-
1
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium, "Structure, function and diversity of the healthy human microbiome, " Nature, vol. 486, no. 7402, pp. 207-214, 2012.
-
(2012)
Nature
, vol.486
, Issue.7402
, pp. 207-214
-
-
-
2
-
-
84866146940
-
Diversity, stability and resilience of the human gut microbiota
-
C. A. Lozupone, J. I. Stombaugh, J. I. Gordon, J. K. Jansson, and R. Knight, "Diversity, stability and resilience of the human gut microbiota, " Nature, vol. 489, no. 7415, pp. 220-230, 2012.
-
(2012)
Nature
, vol.489
, Issue.7415
, pp. 220-230
-
-
Lozupone, C.A.1
Stombaugh, J.I.2
Gordon, J.I.3
Jansson, J.K.4
Knight, R.5
-
3
-
-
8144226856
-
The gut microbiota as an environmental factor that regulates fat storage
-
F. Bäckhed, H. Ding, T. Wang et al., "The gut microbiota as an environmental factor that regulates fat storage, " Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 44, pp. 15718-15723, 2004.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.44
, pp. 15718-15723
-
-
Bäckhed, F.1
Ding, H.2
Wang, T.3
-
4
-
-
84858376593
-
The impact of the gut microbiota on human health: An integrative view
-
J. C. Clemente, L. K. Ursell, L. W. Parfrey, and R. Knight, "The impact of the gut microbiota on human health: An integrative view, " Cell, vol. 148, no. 6, pp. 1258-1270, 2012.
-
(2012)
Cell
, vol.148
, Issue.6
, pp. 1258-1270
-
-
Clemente, J.C.1
Ursell, L.K.2
Parfrey, L.W.3
Knight, R.4
-
5
-
-
79551683580
-
Modulation of immune homeostasis by commensal bacteria
-
I. I. Ivanov and D. R. Littman, "Modulation of immune homeostasis by commensal bacteria, " CurrentOpinion inMicrobiology, vol. 14, no. 1, pp. 106-114, 2011.
-
(2011)
CurrentOpinion InMicrobiology
, vol.14
, Issue.1
, pp. 106-114
-
-
Ivanov, I.I.1
Littman, D.R.2
-
6
-
-
23344442120
-
Obesity alters gut microbial ecology
-
R. E. Ley, F. Bäckhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight, and J. I. Gordon, "Obesity alters gut microbial ecology, " Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 31, pp. 11070-11075, 2005.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.31
, pp. 11070-11075
-
-
Ley, R.E.1
Bäckhed, F.2
Turnbaugh, P.3
Lozupone, C.A.4
Knight, R.D.5
Gordon, J.I.6
-
7
-
-
84861978076
-
Host-gut microbiota metabolic interactions
-
J. K. Nicholson, E. Holmes, J. Kinross et al., "Host-gut microbiota metabolic interactions, " Science, vol. 336, no. 6086, pp. 1262-1267, 2012.
-
(2012)
Science
, vol.336
, Issue.6086
, pp. 1262-1267
-
-
Nicholson, J.K.1
Holmes, E.2
Kinross, J.3
-
8
-
-
84860216630
-
Microbial exposure during early life has persistent effects on natural killer T cell function
-
T. Olszak, D. An, S. Zeissig et al., "Microbial exposure during early life has persistent effects on natural killer T cell function, " Science, vol. 336, no. 6080, pp. 489-493, 2012.
-
(2012)
Science
, vol.336
, Issue.6080
, pp. 489-493
-
-
Olszak, T.1
An, D.2
Zeissig, S.3
-
9
-
-
0029013322
-
Dietary modulation of the human colonic microbiota: Introducing the concept of prebiotics
-
G. R. Gibson and M. B. Roberfroid, "Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics, " Journal of Nutrition, vol. 125, no. 6, pp. 1401-1412, 1995.
