K.11
-
16
-
-
84859773739
-
Impact of intestinal microbiota on intestinal luminal metabolome
-
Matsumoto, M., Kibe, R., Ooga, T., Aiba, Y., Kurihara, S., Sawaki, E., Koga, Y., and Benno, Y. (2012) Impact of intestinal microbiota on intestinal luminal metabolome. Sci. Rep. 2, 233
-
(2012)
Sci. Rep.
, vol.2
, pp. 233
-
-
Matsumoto, M.1
Kibe, R.2
Ooga, T.3
Aiba, Y.4
Kurihara, S.5
Sawaki, E.6
Koga, Y.7
Benno, Y.8
-
17
-
-
84875876611
-
Cerebral low-molecular metabolites influenced by intestinal microbiota: A pilot study
-
Matsumoto, M., Kibe, R., Ooga, T., Aiba, Y., Sawaki, E., Koga, Y., and Benno, Y. (2013) Cerebral low-molecular metabolites influenced by intestinal microbiota: a pilot study. Front. Syst. Neurosci. 7, 9
-
(2013)
Front. Syst. Neurosci.
, vol.7
, pp. 9
-
-
Matsumoto, M.1
Kibe, R.2
Ooga, T.3
Aiba, Y.4
Sawaki, E.5
Koga, Y.6
Benno, Y.7
-
18
-
-
84973480887
-
Analysis of exhaled breath volatile organic compounds in inflammatory bowel disease: A pilot study
-
Hicks, L. C., Huang, J., Kumar, S., Powles, S. T., Orchard, T. R., Hanna, G. B., and Williams, H. R. (2015) Analysis of exhaled breath volatile organic compounds in inflammatory bowel disease: a pilot study. J. Crohns Colitis 9, 731-737
-
(2015)
J. Crohns Colitis
, vol.9
, pp. 731-737
-
-
Hicks, L.C.1
Huang, J.2
Kumar, S.3
Powles, S.T.4
Orchard, T.R.5
Hanna, G.B.6
Williams, H.R.7
-
19
-
-
84940941884
-
MALDITOF mass spectrometry: An emerging technology for microbial identification and diagnosis
-
Singhal, N., Kumar, M., Kanaujia, P. K., and Virdi, J. S. (2015) MALDITOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front. Microbiol. 6, 791
-
(2015)
Front. Microbiol.
, vol.6
, pp. 791
-
-
Singhal, N.1
Kumar, M.2
Kanaujia, P.K.3
Virdi, J.S.4
-
20
-
-
77957809580
-
Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species
-
Stevenson, L. G., Drake, S. K., Shea, Y. R., Zelazny, A. M., and Murray, P. R. (2010) Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of clinically important yeast species. J. Clin. Microbiol. 48, 3482-3486
-
(2010)
J. Clin. Microbiol.
, vol.48
, pp. 3482-3486
-
-
Stevenson, L.G.1
Drake, S.K.2
Shea, Y.R.3
Zelazny, A.M.4
Murray, P.R.5
-
21
-
-
84879428313
-
Identification of rare pathogenic bacteria in a clinical microbiology laboratory: Impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry
-
Seng, P., Abat, C., Rolain, J. M., Colson, P., Lagier, J.-C., Gouriet, F., Fournier, P. E., Drancourt, M., La Scola, B., and Raoult, D. (2013) Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Clin. Microbiol. 51, 2182-2194
-
(2013)
