-
1
-
-
78751580602
-
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
-
Walker, A. W.; Ince, J.; Duncan, S. H.; Webster, L. M.; Holtrop, G.; Ze, X.; Brown, D.; Stares, M. D.; Scott, P.; Bergerat, A.; et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 2011, 5, 220-230.
-
(2011)
ISME J
, vol.5
, pp. 220-230
-
-
Walker, A.W.1
Ince, J.2
Duncan, S.H.3
Webster, L.M.4
Holtrop, G.5
Ze, X.6
Brown, D.7
Stares, M.D.8
Scott, P.9
Bergerat, A.10
-
2
-
-
70350332205
-
Diets enriched in oat bran or wheat bran temporally and differentially alter the composition of the fecal community of rats
-
Abnous, K.; Brooks, S. P.; Kwan, J.; Matias, F.; Green-Johnson, J.; Selinger, L. B.; Thomas, M.; Kalmokoff, M. Diets enriched in oat bran or wheat bran temporally and differentially alter the composition of the fecal community of rats. J. Nutr. 2009, 139, 2024-2031.
-
(2009)
J. Nutr
, vol.139
, pp. 2024-2031
-
-
Abnous, K.1
Brooks, S.P.2
Kwan, J.3
Matias, F.4
Green-Johnson, J.5
Selinger, L.B.6
Thomas, M.7
Kalmokoff, M.8
-
3
-
-
79953025661
-
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
-
Swanson, K. S.; Dowd, S. E.; Suchodolski, J. S.; Middelbos, I. S.; Vester, B. M.; Barry, K. A.; Nelson, K. E.; Torralba, M.; Henrissat, B.; Coutinho, P. M.; et al. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J. 2011, 5, 639-649.
-
(2011)
ISME J
, vol.5
, pp. 639-649
-
-
Swanson, K.S.1
Dowd, S.E.2
Suchodolski, J.S.3
Middelbos, I.S.4
Vester, B.M.5
Barry, K.A.6
Nelson, K.E.7
Torralba, M.8
Henrissat, B.9
Coutinho, P.M.10
-
4
-
-
70350110294
-
High-fat diet determines the composition of the murine gut microbiome independently of obesity
-
Hildebrandt, M. A.; Hoffmann, C.; Sherrill-Mix, S. A.; Keilbaugh, S. A.; Hamady, M.; Chen, Y. Y.; Knight, R.; Ahima, R. S.; Bushman, F.; Wu, G. D. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009, 137, 1716-1724. e2.
-
(2009)
Gastroenterology
, vol.137
-
-
Hildebrandt, M.A.1
Hoffmann, C.2
Sherrill-Mix, S.A.3
Keilbaugh, S.A.4
Hamady, M.5
Chen, Y.Y.6
Knight, R.7
Ahima, R.S.8
Bushman, F.9
Wu, G.D.10
-
5
-
-
84892828465
-
Diet rapidly and reproducibly alters the human gut microbiome
-
David, L. A.; Maurice, C. F.; Carmody, R. N.; Gootenberg, D. B.; Button, J. E.; Wolfe, B. E.; Ling, A. V.; Devlin, A. S.; Varma, Y.; Fischbach, M. A.; et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505, 559-563.
-
(2014)
Nature
, vol.505
, pp. 559-563
-
-
David, L.A.1
Maurice, C.F.2
Carmody, R.N.3
Gootenberg, D.B.4
Button, J.E.5
Wolfe, B.E.6
Ling, A.V.7
Devlin, A.S.8
Varma, Y.9
Fischbach, M.A.10
-
6
-
-
84863537082
-
454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber
-
Hooda, S.; Boler, B. M.; Serao, M. C.; Brulc, J. M.; Staeger, M. A.; Boileau, T. W.; Dowd, S. E.; Fahey, G. C., Jr.; Swanson, K. S. 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. J. Nutr. 2012, 142, 1259-1265.
-
(2012)
J. Nutr
, vol.142
, pp. 1259-1265
-
-
Hooda, S.1
Boler, B.M.2
Serao, M.C.3
Brulc, J.M.4
Staeger, M.A.5
Boileau, T.W.6
Dowd, S.E.7
Fahey, G.C.8
Swanson, K.S.9
-
7
-
-
84884590677
-
In vitro characterization of the impact of selected dietary fibers on fecal microbiota composition and short chain fatty acid production
-
Yang, J.; Martinez, I.; Walter, J.; Keshavarzian, A.; Rose, D. J. In vitro characterization of the impact of selected dietary fibers on fecal microbiota composition and short chain fatty acid production. Anaerobe 2013, 23, 74-81.
-
(2013)
Anaerobe
, vol.23
, pp. 74-81
-
-
Yang, J.1
Martinez, I.2
Walter, J.3
Keshavarzian, A.4
Rose, D.J.5
-
8
-
-
78649734540
-
Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects
-
Martinez, I.; Kim, J.; Duffy, P. R.; Schlegel, V. L.; Walter, J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS ONE 2010, 5, e15046.