-
(1995)
Journal of Nutrition
, vol.125
, Issue.6
, pp. 1401-1412
-
-
Gibson, G.R.1
Roberfroid, M.B.2
-
10
-
-
20744451860
-
Dietary fibres as prebiotics : Implications for colorectal cancer
-
C. C. Lim, L. R. Ferguson, and G. W. Tannock, "Dietary fibres as "prebiotics": implications for colorectal cancer, " Molecular Nutrition & Food Research, vol. 49, no. 6, pp. 609-619, 2005.
-
(2005)
Molecular Nutrition & Food Research
, vol.49
, Issue.6
, pp. 609-619
-
-
Lim, C.C.1
Ferguson, L.R.2
Tannock, G.W.3
-
11
-
-
17044414554
-
Prebiotics and other microbial substrates for gut functionality
-
A. C. Ouwehand, M. Derrien, W. de Vos, K. Tiihonen, and N. Rautonen, "Prebiotics and other microbial substrates for gut functionality, " Current Opinion in Biotechnology, vol. 16, no. 2, pp. 212-217, 2005.
-
(2005)
Current Opinion in Biotechnology
, vol.16
, Issue.2
, pp. 212-217
-
-
Ouwehand, A.C.1
Derrien, M.2
De Vos, W.3
Tiihonen, K.4
Rautonen, N.5
-
12
-
-
0019128183
-
Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man
-
W. E. Roediger, "Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man, " Gut, vol. 21, no. 9, pp. 793-798, 1980.
-
(1980)
Gut
, vol.21
, Issue.9
, pp. 793-798
-
-
Roediger, W.E.1
-
13
-
-
84880332709
-
Carbohydrates and the human gut microbiota
-
C. Chassard and C. Lacroix, "Carbohydrates and the human gut microbiota, " Current Opinion in Clinical Nutrition and Metabolic Care, vol. 16, no. 4, pp. 453-460, 2013.
-
(2013)
Current Opinion in Clinical Nutrition and Metabolic Care
, vol.16
, Issue.4
, pp. 453-460
-
-
Chassard, C.1
Lacroix, C.2
-
14
-
-
78149285318
-
Butyrate andother shortchain fatty acids as modulators of immunity: What relevance for health
-
K. Meijer, P. deVos, andM. G. Priebe, "Butyrate andother shortchain fatty acids as modulators of immunity: what relevance for health" Current Opinion in Clinical Nutrition andMetabolic Care, vol. 13, no. 6, pp. 715-721, 2010.
-
(2010)
Current Opinion in Clinical Nutrition AndMetabolic Care
, vol.13
, Issue.6
, pp. 715-721
-
-
Meijer, K.1
DeVos, P.2
Priebe, M.G.3
-
15
-
-
0034628432
-
Stableisotope probing as a tool inmicrobial ecology
-
S. Radajewski, P. Ineson, N. R. Parekh, and J. C. Murrell, "Stableisotope probing as a tool inmicrobial ecology, " Nature, vol. 403, no. 6770, pp. 646-649, 2000.
-
(2000)
Nature
, vol.403
, Issue.6770
, pp. 646-649
-
-
Radajewski, S.1
Ineson, P.2
Parekh, N.R.3
Murrell, J.C.4
-
16
-
-
0032560228
-
Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers
-
H. T. S. Boschker, S. C. Nold, P. Wellsbury et al., "Direct linking of microbial populations to specific biogeochemical processes by 13C-labelling of biomarkers, " Nature, vol. 392, no. 6678, pp. 801-805, 1998.
-
(1998)
Nature
, vol.392
, Issue.6678
, pp. 801-805
-
-
Boschker, H.T.S.1
Nold, S.C.2
Wellsbury, P.3
-
17
-
-
19144372182
-
Stable isotope probing-linking microbial identity to function
-
M. G. Dumont and J. C. Murrell, "Stable isotope probing-linking microbial identity to function, " Nature Reviews Microbiology, vol. 3, no. 6, pp. 499-504, 2005.