J. Clin. Microbiol.
, vol.51
, pp. 2182-2194
-
-
Seng, P.1
Abat, C.2
Rolain, J.M.3
Colson, P.4
Lagier, J.-C.5
Gouriet, F.6
Fournier, P.E.7
Drancourt, M.8
La Scola, B.9
Raoult, D.10
-
22
-
-
84901218397
-
MALDI-TOF identification of the human gut microbiome in people with and without diarrhea in Senegal
-
Samb-Ba, B., Mazenot, C., Gassama-Sow, A., Dubourg, G., Richet, H., Hugon, P., Lagier, J.-C., Raoult, D., and Fenollar, F. (2014) MALDI-TOF identification of the human gut microbiome in people with and without diarrhea in Senegal. PLoS ONE 9, e87419
-
(2014)
PLoS ONE
, vol.9
, pp. e87419
-
-
Samb-Ba, B.1
Mazenot, C.2
Gassama-Sow, A.3
Dubourg, G.4
Richet, H.5
Hugon, P.6
Lagier, J.-C.7
Raoult, D.8
Fenollar, F.9
-
23
-
-
38549117301
-
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
Caspi, R., Foerster, H., Fulcher, C. A., Kaipa, P., Krummenacker, M., Latendresse, M., Paley, S., Rhee, S. Y., Shearer, A. G., Tissier, C., Walk, T. C., Zhang, P., and Karp, P. D. (2008) The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 36, D623-D631
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D623-D631
-
-
Caspi, R.1
Foerster, H.2
Fulcher, C.A.3
Kaipa, P.4
Krummenacker, M.5
Latendresse, M.6
Paley, S.7
Rhee, S.Y.8
Shearer, A.G.9
Tissier, C.10
Walk, T.C.11
Zhang, P.12
Karp, P.D.13
-
24
-
-
84876148784
-
HMDB 3.0-The human metabolome database in 2013
-
Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., Djoumbou, Y., Mandal, R., Aziat, F., Dong, E., Bouatra, S., Sinelnikov, I., Arndt, D., Xia, J., Liu, P., et al. (2013) HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res. 41, D801-D807
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D801-D807
-
-
Wishart, D.S.1
Jewison, T.2
Guo, A.C.3
Wilson, M.4
Knox, C.5
Liu, Y.6
Djoumbou, Y.7
Mandal, R.8
Aziat, F.9
Dong, E.10
Bouatra, S.11
Sinelnikov, I.12
Arndt, D.13
Xia, J.14
Liu, P.15
-
25
-
-
36348980985
-
Current progress in computational metabolomics
-
Wishart, D. S. (2007) Current progress in computational metabolomics. Brief Bioinform. 8, 279-293
-
(2007)
Brief Bioinform.
, vol.8
, pp. 279-293
-
-
Wishart, D.S.1
-
26
-
-
84939536885
-
Computational approaches to natural product discovery
-
Medema, M. H., and Fischbach, M. A. (2015) Computational approaches to natural product discovery. Nat. Chem. Biol. 11, 639-648
-
(2015)
Nat. Chem. Biol.
, vol.11
, pp. 639-648
-
-
Medema, M.H.1
Fischbach, M.A.2
-
27
-
-
84939493603
-
IMG-ABC: A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites
-
Hadjithomas, M., Chen, I.-M., Chu, K., Ratner, A., Palaniappan, K., Szeto, E., Huang, J., Reddy, T. B., Cimermančič, P., Fischbach, M. A., Ivanova, N. N., Markowitz, V. M., Kyrpides, N. C., and Pati, A. (2015) IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio. 6, e00932
-
(2015)
MBio.
, vol.6
, pp. e00932
-
-
Hadjithomas, M.1
Chen, I.-M.2
Chu, K.3
Ratner, A.4
Palaniappan, K.5
Szeto, E.6
Huang, J.7
Reddy, T.B.8
Cimermančič, P.9
Fischbach, M.A.10
Ivanova, N.N.11
Markowitz, V.M.12
Kyrpides, N.C.13
Pati, A.14
-
28
-
-
84872535919
-
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
-
Maurice, C. F., Haiser, H. J., and Turnbaugh, P. J. (2013) Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50
-
(2013)
Cell
, vol.152
, pp. 39-50
-
-
Maurice, C.F.1
Haiser, H.J.2
Turnbaugh, P.J.3
-
29
-
-
84880439384
-
Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta
-
Haiser, H. J., Gootenberg, D. B., Chatman, K., Sirasani, G., Balskus, E. P., and Turnbaugh, P. J. (2013) Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295-298
-
(2013)
Science
, vol.341
, pp. 295-298
-
-
Haiser, H.J.1
Gootenberg, D.B.2
Chatman, K.3
Sirasani, G.4
Balskus, E.P.5
Turnbaugh, P.J.6
-
30
-
-
74949136754
-
In vitro interaction of L-dopa with bacterial adhesins of Helicobacter pylori: An explanation for clinical differences in bioavailability?