-
(2010)
PLoS ONE
, vol.5
-
-
Martinez, I.1
Kim, J.2
Duffy, P.R.3
Schlegel, V.L.4
Walter, J.5
-
9
-
-
55949117839
-
Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch
-
Abell, G. C.; Cooke, C. M.; Bennett, C. N.; Conlon, M. A.; McOrist, A. L. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 2008, 66, 505-515.
-
(2008)
FEMS Microbiol. Ecol
, vol.66
, pp. 505-515
-
-
Abell, G.C.1
Cooke, C.M.2
Bennett, C.N.3
Conlon, M.A.4
McOrist, A.L.5
-
10
-
-
79955981721
-
Dietary resistant and butyrylated starches have different effects on the faecal bacterial flora of azoxymethane-treated rats
-
Abell, G. C.; Christophersen, C. T.; McOrist, A. L.; Clarke, J. M. Dietary resistant and butyrylated starches have different effects on the faecal bacterial flora of azoxymethane-treated rats. Br. J. Nutr. 2011, 105, 1480-1485.
-
(2011)
Br. J. Nutr
, vol.105
, pp. 1480-1485
-
-
Abell, G.C.1
Christophersen, C.T.2
McOrist, A.L.3
Clarke, J.M.4
-
11
-
-
84876415448
-
Temporal change in the gut community of rats fed high amylose cornstarch is driven by endogenous urea rather than strictly on carbohydrate availability
-
Kalmokoff, M.; Zwicker, B.; O'Hara, M.; Matias, F.; Green, J.; Shastri, P.; Green-Johnson, J.; Brooks, S. P. Temporal change in the gut community of rats fed high amylose cornstarch is driven by endogenous urea rather than strictly on carbohydrate availability. J. Appl. Microbiol. 2013, 114, 1516-1528.
-
(2013)
J. Appl. Microbiol
, vol.114
, pp. 1516-1528
-
-
Kalmokoff, M.1
Zwicker, B.2
O'Hara, M.3
Matias, F.4
Green, J.5
Shastri, P.6
Green-Johnson, J.7
Brooks, S.P.8
-
12
-
-
36549034874
-
Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet
-
Klieve, A. V.; O'Leary, M. N.; McMillen, L.; Ouwerkerk, D. Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet. J. Appl. Microbiol. 2007, 103, 2065-2073.
-
(2007)
J. Appl. Microbiol
, vol.103
, pp. 2065-2073
-
-
Klieve, A.V.1
O'Leary, M.N.2
McMillen, L.3
Ouwerkerk, D.4
-
13
-
-
0032901238
-
Short-chain fructo-oligosaccharide administration dose-dependently increases fecal bifidobacteria in healthy humans
-
Bouhnik, Y.; Vahedi, K.; Achour, L.; Attar, A.; Salfati, J.; Pochart, P.; Marteau, P.; Flourie, B.; Bornet, F.; Rambaud, J. C. Short-chain fructo-oligosaccharide administration dose-dependently increases fecal bifidobacteria in healthy humans. J. Nutr. 1999, 129, 113-116.
-
(1999)
J. Nutr
, vol.129
, pp. 113-116
-
-
Bouhnik, Y.1
Vahedi, K.2
Achour, L.3
Attar, A.4
Salfati, J.5
Pochart, P.6
Marteau, P.7
Flourie, B.8
Bornet, F.9
Rambaud, J.C.10
-
14
-
-
40549138422
-
Prebiotic evaluation of a novel galactooligosaccharide mixture produced by the enzymatic activity of Bifidobacterium bifidum NCIMB 41171, in healthy humans: A randomized, double-blind, crossover, placebo-controlled intervention study
-
Depeint, F.; Tzortzis, G.; Vulevic, J.; I'Anson, K.; Gibson, G. R. Prebiotic evaluation of a novel galactooligosaccharide mixture produced by the enzymatic activity of Bifidobacterium bifidum NCIMB 41171, in healthy humans: A randomized, double-blind, crossover, placebo-controlled intervention study. Am. J. Clin. Nutr. 2008, 87, 785-791.
-
(2008)
Am. J. Clin. Nutr
, vol.87
, pp. 785-791
-
-
Depeint, F.1
Tzortzis, G.2
Vulevic, J.3
I'Anson, K.4
Gibson, G.R.5
-
15
-
-
32844461981
-
Effect of isomalt consumption on faecal microflora and colonic metabolism in healthy volunteers
-
Gostner, A.; Blaut, M.; Schaffer, V.; Kozianowski, G.; Theis, S.; Klingeberg, M.; Dombrowski, Y.; Martin, D.; Ehrhardt, S.; Taras, D.; et al. Effect of isomalt consumption on faecal microflora and colonic metabolism in healthy volunteers. Br. J. Nutr. 2006, 95, 40-50.