-
(2005)
Nature Reviews Microbiology
, vol.3
, Issue.6
, pp. 499-504
-
-
Dumont, M.G.1
Murrell, J.C.2
-
18
-
-
31944450239
-
Beyond diversity: Functional microbiomics of the human colon
-
M. Egert, A. A. De Graaf, H. Smidt, W. M. De Vos, and K. Venema, "Beyond diversity: functional microbiomics of the human colon, " Trends in Microbiology, vol. 14, no. 2, pp. 86-91, 2006.
-
(2006)
Trends in Microbiology
, vol.14
, Issue.2
, pp. 86-91
-
-
Egert, M.1
De Graaf, A.A.2
Smidt, H.3
De Vos, W.M.4
Venema, K.5
-
19
-
-
34249948237
-
Who eats what, where and when Isotope-labelling experiments are coming of age
-
J. D. Neufeld, M. Wagner, and J. C. Murrell, "Who eats what, where and when Isotope-labelling experiments are coming of age, " ISME Journal, vol. 1, no. 2, pp. 103-110, 2007.
-
(2007)
ISME Journal
, vol.1
, Issue.2
, pp. 103-110
-
-
Neufeld, J.D.1
Wagner, M.2
Murrell, J.C.3
-
20
-
-
0036452120
-
Technical considerations for RNA-based stable isotope probing: An approach to associating microbial diversity with microbial community function
-
M. Manefield, A. S. Whiteley, N. Ostle, P. Ineson, and M. J. Bailey, "Technical considerations for RNA-based stable isotope probing: An approach to associating microbial diversity with microbial community function, " Rapid Communications in Mass Spectrometry, vol. 16, no. 23, pp. 2179-2183, 2002.
-
(2002)
Rapid Communications in Mass Spectrometry
, vol.16
, Issue.23
, pp. 2179-2183
-
-
Manefield, M.1
Whiteley, A.S.2
Ostle, N.3
Ineson, P.4
Bailey, M.J.5
-
21
-
-
0842266326
-
Enhanced sensitivity of DNA-and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients
-
T. Lueders, M. Manefield, and M. W. Friedrich, "Enhanced sensitivity of DNA-and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients, " EnvironmentalMicrobiology, vol. 6, no. 1, pp. 73-78, 2004.
-
(2004)
EnvironmentalMicrobiology
, vol.6
, Issue.1
, pp. 73-78
-
-
Lueders, T.1
Manefield, M.2
Friedrich, M.W.3
-
22
-
-
34248529798
-
RNA stable-isotope probing
-
A. S. Whiteley, B. Thomson, T. Lueders, and M. Manefield, "RNA stable-isotope probing, " Nature Protocols, vol. 2, no. 4, pp. 838-844, 2007.
-
(2007)
Nature Protocols
, vol.2
, Issue.4
, pp. 838-844
-
-
Whiteley, A.S.1
Thomson, B.2
Lueders, T.3
Manefield, M.4
-
23
-
-
33947199799
-
Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing
-
M. Egert, A. A. De Graaf, A. Maathuis et al., "Identification of glucose-fermenting bacteria present in an in vitro model of the human intestine by RNA-stable isotope probing, " FEMS Microbiology Ecology, vol. 60, no. 1, pp. 126-135, 2007.
-
(2007)
FEMS Microbiology Ecology
, vol.60
, Issue.1
, pp. 126-135
-
-
Egert, M.1
De Graaf, A.A.2
Maathuis, A.3
-
24
-
-
63849262393
-
Linking phylogenetic identities of bacteria to starch fermentation in an in vitromodel of the large intestine by RNA-based stable isotope probing
-
P. Kovatcheva-Datchary, M. Egert, A. Maathuis et al., "Linking phylogenetic identities of bacteria to starch fermentation in an in vitromodel of the large intestine by RNA-based stable isotope probing, " Environmental Microbiology, vol. 11, no. 4, pp. 914-926, 2009.
-
(2009)
Environmental Microbiology
, vol.11
, Issue.4
, pp. 914-926
-
-
Kovatcheva-Datchary, P.1
Egert, M.2
Maathuis, A.3
-
25
-
-
84896038035
-
RNA-stableisotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel
-
G. W. Tannock, B. Lawley, K. Munro et al., "RNA-stableisotope probing shows utilization of carbon from inulin by specific bacterial populations in the rat large bowel, " Applied and Environmental Microbiology, vol. 80, no. 7, pp. 2240-2247, 2014.