-
Niehues, M., and Hensel, A. (2009) In vitro interaction of L-dopa with bacterial adhesins of Helicobacter pylori: an explanation for clinical differences in bioavailability? J. Pharm. Pharmacol. 61, 1303-1307
-
(2009)
J. Pharm. Pharmacol.
, vol.61
, pp. 1303-1307
-
-
Niehues, M.1
Hensel, A.2
-
31
-
-
84907487928
-
Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics
-
Carmody, R. N., and Turnbaugh, P. J. (2014) Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J. Clin. Invest. 124, 4173-4181
-
(2014)
J. Clin. Invest.
, vol.124
, pp. 4173-4181
-
-
Carmody, R.N.1
Turnbaugh, P.J.2
-
32
-
-
84893686882
-
Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
-
McHardy, I. H., Goudarzi, M., Tong, M., Ruegger, P. M., Schwager, E., Weger, J. R., Graeber, T. G., Sonnenburg, J. L., Horvath, S., Huttenhower, C., McGovern, D. P., Fornace, A. J., Jr., Borneman, J., and Braun, J. (2013) Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 1, 17
-
(2013)
Microbiome
, vol.1
, pp. 17
-
-
McHardy, I.H.1
Goudarzi, M.2
Tong, M.3
Ruegger, P.M.4
Schwager, E.5
Weger, J.R.6
Graeber, T.G.7
Sonnenburg, J.L.8
Horvath, S.9
Huttenhower, C.10
McGovern, D.P.11
Fornace, A.J.12
Borneman, J.13
Braun, J.14
-
33
-
-
84978852361
-
The human gut microbiome and its dysfunctions through the meta-omics prism
-
Mondot, S., and Lepage, P. (2016) The human gut microbiome and its dysfunctions through the meta-omics prism. Ann. N.Y. Acad. Sci. 1372, 9-19
-
(2016)
Ann. N.Y. Acad. Sci.
, vol.1372
, pp. 9-19
-
-
Mondot, S.1
Lepage, P.2
-
34
-
-
84884650652
-
Diet, microbes, and host genetics: The perfect storm in inflammatory bowel diseases
-
Leone, V., Chang, E. B., and Devkota, S. (2013) Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases. J. Gastroenterol. 48, 315-321
-
(2013)
J. Gastroenterol.
, vol.48
, pp. 315-321
-
-
Leone, V.1
Chang, E.B.2
Devkota, S.3
-
35
-
-
84863436944
-
Dietaryfat- induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice
-
Devkota, S., Wang, Y., Musch, M. W., Leone, V., Fehlner-Peach, H., Nadimpalli, A., Antonopoulos, D. A., Jabri, B., and Chang, E. B. (2012) Dietaryfat- induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Nature 487, 104-108
-
(2012)
Nature
, vol.487
, pp. 104-108
-
-
Devkota, S.1
Wang, Y.2
Musch, M.W.3
Leone, V.4
Fehlner-Peach, H.5
Nadimpalli, A.6
Antonopoulos, D.A.7
Jabri, B.8
Chang, E.B.9
-
36
-
-
33847378014
-
Rapid and noninvasive metabonomic characterization of inflammatory bowel disease
-
Marchesi, J. R., Holmes, E., Khan, F., Kochhar, S., Scanlan, P., Shanahan, F., Wilson, I. D., and Wang, Y. (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J. Proteome Res. 6, 546-551
-
(2007)
J. Proteome Res.
, vol.6
, pp. 546-551
-
-
Marchesi, J.R.1
Holmes, E.2
Khan, F.3
Kochhar, S.4
Scanlan, P.5
Shanahan, F.6
Wilson, I.D.7
Wang, Y.8
-
37
-
-
84977507546
-
Microbial metabolism of dietary components to bioactive metabolites: Opportunities for new therapeutic interventions
-
Zhang, L. S., and Davies, S. S. (2016) Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions. Genome Med. 8, 46
-
(2016)
Genome Med.