-
(2006)
Br. J. Nutr
, vol.95
, pp. 40-50
-
-
Gostner, A.1
Blaut, M.2
Schaffer, V.3
Kozianowski, G.4
Theis, S.5
Klingeberg, M.6
Dombrowski, Y.7
Martin, D.8
Ehrhardt, S.9
Taras, D.10
-
16
-
-
34548394098
-
Effects of low doses of lactitol on faecal microflora, pH, short chain fatty acids and gastrointestinal symptomology
-
Finney, M.; Smullen, J.; Foster, H. A.; Brokx, S.; Storey, D. M. Effects of low doses of lactitol on faecal microflora, pH, short chain fatty acids and gastrointestinal symptomology. Eur. J. Nutr. 2007, 46, 307-314.
-
(2007)
Eur. J. Nutr
, vol.46
, pp. 307-314
-
-
Finney, M.1
Smullen, J.2
Foster, H.A.3
Brokx, S.4
Storey, D.M.5
-
17
-
-
0036197779
-
Oral administration of arabinogalactan affects immune status and fecal microbial populations in dogs
-
Grieshop, C. M.; Flickinger, E. A.; Fahey, G. C., Jr. Oral administration of arabinogalactan affects immune status and fecal microbial populations in dogs. J. Nutr. 2002, 132, 478-482.
-
(2002)
J. Nutr
, vol.132
, pp. 478-482
-
-
Grieshop, C.M.1
Flickinger, E.A.2
Fahey, G.C.3
-
18
-
-
33747343668
-
Review article: Prebiotics in the gastrointestinal tract
-
Macfarlane, S.; Macfarlane, G. T.; Cummings, J. H. Review article: Prebiotics in the gastrointestinal tract. Aliment. Pharmacol. Ther. 2006, 24, 701-714.
-
(2006)
Aliment. Pharmacol. Ther
, vol.24
, pp. 701-714
-
-
Macfarlane, S.1
Macfarlane, G.T.2
Cummings, J.H.3
-
19
-
-
80755152887
-
Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice
-
Everard, A.; Lazarevic, V.; Derrien, M.; Girard, M.; Muccioli, G. G.; Neyrinck, A. M.; Possemiers, S.; Van Holle, A.; Francois, P.; de Vos, W. M.; et al. Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes 2011, 60, 2775-2786.
-
(2011)
Diabetes
, vol.60
, pp. 2775-2786
-
-
Everard, A.1
Lazarevic, V.2
Derrien, M.3
Girard, M.4
Muccioli, G.G.5
Neyrinck, A.M.6
Possemiers, S.7
Van Holle, A.8
Francois, P.9
de Vos, W.M.10
-
20
-
-
33845901507
-
Microbial ecology: Human gut microbes associated with obesity
-
Ley, R. E.; Turnbaugh, P. J.; Klein, S.; Gordon, J. I. Microbial ecology: Human gut microbes associated with obesity. Nature 2006, 444, 1022-1023.
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
Gordon, J.I.4
-
21
-
-
56549122798
-
Human colonic microbiota associated with diet, obesity and weight loss
-
Duncan, S. H.; Lobley, G. E.; Holtrop, G.; Ince, J.; Johnstone, A. M.; Louis, P.; Flint, H. J. Human colonic microbiota associated with diet, obesity and weight loss. Int. J. Obes. (Lond.) 2008, 32, 1720-1724.
-
(2008)
Int. J. Obes. (Lond.)
, vol.32
, pp. 1720-1724
-
-
Duncan, S.H.1
Lobley, G.E.2
Holtrop, G.3
Ince, J.4
Johnstone, A.M.5
Louis, P.6
Flint, H.J.7
-
22
-
-
33947136322
-
Prebiotics: The concept revisited
-
Roberfroid, M. Prebiotics: The concept revisited. J. Nutr. 2007, 137, 830S-837S.
-
(2007)
J. Nutr
, vol.137
, pp. 830S-837S
-
-
Roberfroid, M.1
-
23
-
-
0016337140
-
Nutritional features of the intestinal anaerobe Ruminococcus bromii
-
Herbeck, J. L.; Bryant, M. P. Nutritional features of the intestinal anaerobe Ruminococcus bromii. Appl. Microbiol. 1974, 28, 1018-1022.
-
(1974)
Appl. Microbiol
, vol.28
, pp. 1018-1022
-
-
Herbeck, J.L.1
Bryant, M.P.2
-
24
-
-
79959855078
-
Predicting a human gut microbiota's response to diet in gnotobiotic mice
-
Faith, J. J.; McNulty, N. P.; Rey, F. E.; Gordon, J. I. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 2011, 333, 101-104.