-
(2014)
Applied and Environmental Microbiology
, vol.80
, Issue.7
, pp. 2240-2247
-
-
Tannock, G.W.1
Lawley, B.2
Munro, K.3
-
26
-
-
84927925180
-
Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing
-
W. Young, M. Egert, S. A. Bassett, and R. Bibiloni, "Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing, " Nutrients, vol. 7, no. 4, pp. 2109-2124, 2015.
-
(2015)
Nutrients
, vol.7
, Issue.4
, pp. 2109-2124
-
-
Young, W.1
Egert, M.2
Bassett, S.A.3
Bibiloni, R.4
-
27
-
-
35448978380
-
Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research
-
J.-P. Godin, L.-B. Fay, and G. Hopfgartner, "Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research, " Mass Spectrometry Reviews, vol. 26, no. 6, pp. 751-774, 2007.
-
(2007)
Mass Spectrometry Reviews
, vol.26
, Issue.6
, pp. 751-774
-
-
Godin, J.-P.1
Fay, L.-B.2
Hopfgartner, G.3
-
28
-
-
4644335583
-
A new concept for isotope ratio monitoring liquid chromatography/mass spectrometry
-
M. Krummen, A. W. Hilkert, D. Juchelka, A. Duhr, H.-J. Schlüter, and R. Pesch, "A new concept for isotope ratio monitoring liquid chromatography/mass spectrometry, " Rapid Communications inMass Spectrometry, vol. 18, no. 19, pp. 2260-2266, 2004.
-
(2004)
Rapid Communications InMass Spectrometry
, vol.18
, Issue.19
, pp. 2260-2266
-
-
Krummen, M.1
Hilkert, A.W.2
Juchelka, D.3
Duhr, A.4
Schlüter, H.-J.5
Pesch, R.6
-
29
-
-
80052049827
-
Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil
-
F. Liu and R. Conrad, "Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil, " ISME Journal, vol. 5, no. 9, pp. 1526-1539, 2011.
-
(2011)
ISME Journal
, vol.5
, Issue.9
, pp. 1526-1539
-
-
Liu, F.1
Conrad, R.2
-
30
-
-
0036470363
-
Stable carbon isotopes of lipid biomarkers: Analysis of metabolites and metabolic fates of environmental microorganisms
-
C. L. Zhang, "Stable carbon isotopes of lipid biomarkers: Analysis of metabolites and metabolic fates of environmental microorganisms, " Current Opinion in Biotechnology, vol. 13, no. 1, pp. 25-30, 2002.
-
(2002)
Current Opinion in Biotechnology
, vol.13
, Issue.1
, pp. 25-30
-
-
Zhang, C.L.1
-
31
-
-
17644421480
-
Quantification of methanogenic pathways using stable carbon isotopic signatures: A review and a proposal
-
R. Conrad, "Quantification of methanogenic pathways using stable carbon isotopic signatures: A review and a proposal, " Organic Geochemistry, vol. 36, no. 5, pp. 739-752, 2005.
-
(2005)
Organic Geochemistry
, vol.36
, Issue.5
, pp. 739-752
-
-
Conrad, R.1
-
32
-
-
84920404296
-
How informative is the mouse for human gut microbiota research
-
T. L. A. Nguyen, S. Vieira-Silva, A. Liston, and J. Raes, "How informative is the mouse for human gut microbiota research" DMM Disease Models and Mechanisms, vol. 8, no. 1, pp. 1-16, 2015.
-
(2015)
DMM Disease Models and Mechanisms
, vol.8
, Issue.1
, pp. 1-16
-
-
Nguyen, T.L.A.1
Vieira-Silva, S.2
Liston, A.3
Raes, J.4
-
33
-
-
84876237691
-
Exploring hostmicrobiota interactions in animal models and humans
-
A. D. Kostic, M. R. Howitt, andW. S. Garrett, "Exploring hostmicrobiota interactions in animal models and humans, " Genes &Development, vol. 27, no. 7, pp. 701-718, 2013.