, vol.8
, pp. 46
-
-
Zhang, L.S.1
Davies, S.S.2
-
38
-
-
68149099597
-
Metabolomics reveals metabolic biomarkers of Crohn's disease
-
Jansson, J., Willing, B., Lucio, M., Fekete, A., Dicksved, J., Halfvarson, J., Tysk, C., and Schmitt-Kopplin, P. (2009) Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS ONE 4, e6386
-
(2009)
PLoS ONE
, vol.4
, pp. e6386
-
-
Jansson, J.1
Willing, B.2
Lucio, M.3
Fekete, A.4
Dicksved, J.5
Halfvarson, J.6
Tysk, C.7
Schmitt-Kopplin, P.8
-
39
-
-
0015349085
-
Tryptophan metabolism in microorganisms
-
Nozaki, M., and Ishimura, Y. (1972) Tryptophan metabolism in microorganisms. Biochem. J. 128, 24P-25P
-
(1972)
Biochem. J.
, vol.128
, pp. 24P-25P
-
-
Nozaki, M.1
Ishimura, Y.2
-
40
-
-
76249101130
-
The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation
-
Bansal, T., Alaniz, R. C., Wood, T. K., and Jayaraman, A. (2010) The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation. Proc. Natl. Acad. Sci. U.S.A. 107, 228-233
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 228-233
-
-
Bansal, T.1
Alaniz, R.C.2
Wood, T.K.3
Jayaraman, A.4
-
41
-
-
84894263389
-
Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon
-
Shimada, Y., Kinoshita, M., Harada, K., Mizutani, M., Masahata, K., Kayama, H., and Takeda, K. (2013) Commensal bacteria-dependent indole production enhances epithelial barrier function in the colon. PLoS ONE 8, e80604
-
(2013)
PLoS ONE
, vol.8
, pp. e80604
-
-
Shimada, Y.1
Kinoshita, M.2
Harada, K.3
Mizutani, M.4
Masahata, K.5
Kayama, H.6
Takeda, K.7
-
42
-
-
84938675563
-
Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles
-
Hubbard, T. D., Murray, I. A., Bisson, W. H., Lahoti, T. S., Gowda, K., Amin, S. G., Patterson, A. D., and Perdew, G. H. (2015) Adaptation of the human aryl hydrocarbon receptor to sense microbiota-derived indoles. Sci. Rep. 5, 12689
-
(2015)
Sci. Rep.
, vol.5
, pp. 12689
-
-
Hubbard, T.D.1
Murray, I.A.2
Bisson, W.H.3
Lahoti, T.S.4
Gowda, K.5
Amin, S.G.6
Patterson, A.D.7
Perdew, G.H.8
-
43
-
-
84930818280
-
Aryl hydrocarbon receptor activation down-regulates IL-7 and reduces inflammation in a mouse model of DSS-induced colitis
-
Ji, T., Xu, C., Sun, L., Yu, M., Peng, K., Qiu, Y., Xiao, W., and Yang, H. (2015) Aryl hydrocarbon receptor activation down-regulates IL-7 and reduces inflammation in a mouse model of DSS-induced colitis. Dig. Dis. Sci. 60, 1958-1966
-
(2015)
Dig. Dis. Sci.