-
(2011)
Science
, vol.333
, pp. 101-104
-
-
Faith, J.J.1
McNulty, N.P.2
Rey, F.E.3
Gordon, J.I.4
-
25
-
-
0025855242
-
The control and consequences of bacterial fermentation in the human colon
-
Cummings, J. H.; Macfarlane, G. T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 1991, 70, 443-459.
-
(1991)
J. Appl. Bacteriol
, vol.70
, pp. 443-459
-
-
Cummings, J.H.1
Macfarlane, G.T.2
-
26
-
-
0022544586
-
Protein degradation by human intestinal bacteria
-
Macfarlane, G. T.; Cummings, J. H.; Allison, C. Protein degradation by human intestinal bacteria. J. Gen. Microbiol. 1986, 132, 1647-1656.
-
(1986)
J. Gen. Microbiol
, vol.132
, pp. 1647-1656
-
-
Macfarlane, G.T.1
Cummings, J.H.2
Allison, C.3
-
27
-
-
10744220291
-
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533
-
Pridmore, R. D.; Berger, B.; Desiere, F.; Vilanova, D.; Barretto, C.; Pittet, A. C.; Zwahlen, M. C.; Rouvet, M.; Altermann, E.; Barrangou, R.; et al. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc. Natl. Acad. Sci. USA 2004, 101, 2512-2517.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 2512-2517
-
-
Pridmore, R.D.1
Berger, B.2
Desiere, F.3
Vilanova, D.4
Barretto, C.5
Pittet, A.C.6
Zwahlen, M.C.7
Rouvet, M.8
Altermann, E.9
Barrangou, R.10
-
28
-
-
73649168807
-
Some nutritional characteristics of predominant culturable ruminal bacteria
-
Bryant, M. P.; Robinson, I. M. Some nutritional characteristics of predominant culturable ruminal bacteria. J. Bacteriol. 1962, 84, 605-614.
-
(1962)
J. Bacteriol
, vol.84
, pp. 605-614
-
-
Bryant, M.P.1
Robinson, I.M.2
-
29
-
-
0014541465
-
Pectin-fermenting bacteria isolated from the bovine rumen
-
Dehority, B. A. Pectin-fermenting bacteria isolated from the bovine rumen. J. Bacteriol. 1969, 99, 189-196.
-
(1969)
J. Bacteriol
, vol.99
, pp. 189-196
-
-
Dehority, B.A.1
-
30
-
-
0022405071
-
Nitrogen utilization in bacterial isolates from the equine cecum
-
Maczulak, A. E.; Dawson, K. A.; Baker, J. P. Nitrogen utilization in bacterial isolates from the equine cecum. Appl. Environ. Microbiol. 1985, 50, 1439-1443.
-
(1985)
Appl. Environ. Microbiol
, vol.50
, pp. 1439-1443
-
-
Maczulak, A.E.1
Dawson, K.A.2
Baker, J.P.3
-
31
-
-
0018338356
-
The biology of gastrointestinal Bacteroides
-
Macy, J. M.; Probst, I. The biology of gastrointestinal Bacteroides. Annu. Rev. Microbiol. 1979, 33, 561-594.
-
(1979)
Annu. Rev. Microbiol
, vol.33
, pp. 561-594
-
-
Macy, J.M.1
Probst, I.2
-
32
-
-
0026586542
-
Comparison of fermentation reactions in different regions of the human colon
-
Macfarlane, G. T.; Gibson, G. R.; Cummings, J. H. Comparison of fermentation reactions in different regions of the human colon. J. Appl. Bacteriol. 1992, 72, 57-64.
-
(1992)
J. Appl. Bacteriol
, vol.72
, pp. 57-64
-
-
Macfarlane, G.T.1
Gibson, G.R.2
Cummings, J.H.3
-
33
-
-
63849241608
-
Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine
-
Louis, P.; Flint, H. J. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 2009, 294, 1-8.
-
(2009)
FEMS Microbiol. Lett
, vol.294
, pp. 1-8
-
-
Louis, P.1
Flint, H.J.2
-
34
-
-
0029883793
-
Resistant starch lowers fecal concentrations of ammonia and phenols in humans
-
Birkett, A.; Muir, J.; Phillips, J.; Jones, G.; O'Dea, K. Resistant starch lowers fecal concentrations of ammonia and phenols in humans. Am. J. Clin. Nutr. 1996, 63, 766-772.
-
(1996)
Am. J. Clin. Nutr
, vol.63
, pp. 766-772
-
-
Birkett, A.1
Muir, J.2
Phillips, J.3
Jones, G.4
O'Dea, K.5
-
35
-
-
0029758538
-
The NAD(P)H-dependent glutamate dehydrogenase activities of Prevotella ruminicola b(1)4 can be attributed to one enzyme (GDHA), and gdhA expression is regulated in response to the nitrogen source available for growth
-
Wen, Z.; Morrison, M. The NAD(P)H-dependent glutamate dehydrogenase activities of Prevotella ruminicola b(1)4 can be attributed to one enzyme (GDHA), and gdhA expression is regulated in response to the nitrogen source available for growth. Appl. Environ. Microbiol. 1996, 62, 3826-3833.