-
(2013)
Genes &Development
, vol.27
, Issue.7
, pp. 701-718
-
-
Kostic, A.D.1
Howitt, M.R.2
Garrett, W.S.3
-
34
-
-
0008753508
-
Two sequential repressions ofDNA synthesis in the establishment of lysogeny by phage P22 and its mutants
-
H. O. Smith and M. Levine, "Two sequential repressions ofDNA synthesis in the establishment of lysogeny by phage P22 and its mutants, " Proceedings of the National Academy of Sciences of the United States of, vol. 52, pp. 356-363, 1964.
-
(1964)
Proceedings of the National Academy of Sciences of the United States of
, vol.52
, pp. 356-363
-
-
Smith, H.O.1
Levine, M.2
-
35
-
-
0024444791
-
Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA
-
U. Edwards, T. Rogall, H. Blöcker, M. Emde, and E. C. Böttger, "Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA, " Nucleic Acids Research, vol. 17, no. 19, pp. 7843-7853, 1989.
-
(1989)
Nucleic Acids Research
, vol.17
, Issue.19
, pp. 7843-7853
-
-
Edwards, U.1
Rogall, T.2
Blöcker, H.3
Emde, M.4
Böttger, E.C.5
-
36
-
-
0029097821
-
Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments
-
G. Muyzer, A. Teske, C. O. Wirsen, and H. W. Jannasch, "Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments, " Archives of Microbiology, vol. 164, no. 3, pp. 165-172, 1995.
-
(1995)
Archives of Microbiology
, vol.164
, Issue.3
, pp. 165-172
-
-
Muyzer, G.1
Teske, A.2
Wirsen, C.O.3
Jannasch, H.W.4
-
37
-
-
85015584068
-
Effect of rotor type on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation
-
E. Herrmann, P. Koch, C. U. Riedel, W. Young, and M. Egert, "Effect of rotor type on the separation of isotope-labeled and unlabeled Escherichia coli RNA by isopycnic density ultracentrifugation, " Canadian Journal ofMicrobiology, vol. 63, no. 1, pp. 83-87, 2017.
-
(2017)
Canadian Journal OfMicrobiology
, vol.63
, Issue.1
, pp. 83-87
-
-
Herrmann, E.1
Koch, P.2
Riedel, C.U.3
Young, W.4
Egert, M.5
-
38
-
-
84991239272
-
-
Illumina
-
Illumina, "16S Metagenomic Sequencing Library Preparation, " http://www. illumina. com/content/dam/illumina-support/documents/ documentation/chemistry documentation/16s/16s-metagenomic-library-prep-guide-15044223-b. pdf.
-
16S Metagenomic Sequencing Library Preparation
-
-
-
39
-
-
84871808499
-
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
-
A. Klindworth, E. Pruesse, T. Schweer et al., "Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies, " Nucleic Acids Research, vol. 41, no. 1, 2013.
-
(2013)
Nucleic Acids Research
, vol.41
, Issue.1
-
-
Klindworth, A.1
Pruesse, E.2
Schweer, T.3
-
40
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
J. G. Caporaso, J. Kuczynski, J. Stombaugh et al., "QIIME allows analysis of high-throughput community sequencing data, " Nature Methods, vol. 7, no. 5, pp. 335-336, 2010.
-
(2010)
Nature Methods
, vol.7
, Issue.5
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
41
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
R. C. Edgar, "Search and clustering orders of magnitude faster than BLAST, " Bioinformatics, vol. 26, no. 19, pp. 2460-2461, 2010.
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2460-2461
-
-
Edgar, R.C.1
-
42
-
-
13444304367
-
The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis
-
J. R. Cole, B. Chai, R. J. Farris et al., "The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis, " Nucleic Acids Research, vol. 33, pp. D294-D296, 2005.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. D294-D296
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
-
43
-
-
79961135005
-
-
R Development Core Team, The R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team, R: A Language and Environment for Statistical Computing, The R Foundation for Statistical Computing, Vienna, Austria, 2011, http://www. R-project. org/.