, vol.60
, pp. 1958-1966
-
-
Ji, T.1
Xu, C.2
Sun, L.3
Yu, M.4
Peng, K.5
Qiu, Y.6
Xiao, W.7
Yang, H.8
-
44
-
-
84966526506
-
CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands
-
Lamas, B., Richard, M. L., Leducq, V., Pham, H.-P., Michel, M.-L., Da Costa, G., Bridonneau, C., Jegou, S., Hoffmann, T. W., Natividad, J. M., Brot, L., Taleb, S., Couturier-Maillard, A., Nion-Larmurier, I., Merabtene, F., et al. (2016) CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat. Med. 22, 598-605
-
(2016)
Nat. Med.
, vol.22
, pp. 598-605
-
-
Lamas, B.1
Richard, M.L.2
Leducq, V.3
Pham, H.-P.4
Michel, M.-L.5
Da Costa, G.6
Bridonneau, C.7
Jegou, S.8
Hoffmann, T.W.9
Natividad, J.M.10
Brot, L.11
Taleb, S.12
Couturier-Maillard, A.13
Nion-Larmurier, I.14
Merabtene, F.15
-
45
-
-
79952601424
-
Normal gut microbiota modulates brain development and behavior
-
Diaz Heijtz, R., Wang, S., Anuar, F., Qian, Y., Björkholm, B., Samuelsson, A., Hibberd, M. L., Forssberg, H., and Pettersson, S. (2011) Normal gut microbiota modulates brain development and behavior. Proc. Natl. Acad. Sci. U.S.A. 108, 3047-3052
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 3047-3052
-
-
Diaz Heijtz, R.1
Wang, S.2
Anuar, F.3
Qian, Y.4
Björkholm, B.5
Samuelsson, A.6
Hibberd, M.L.7
Forssberg, H.8
Pettersson, S.9
-
46
-
-
84911884131
-
The gut microbiota influences blood-brain barrier permeability in mice
-
Braniste, V., Al-Asmakh, M., Kowal, C., Anuar, F., Abbaspour, A., Tóth, M., Korecka, A., Bakocevic, N., Ng, L. G., Guan, N. L., Kundu, P., Gulyás, B., Halldin, C., Hultenby, K., Nilsson, H., et al. (2014) The gut microbiota influences blood-brain barrier permeability in mice. Sci. Transl. Med. 6, 263ra158
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 263ra158
-
-
Braniste, V.1
Al-Asmakh, M.2
Kowal, C.3
Anuar, F.4
Abbaspour, A.5
Tóth, M.6
Korecka, A.7
Bakocevic, N.8
Ng, L.G.9
Guan, N.L.10
Kundu, P.11
Gulyás, B.12
Halldin, C.13
Hultenby, K.14
Nilsson, H.15
-
47
-
-
84964389293
-
From gut dysbiosis to altered brain function and mental illness: Mechanisms and pathways
-
Rogers, G. B., Keating, D. J., Young, R. L., Wong, M.-L., Licinio, J., and Wesselingh, S. (2016) From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways. Mol. Psychiatry 21, 738-748
-
(2016)
Mol. Psychiatry
, vol.21
, pp. 738-748
-
-
Rogers, G.B.1
Keating, D.J.2
Young, R.L.3
Wong, M.-L.4
Licinio, J.5
Wesselingh, S.6
-
48
-
-
80051535923
-
The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice
-
Bercik, P., Denou, E., Collins, J., Jackson, W., Lu, J., Jury, J., Deng, Y., Blennerhassett, P., Macri, J., McCoy, K. D., Verdu, E. F., and Collins, S. M. (2011) The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 141, 599-609.e3
-
(2011)
Gastroenterology
, vol.141
, pp. 599e3-599e3
-
-
Bercik, P.1
Denou, E.2
Collins, J.3
Jackson, W.4
Lu, J.5
Jury, J.6
Deng, Y.7
Blennerhassett, P.8
Macri, J.9
McCoy, K.D.10
Verdu, E.F.11
Collins, S.M.12
-
49
-
-
84896728399
-
Altered gut microbiota and activity in a murine model of autism spectrum disorders
-
de Theije, C. G., Wopereis, H., Ramadan, M., van Eijndthoven, T., Lambert, J., Knol, J., Garssen, J., Kraneveld, A. D., and Oozeer, R. (2014) Altered gut microbiota and activity in a murine model of autism spectrum disorders. Brain Behav. Immun. 37, 197-206
-
(2014)
Brain Behav. Immun.