-
(1996)
Appl. Environ. Microbiol
, vol.62
, pp. 3826-3833
-
-
Wen, Z.1
Morrison, M.2
-
36
-
-
0027487229
-
Ain-93 purified diets for laboratory rodents: Final report of the american institute of nutrition ad hoc writing committee on the reformulation of the AIN-76A rodent diet
-
Reeves, P. G.; Nielsen, F. H.; Fahey, G. C., Jr. Ain-93 purified diets for laboratory rodents: Final report of the american institute of nutrition ad hoc writing committee on the reformulation of the AIN-76A rodent diet. J. Nutr. 1993, 123, 1939-1951.
-
(1993)
J. Nutr
, vol.123
, pp. 1939-1951
-
-
Reeves, P.G.1
Nielsen, F.H.2
Fahey, G.C.3
-
37
-
-
0023472497
-
Fecal short-chain fatty acid (SCFA) analysis by capillary gas-liquid chromatography
-
Scheppach, W. M.; Fabian, C. E.; Kasper, H. W. Fecal short-chain fatty acid (SCFA) analysis by capillary gas-liquid chromatography. Am. J. Clin. Nutr. 1987, 46, 641-646.
-
(1987)
Am. J. Clin. Nutr
, vol.46
, pp. 641-646
-
-
Scheppach, W.M.1
Fabian, C.E.2
Kasper, H.W.3
-
38
-
-
74549125386
-
Seaview version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building
-
Gouy, M.; Guindon, S.; Gascuel, O. Seaview version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010, 27, 221-224.
-
(2010)
Mol. Biol. Evol
, vol.27
, pp. 221-224
-
-
Gouy, M.1
Guindon, S.2
Gascuel, O.3
-
39
-
-
67249096511
-
Esprit: Estimating species richness using large collections of 16s rna pyrosequences
-
Sun, Y.; Cai, Y.; Liu, L.; Yu, F.; Farrell, M. L.; McKendree, W.; Farmerie, W. Esprit: Estimating species richness using large collections of 16s rna pyrosequences. Nucleic Acids Res. 2009, 37, e76.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sun, Y.1
Cai, Y.2
Liu, L.3
Yu, F.4
Farrell, M.L.5
McKendree, W.6
Farmerie, W.7
-
40
-
-
84891813947
-
The silva and "all-species living tree project (ltp)" taxonomic frameworks
-
Yilmaz, P.; Parfrey, L. W.; Yarza, P.; Gerken, J.; Pruesse, E.; Quast, C.; Schweer, T.; Peplies, J.; Ludwig, W.; Glockner, F. O. The silva and "all-species living tree project (ltp)" taxonomic frameworks. Nucleic Acids Res. 2014, 42, D643-D648.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D643-D648
-
-
Yilmaz, P.1
Parfrey, L.W.2
Yarza, P.3
Gerken, J.4
Pruesse, E.5
Quast, C.6
Schweer, T.7
Peplies, J.8
Ludwig, W.9
Glockner, F.O.10
-
41
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D.; Westcott, S. L.; Ryabin, T.; Hall, J. R.; Hartmann, M.; Hollister, E. B.; Lesniewski, R. A.; Oakley, B. B.; Parks, D. H.; Robinson, C. J.; et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75, 7537-7541.
-
(2009)
Appl. Environ. Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
-
42
-
-
0037251969
-
The ribosomal database project (rdp-ii): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
-
Cole, J. R.; Chai, B.; Marsh, T. L.; Farris, R. J.; Wang, Q.; Kulam, S. A.; Chandra, S.; McGarrell, D. M.; Schmidt, T. M.; Garrity, G. M.; et al. The ribosomal database project (rdp-ii): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 2003, 31, 442-443.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 442-443
-
-
Cole, J.R.1
Chai, B.2
Marsh, T.L.3
Farris, R.J.4
Wang, Q.5
Kulam, S.A.6
Chandra, S.7
McGarrell, D.M.8
Schmidt, T.M.9
Garrity, G.M.10
-
43
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 1990, 215, 403-410.
-
(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
-
44
-
-
80052549504
-
Integrative analysis of environmental sequences using MEGAN4
-
Huson, D. H.; Mitra, S.; Ruscheweyh, H. J.; Weber, N.; Schuster, S. C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011, 21, 1552-1560.