-
(2011)
R: A Language and Environment for Statistical Computing
-
-
-
44
-
-
34547227615
-
Characterization of methanogenic Archaea and stable isotope fractionation during methane production in the profundal sediment of an oligotrophic lake (Lake Stechlin, Germany)
-
R. Conrad, O.-C. Chan, P. Claus, and P. Casper, "Characterization of methanogenic Archaea and stable isotope fractionation during methane production in the profundal sediment of an oligotrophic lake (Lake Stechlin, Germany), " Limnology and Oceanography, vol. 52, no. 4, pp. 1393-1406, 2007.
-
(2007)
Limnology and Oceanography
, vol.52
, Issue.4
, pp. 1393-1406
-
-
Conrad, R.1
Chan, O.-C.2
Claus, P.3
Casper, P.4
-
45
-
-
0036840287
-
RNA stable isotope probing, a novel means of linking microbial community function to phylogeny
-
M. Manefield, A. S. Whiteley, R. I. Griffiths, and M. J. Bailey, "RNA stable isotope probing, a novel means of linking microbial community function to phylogeny, " Applied and EnvironmentalMicrobiology, vol. 68, no. 11, pp. 5367-5373, 2002.
-
(2002)
Applied and EnvironmentalMicrobiology
, vol.68
, Issue.11
, pp. 5367-5373
-
-
Manefield, M.1
Whiteley, A.S.2
Griffiths, R.I.3
Bailey, M.J.4
-
46
-
-
0025006088
-
Luminal glucose concentrations in the gut under normal conditions
-
R. P. Ferraris, S. Yasharpour, K. C. K. Lloyd, R. Mirzayan, and J. M. Diamond, "Luminal glucose concentrations in the gut under normal conditions, "American Journal of Physiology, vol. 259, no. 5, pp. G822-G837, 1990.
-
(1990)
American Journal of Physiology
, vol.259
, Issue.5
, pp. G822-G837
-
-
Ferraris, R.P.1
Yasharpour, S.2
Lloyd, K.C.K.3
Mirzayan, R.4
Diamond, J.M.5
-
47
-
-
67650021209
-
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
-
M. Hamady and R. Knight, "Microbial community profiling for human microbiome projects: Tools, techniques, and challenges, " Genome Research, vol. 19, no. 7, pp. 1141-1152, 2009.
-
(2009)
Genome Research
, vol.19
, Issue.7
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
48
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
C. Lozupone and R. Knight, "UniFrac: A new phylogenetic method for comparing microbial communities, " Applied and EnvironmentalMicrobiology, vol. 71, no. 12, pp. 8228-8235, 2005.
-
(2005)
Applied and EnvironmentalMicrobiology
, vol.71
, Issue.12
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
49
-
-
84885080349
-
Bacterial community mapping of the mouse gastrointestinal tract
-
S. Gu, D. Chen, J.-N. Zhang et al., "Bacterial community mapping of the mouse gastrointestinal tract, " PLoS ONE, vol. 8, no. 10, Article ID e74957, 2013.
-
(2013)
PLoS ONE
, vol.8
, Issue.10
-
-
Gu, S.1
Chen, D.2
Zhang, J.-N.3
-
50
-
-
85046981892
-
Maternal micronutrients can modify colonic mucosal microbiota maturation inmurine offspring
-
D. Nagy-Szakal, M. C. Ross, S. E. Dowd et al., "Maternal micronutrients can modify colonic mucosal microbiota maturation inmurine offspring, " GutMicrobes, vol. 3, no. 5, pp. 426-433, 2012.
-
(2012)
GutMicrobes
, vol.3
, Issue.5
, pp. 426-433
-
-
Nagy-Szakal, D.1
Ross, M.C.2
Dowd, S.E.3
-
51
-
-
84857164927
-
Effect of Lactobacillus salivarius bacteriocin ABP118 on the mouse and pig intestinal microbiota
-
E. Riboulet-Bisson, M. H. J. Sturme, I. B. Jeffery et al., "Effect of Lactobacillus salivarius bacteriocin ABP118 on the mouse and pig intestinal microbiota, " PLOS ONE, vol. 7, no. 2, Article ID e31113, 2012.