, vol.37
, pp. 197-206
-
-
De Theije, C.G.1
Wopereis, H.2
Ramadan, M.3
Van Eijndthoven, T.4
Lambert, J.5
Knol, J.6
Garssen, J.7
Kraneveld, A.D.8
Oozeer, R.9
-
50
-
-
84971575056
-
Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior
-
Gacias, M., Gaspari, S., Santos, P.-M., Tamburini, S., Andrade, M., Zhang, F., Shen, N., Tolstikov, V., Kiebish, M. A., Dupree, J. L., Zachariou, V., Clemente, J. C., and Casaccia, P. (2016) Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior. Elife 5, e13442
-
(2016)
Elife
, vol.5
, pp. e13442
-
-
Gacias, M.1
Gaspari, S.2
Santos, P.-M.3
Tamburini, S.4
Andrade, M.5
Zhang, F.6
Shen, N.7
Tolstikov, V.8
Kiebish, M.A.9
Dupree, J.L.10
Zachariou, V.11
Clemente, J.C.12
Casaccia, P.13
-
51
-
-
84966658995
-
Type i interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor
-
Rothhammer, V., Mascanfroni, I. D., Bunse, L., Takenaka, M. C., Kenison, J. E., Mayo, L., Chao, C.-C., Patel, B., Yan, R., Blain, M., Alvarez, J. I., Kebir, H., Anandasabapathy, N., Izquierdo, G., Jung, S., et al. (2016) Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor. Nat. Med. 22, 586-597
-
(2016)
Nat. Med.
, vol.22
, pp. 586-597
-
-
Rothhammer, V.1
Mascanfroni, I.D.2
Bunse, L.3
Takenaka, M.C.4
Kenison, J.E.5
Mayo, L.6
Chao, C.-C.7
Patel, B.8
Yan, R.9
Blain, M.10
Alvarez, J.I.11
Kebir, H.12
Anandasabapathy, N.13
Izquierdo, G.14
Jung, S.15
-
52
-
-
79953733693
-
Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease
-
Wang, Z., Klipfell, E., Bennett, B. J., Koeth, R., Levison, B. S., Dugar, B., Feldstein, A. E., Britt, E. B., Fu, X., Chung, Y.-M., Wu, Y., Schauer, P., Smith, J. D., Allayee, H., Tang, W. H., et al. (2011) Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57-63
-
(2011)
Nature
, vol.472
, pp. 57-63
-
-
Wang, Z.1
Klipfell, E.2
Bennett, B.J.3
Koeth, R.4
Levison, B.S.5
Dugar, B.6
Feldstein, A.E.7
Britt, E.B.8
Fu, X.9
Chung, Y.-M.10
Wu, Y.11
Schauer, P.12
Smith, J.D.13
Allayee, H.14
Tang, W.H.15
-
53
-
-
84877331372
-
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis
-
Koeth, R. A., Wang, Z., Levison, B. S., Buffa, J. A., Org, E., Sheehy, B. T., Britt, E. B., Fu, X., Wu, Y., Li, L., Smith, J. D., DiDonato, J. A., Chen, J., Li, H., Wu, G. D., et al. (2013) Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 19, 576-585
-
(2013)
Nat. Med.
, vol.19
, pp. 576-585
-
-
Koeth, R.A.1
Wang, Z.2
Levison, B.S.3
Buffa, J.A.4
Org, E.5
Sheehy, B.T.6
Britt, E.B.7
Fu, X.8
Wu, Y.9
Li, L.10
Smith, J.D.11
DiDonato, J.A.12
Chen, J.13
Li, H.14
Wu, G.D.15
-
54
-
-
84959573656
-
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease
-
Feng, Q., Liu, Z., Zhong, S., Li, R., Xia, H., Jie, Z., Wen, B., Chen, X., Yan, W., Fan, Y., Guo, Z., Meng, N., Chen, J., Yu, X., Zhang, Z., et al. (2016) Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. Sci. Rep. 6, 22525
-
(2016)
Sci. Rep.