-
(2011)
Genome Res
, vol.21
, pp. 1552-1560
-
-
Huson, D.H.1
Mitra, S.2
Ruscheweyh, H.J.3
Weber, N.4
Schuster, S.C.5
-
45
-
-
25644458211
-
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
-
Overbeek, R.; Begley, T.; Butler, R. M.; Choudhuri, J. V.; Chuang, H. Y.; de Cohoon, M.; Crécy-Lagard, V.; Diaz, N.; Disz, T.; Edwards, R.; et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005, 33, 5691-5702.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5691-5702
-
-
Overbeek, R.1
Begley, T.2
Butler, R.M.3
Choudhuri, J.V.4
Chuang, H.Y.5
de Cohoon, M.6
Crécy-Lagard, V.7
Diaz, N.8
Disz, T.9
Edwards, R.10
-
46
-
-
84888808639
-
-
Victorian Bioinformatics Consortium: Melbourne, Australia
-
Glasman, S.; Seeman, T. Velvetoptimiser, v2. 2. 5; Victorian Bioinformatics Consortium: Melbourne, Australia, 2012.
-
(2012)
Velvetoptimiser, v2.2. 5
-
-
Glasman, S.1
Seeman, T.2
-
47
-
-
84891763855
-
The carbohydrate-active enzymes database (CAZY) in 2013
-
Lombard, V.; Golaconda Ramulu, H.; Drula, E.; Coutinho, P. M.; Henrissat, B. The carbohydrate-active enzymes database (CAZY) in 2013. Nucleic Acids Res. 2014, 42, D490-D495.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D490-D495
-
-
Lombard, V.1
Golaconda Ramulu, H.2
Drula, E.3
Coutinho, P.M.4
Henrissat, B.5
-
49
-
-
60749116898
-
Bray-curtis ordination: An effective strategy for analysis of multivariate ecological data
-
Beals, E. W. Bray-curtis ordination: An effective strategy for analysis of multivariate ecological data. Adv. Ecol. Res. 1984, 14, 1-55.
-
(1984)
Adv. Ecol. Res
, vol.14
, pp. 1-55
-
-
Beals, E.W.1
-
50
-
-
33644606606
-
Fastgroupii: A web-based bioinformatics platform for analyses of large 16s rdna libraries
-
Yu, Y.; Breitbart, M.; McNairnie, P.; Rohwer, F. Fastgroupii: A web-based bioinformatics platform for analyses of large 16s rdna libraries. BMC Bioinform. 2006, 7, 57.
-
(2006)
BMC Bioinform
, vol.7
-
-
Yu, Y.1
Breitbart, M.2
McNairnie, P.3
Rohwer, F.4
-
52
-
-
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. The metagenomics rast server-A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 2008, 9, 386.
-
(2008)
BMC Bioinform
, vol.9
-
-
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
-
53
-
-
84874087906
-
Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds
-
Xu, B.; Xu, W.; Yang, F.; Li, J.; Yang, Y.; Tang, X.; Mu, Y.; Zhou, J.; Huang, Z. Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds. PLoS ONE 2013, 8, e56565.
-
(2013)
PLoS ONE
, vol.8
-
-
Xu, B.1
Xu, W.2
Yang, F.3
Li, J.4
Yang, Y.5
Tang, X.6
Mu, Y.7
Zhou, J.8
Huang, Z.9
-
54
-
-
79955794476
-
Comparative fecal metagenomics unveils unique functional capacity of the swine gut
-
Lamendella, R.; Domingo, J. W.; Ghosh, S.; Martinson, J.; Oerther, D. B. Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol. 2011, 11, 103.
-
(2011)
BMC Microbiol
, vol.11
-
-
Lamendella, R.1
Domingo, J.W.2
Ghosh, S.3
Martinson, J.4
Oerther, D.B.5
-
55
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K.; Itoh, T.; Kuwahara, T.; Oshima, K.; Toh, H.; Toyoda, A.; Takami, H.; Morita, H.; Sharma, V. K.; Srivastava, T. P.; et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007, 14, 169-181.
-
(2007)
DNA Res
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
Itoh, T.2
Kuwahara, T.3
Oshima, K.4
Toh, H.5
Toyoda, A.6
Takami, H.7
Morita, H.8
Sharma, V.K.9
Srivastava, T.P.10
-
56
-
-
0034175728
-
Biochemical and genetic characterization of the flagellar filaments from the rumen anaerobe Butyrivibrio fibrisolvens OR77
-
Kalmokoff, M.; Allard, S.; Austin, J.; Whitford, M.; Hefford, M.; Teather, R. Biochemical and genetic characterization of the flagellar filaments from the rumen anaerobe Butyrivibrio fibrisolvens OR77. Anaerobe 2000, 6, 93-109.