-
(2012)
PLOS ONE
, vol.7
, Issue.2
-
-
Riboulet-Bisson, E.1
Sturme, M.H.J.2
Jeffery, I.B.3
-
52
-
-
84874672692
-
Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization
-
C. Ubeda, V. Bucci, S. Caballero et al., "Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization, " Infection and Immunity, vol. 81, no. 3, pp. 965-973, 2013.
-
(2013)
Infection and Immunity
, vol.81
, Issue.3
, pp. 965-973
-
-
Ubeda, C.1
Bucci, V.2
Caballero, S.3
-
53
-
-
84865445024
-
Intestinal aganglionosis is associated with early and sustained disruption of the colonic microbiome
-
N. L. Ward, A. Pieretti, S. E. Dowd, S. B. Cox, and A. M. Goldstein, "Intestinal aganglionosis is associated with early and sustained disruption of the colonic microbiome, " Neurogastroenterology and Motility, vol. 24, no. 9, pp. 874-e400, 2012.
-
(2012)
Neurogastroenterology and Motility
, vol.24
, Issue.9
, pp. 874-8400
-
-
Ward, N.L.1
Pieretti, A.2
Dowd, S.E.3
Cox, S.B.4
Goldstein, A.M.5
-
54
-
-
84921626523
-
Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity
-
A. Everard, V. Lazarevic, N. Gaä et al., "Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity, " ISME Journal, vol. 8, no. 10, pp. 2116-2130, 2014.
-
(2014)
ISME Journal
, vol.8
, Issue.10
, pp. 2116-2130
-
-
Everard, A.1
Lazarevic, V.2
Gaä, N.3
-
55
-
-
77950669604
-
Theeffect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice
-
P. J. Turnbaugh, V. K. Ridaura, J. J. Faith, F. E. Rey, R. Knight, and J. I. Gordon, "Theeffect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice, " Science Translational Medicine, vol. 1, no. 6, p. 6ra14, 2009.
-
(2009)
Science Translational Medicine
, vol.1
, Issue.6
, pp. 6ra14
-
-
Turnbaugh, P.J.1
Ridaura, V.K.2
Faith, J.J.3
Rey, F.E.4
Knight, R.5
Gordon, J.I.6
-
56
-
-
4544291744
-
Allobaculum stercoricanis gen. Nov., sp. Nov., isolated from canine feces
-
H. L. Greetham, G. R. Gibson, C. Giffard et al., "Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces, " Anaerobe, vol. 10, no. 5, pp. 301-307, 2004.
-
(2004)
Anaerobe
, vol.10
, Issue.5
, pp. 301-307
-
-
Greetham, H.L.1
Gibson, G.R.2
Giffard, C.3
-
57
-
-
0028126829
-
Thephylogeny of the genus Clostridium: Proposal of five new genera and eleven new species combinations
-
M. D. Collins, P. A. Lawson, A. Willems et al., "Thephylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, " International Journal of Systematic Bacteriology, vol. 44, no. 4, pp. 812-826, 1994.
-
(1994)
International Journal of Systematic Bacteriology
, vol.44
, Issue.4
, pp. 812-826
-
-
Collins, M.D.1
Lawson, P.A.2
Willems, A.3
-
58
-
-
0003472790
-
-
Academic Press, Cambridge, Mass, USA
-
J. I. Rood, B. A. McClane, J. G. Songer, and R. W. Titball, The Clostridia:Molecular Biology and Pathogenesis, Academic Press, Cambridge, Mass, USA, 1997.
-
(1997)
The Clostridia:Molecular Biology and Pathogenesis
-
-
Rood, J.I.1
McClane, B.A.2
Songer, J.G.3
Titball, R.W.4
-
59
-
-
68949203136
-
The family Lachnospiraceae, including the Genera Butyrivibrio, Lachnospira and Roseburia
-
M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt, Eds., Springer, New York, NY, USA
-
M. Cotta and R. Foster, "The family Lachnospiraceae, including the Genera Butyrivibrio, Lachnospira and Roseburia, " in The Prokaryotes, M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt, Eds., pp. 1002-1021, Springer, New York, NY, USA, 2006.