, vol.6
, pp. 22525
-
-
Feng, Q.1
Liu, Z.2
Zhong, S.3
Li, R.4
Xia, H.5
Jie, Z.6
Wen, B.7
Chen, X.8
Yan, W.9
Fan, Y.10
Guo, Z.11
Meng, N.12
Chen, J.13
Yu, X.14
Zhang, Z.15
-
55
-
-
33747618036
-
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice
-
Dumas, M.-E., Barton, R. H., Toye, A., Cloarec, O., Blancher, C., Rothwell, A., Fearnside, J., Tatoud, R., Blanc, V., Lindon, J. C., Mitchell, S. C., Holmes, E., McCarthy, M. I., Scott, J., Gauguier, D., and Nicholson, J. K. (2006) Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc. Natl. Acad. Sci. U.S.A. 103, 12511-12516
-
(2006)
Proc. Natl. Acad. Sci. U.S.A.
, vol.103
, pp. 12511-12516
-
-
Dumas, M.-E.1
Barton, R.H.2
Toye, A.3
Cloarec, O.4
Blancher, C.5
Rothwell, A.6
Fearnside, J.7
Tatoud, R.8
Blanc, V.9
Lindon, J.C.10
Mitchell, S.C.11
Holmes, E.12
McCarthy, M.I.13
Scott, J.14
Gauguier, D.15
Nicholson, J.K.16
-
56
-
-
84936845643
-
Urinary 1H-NMR-based metabolic profiling of children with NAFLD undergoing VSL#3 treatment
-
Miccheli, A., Capuani, G., Marini, F., Tomassini, A., Praticò, G., Ceccarelli, S., Gnani, D., Baviera, G., Alisi, A., Putignani, L., and Nobili, V. (2015) Urinary 1H-NMR-based metabolic profiling of children with NAFLD undergoing VSL#3 treatment. Int. J. Obes. 39, 1118-1125
-
(2015)
Int. J. Obes.
, vol.39
, pp. 1118-1125
-
-
Miccheli, A.1
Capuani, G.2
Marini, F.3
Tomassini, A.4
Praticò, G.5
Ceccarelli, S.6
Gnani, D.7
Baviera, G.8
Alisi, A.9
Putignani, L.10
Nobili, V.11
-
57
-
-
84900032263
-
Randomised clinical trial: The beneficial effects of VSL#3 in obese children with non-alcoholic steatohepatitis
-
Alisi, A., Bedogni, G., Baviera, G., Giorgio, V., Porro, E., Paris, C., Giammaria, P., Reali, L., Anania, F., and Nobili, V. (2014) Randomised clinical trial: the beneficial effects of VSL#3 in obese children with non-alcoholic steatohepatitis. Aliment. Pharmacol. Ther. 39, 1276-1285
-
(2014)
Aliment. Pharmacol. Ther.
, vol.39
, pp. 1276-1285
-
-
Alisi, A.1
Bedogni, G.2
Baviera, G.3
Giorgio, V.4
Porro, E.5
Paris, C.6
Giammaria, P.7
Reali, L.8
Anania, F.9
Nobili, V.10
-
58
-
-
84908293710
-
Differential modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of host peripheral lipid metabolism and histone acetylation in mouse gut organoids
-
Lukovac, S., Belzer, C., Pellis, L., Keijser, B. J., de Vos, W. M., Montijn, R. C., and Roeselers, G. (2014) Differential modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of host peripheral lipid metabolism and histone acetylation in mouse gut organoids. MBio 5, e01438
-
(2014)
MBio
, vol.5
, pp. e01438
-
-
Lukovac, S.1
Belzer, C.2
Pellis, L.3
Keijser, B.J.4
De Vos, W.M.5
Montijn, R.C.6
Roeselers, G.7
|