-
(2000)
Anaerobe
, vol.6
, pp. 93-109
-
-
Kalmokoff, M.1
Allard, S.2
Austin, J.3
Whitford, M.4
Hefford, M.5
Teather, R.6
-
57
-
-
0024023148
-
Cloning, nucleotide sequence, and taxonomic implications of the flagellin gene of Roseburia cecicola
-
Martin, J. H.; Savage, D. C. Cloning, nucleotide sequence, and taxonomic implications of the flagellin gene of Roseburia cecicola. J. Bacteriol. 1988, 170, 2612-2617.
-
(1988)
J. Bacteriol
, vol.170
, pp. 2612-2617
-
-
Martin, J.H.1
Savage, D.C.2
-
58
-
-
84978342799
-
Dietary fibre: Properties and sources
-
Academic Press: New York, NY, USA
-
Mongeau, R.; Brooks, S. P. J. Dietary fibre: Properties and sources. In Encyclopaedia of Food Sciences and Nutrition; Academic Press: New York, NY, USA, 2003; pp. 1813-1823.
-
(2003)
Encyclopaedia of Food Sciences and Nutrition
, pp. 1813-1823
-
-
Mongeau, R.1
Brooks, S.P.J.2
-
59
-
-
0024486198
-
Relationship between dietary fiber levels and protein digestibility in selected foods as determined in rats
-
Mongeau, R.; Sarwar, G.; Peace, R. W.; Brassard, R. Relationship between dietary fiber levels and protein digestibility in selected foods as determined in rats. Plant Foods Hum. Nutr. 1989, 39, 45-51.
-
(1989)
Plant Foods Hum. Nutr
, vol.39
, pp. 45-51
-
-
Mongeau, R.1
Sarwar, G.2
Peace, R.W.3
Brassard, R.4
-
60
-
-
84856706646
-
Molecular methods to measure intestinal bacteria: A review
-
Inglis, G. D.; Thomas, M. C.; Thomas, D. K.; Kalmokoff, M. L.; Brooks, S. P.; Selinger, L. B. Molecular methods to measure intestinal bacteria: A review. J. AOAC Int. 2012, 95, 5-23.
-
(2012)
J. AOAC Int
, vol.95
, pp. 5-23
-
-
Inglis, G.D.1
Thomas, M.C.2
Thomas, D.K.3
Kalmokoff, M.L.4
Brooks, S.P.5
Selinger, L.B.6
-
61
-
-
84941140948
-
RNAdb: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
-
Stoddard, S. F.; Smith, B. J.; Hein, R.; Roller, B. R.; Schmidt, T. M. RNAdb: Improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. Nucleic Acids Res. 2015, 43, D593-D598.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D593-D598
-
-
Stoddard, S.F.1
Smith, B.J.2
Hein, R.3
Roller, B.R.4
Schmidt, T.M.5
-
62
-
-
0036271968
-
Extensive profiling of a complex microbial community by high-throughput sequencing
-
Hill, J. E.; Seipp, R. P.; Betts, M.; Hawkins, L.; Van Kessel, A. G.; Crosby, W. L.; Hemmingsen, S. M. Extensive profiling of a complex microbial community by high-throughput sequencing. Appl. Environ. Microbiol. 2002, 68, 3055-3066.
-
(2002)
Appl. Environ. Microbiol
, vol.68
, pp. 3055-3066
-
-
Hill, J.E.1
Seipp, R.P.2
Betts, M.3
Hawkins, L.4
Van Kessel, A.G.5
Crosby, W.L.6
Hemmingsen, S.M.7
-
63
-
-
84884363710
-
Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges
-
Shah, V.; Zakrzewski, M.; Wibberg, D.; Eikmeyer, F.; Schluter, A.; Madamwar, D. Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. Microb. Ecol. 2013, 66, 533-550.
-
(2013)
Microb. Ecol
, vol.66
, pp. 533-550
-
-
Shah, V.1
Zakrzewski, M.2
Wibberg, D.3
Eikmeyer, F.4
Schluter, A.5
Madamwar, D.6
-
64
-
-
84879603340
-
Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation
-
Hanreich, A.; Schimpf, U.; Zakrzewski, M.; Schluter, A.; Benndorf, D.; Heyer, R.; Rapp, E.; Puhler, A.; Reichl, U.; Klocke, M. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst. Appl. Microbiol. 2013, 36, 330-338.
-
(2013)
Syst. Appl. Microbiol
, vol.36
, pp. 330-338
-
-
Hanreich, A.1
Schimpf, U.2
Zakrzewski, M.3
Schluter, A.4
Benndorf, D.5
Heyer, R.6
Rapp, E.7
Puhler, A.8
Reichl, U.9
Klocke, M.10
-
65
-
-
22144439446
-
pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon
-
Walker, A. W.; Duncan, S. H.; Leitch, E. C. M.; Child, M. W.; Flint, H. J. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl. Environ. Microbiol. 2005, 71, 3692-3700.
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 3692-3700
-
-
Walker, A.W.1
Duncan, S.H.2
Leitch, E.C.M.3
Child, M.W.4
Flint, H.J.5
-
66
-
-
0018552812
-
Effect of dietary nitrogen on the rumen microbial population in lactating dairy cattle
-
Teather, R. M.; Erfle, J. D.; Boila, R. J.; Sauer, F. D. Effect of dietary nitrogen on the rumen microbial population in lactating dairy cattle. J. Appl. Bacteriol. 1980, 49, 231-238.
-
(1980)
J. Appl. Bacteriol
, vol.49
, pp. 231-238
-
-
Teather, R.M.1
Erfle, J.D.2
Boila, R.J.3
Sauer, F.D.4
-
67
-
-
0001793212
-
Utilization of nitrogen sources by gastrointestinal tract bacteria
-
Hentges, D.J., Ed.; Academic Press: New York, NY, USA
-
Hespell, R.; Smith, C. Utilization of nitrogen sources by gastrointestinal tract bacteria. In Human Intestinal Microflora in Health and Disease; Hentges, D. J., Ed.; Academic Press: New York, NY, USA, 1983; pp. 167-187.
-
(1983)
Human Intestinal Microflora in Health and Disease
, pp. 167-187
-
-
Hespell, R.1
Smith, C.2
-
68
-
-
0001694518
-
Peptides and other nitrogen sources for growth of Bacteroides ruminicola
-
Pittman, K. A.; Bryant, M. P. Peptides and other nitrogen sources for growth of Bacteroides ruminicola. J. Bacteriol. 1964, 88, 401-410.
-
(1964)
J. Bacteriol
, vol.88
, pp. 401-410
-
-
Pittman, K.A.1
Bryant, M.P.2
-
69
-
-
0016167941
-
Human fecal flora: The normal flora of 20 japanese-hawaiians
-
Moore, W. E.; Holdeman, L. V. Human fecal flora: The normal flora of 20 japanese-hawaiians. Appl. Microbiol. 1974, 27, 961-979.
-
(1974)
Appl. Microbiol
, vol.27
, pp. 961-979
-
-
Moore, W.E.1
Holdeman, L.V.2
-
70
-
-
69949111703
-
The core gut microbiome, energy balance and obesity
-
Turnbaugh, P. J.; Gordon, J. I. The core gut microbiome, energy balance and obesity. J. Physiol. 2009, 587, 4153-4158.
-
(2009)
J. Physiol
, vol.587
, pp. 4153-4158
-
-
Turnbaugh, P.J.1
Gordon, J.I.2
-
71
-
-
77649119543
-
Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA: Acetate CoA-transferase gene
-
Louis, P.; Young, P.; Holtrop, G.; Flint, H. J. Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA: Acetate CoA-transferase gene. Environ. Microbiol. 2010, 12, 304-314.
-
(2010)
Environ. Microbiol
, vol.12
, pp. 304-314
-
-
Louis, P.1
Young, P.2
Holtrop, G.3
Flint, H.J.4
-
72
-
-
85047689124
-
Bacteria, colonic fermentation, and gastrointestinal health
-
Macfarlane, G. T.; Macfarlane, S. Bacteria, colonic fermentation, and gastrointestinal health. J. AOAC Int. 2012, 95, 50-60.
-
(2012)
J. AOAC Int
, vol.95
, pp. 50-60
-
-
Macfarlane, G.T.1
Macfarlane, S.2
-
73
-
-
80054862011
-
Bile acid is a host factor that regulates the composition of the cecal microbiota in rats
-
Islam, K. B.; Fukiya, S.; Hagio, M.; Fujii, N.; Ishizuka, S.; Ooka, T.; Ogura, Y.; Hayashi, T.; Yokota, A. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 2011, 141, 1773-1781.
-
(2011)
Gastroenterology
, vol.141
, pp. 1773-1781
-
-
Islam, K.B.1
Fukiya, S.2
Hagio, M.3
Fujii, N.4
Ishizuka, S.5
Ooka, T.6
Ogura, Y.7
Hayashi, T.8
Yokota, A.9
-
74
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh, P. J.; Ley, R. E.; Mahowald, M. A.; Magrini, V.; Mardis, E. R.; Gordon, J. I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444, 1027-1031.
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
75
-
-
77955595990
-
Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation
-
De La Serre, C. B.; Ellis, C. L.; Lee, J.; Hartman, A. L.; Rutledge, J. C.; Raybould, H. E. Propensity to high-fat diet-induced obesity in rats is associated with changes in the gut microbiota and gut inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 2010, 299, G440-G448.
-
(2010)
Am. J. Physiol. Gastrointest. Liver Physiol
, vol.299
, pp. G440-G448
-
-
De La Serre, C.B.1
Ellis, C.L.2
Lee, J.3
Hartman, A.L.4
Rutledge, J.C.5
Raybould, H.E.6
|