-
(2006)
The Prokaryotes
, pp. 1002-1021
-
-
Cotta, M.1
Foster, R.2
-
60
-
-
84927692256
-
The first 1000 cultured species of the human gastrointestinal microbiota
-
M. Rajilíc-Stojanovíc andW. M. de Vos, "The first 1000 cultured species of the human gastrointestinal microbiota, " FEMSMicrobiology Reviews, vol. 38, no. 5, pp. 996-1047, 2014.
-
(2014)
FEMSMicrobiology Reviews
, vol.38
, Issue.5
, pp. 996-1047
-
-
Rajilíc-Stojanovíc, M.1
De Vos, W.M.2
-
61
-
-
5444248493
-
Akkermansia muciniphila gen. Nov., sp. Nov., a human intestinalmucin-degrading bacterium
-
M. Derrien, E. E. Vaughan, C. M. Plugge, and W. M. de Vos, "Akkermansia muciniphila gen. nov., sp. nov., a human intestinalmucin-degrading bacterium, " International Journal of Systematic and Evolutionary Microbiology, vol. 54, no. 5, pp. 1469-1476, 2004.
-
(2004)
International Journal of Systematic and Evolutionary Microbiology
, vol.54
, Issue.5
, pp. 1469-1476
-
-
Derrien, M.1
Vaughan, E.E.2
Plugge, C.M.3
De Vos, W.M.4
-
62
-
-
84983078391
-
Characterization of outer membrane proteome of Akkermansia muciniphila reveals sets of novel proteins exposed to the human intestine
-
N. Ottman, L. Huuskonen, J. Reunanen et al., "Characterization of outer membrane proteome of Akkermansia muciniphila reveals sets of novel proteins exposed to the human intestine, " Frontiers in Microbiology, vol. 7, article 1157, 2016.
-
(2016)
Frontiers in Microbiology
, vol.7
-
-
Ottman, N.1
Huuskonen, L.2
Reunanen, J.3
-
63
-
-
34247371381
-
Understanding the effects of diet on bacterial metabolism in the large intestine
-
P. Louis, K. P. Scott, S. H. Duncan, and H. J. Flint, "Understanding the effects of diet on bacterial metabolism in the large intestine, " Journal of Applied Microbiology, vol. 102, no. 5, pp. 1197-1208, 2007.
-
(2007)
Journal of Applied Microbiology
, vol.102
, Issue.5
, pp. 1197-1208
-
-
Louis, P.1
Scott, K.P.2
Duncan, S.H.3
Flint, H.J.4
-
64
-
-
0029882856
-
Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora
-
T. L. Miller and M. J. Wolin, "Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora, " Applied and Environmental Microbiology, vol. 62, no. 5, pp. 1589-1592, 1996.
-
(1996)
Applied and Environmental Microbiology
, vol.62
, Issue.5
, pp. 1589-1592
-
-
Miller, T.L.1
Wolin, M.J.2
-
65
-
-
0000328650
-
Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine
-
R. I. Mackie, B. R. White, and R. E. Isaacson, Eds., Chapman &Hall, London, UK
-
G. T. Macfarlane and G. R. Gibson, "Carbohydrate fermentation, energy transduction and gas metabolism in the human large intestine, " in GastrointestinalMicrobiology, R. I. Mackie, B. R. White, and R. E. Isaacson, Eds., vol. 1, pp. 269-318, Chapman &Hall, London, UK, 1996.
-
(1996)
GastrointestinalMicrobiology
, vol.1
, pp. 269-318
-
-
Macfarlane, G.T.1
Gibson, G.R.2
-
66
-
-
0037509909
-
Regulation of short-chain fatty acid production
-
S. Macfarlane and G. T. Macfarlane, "Regulation of short-chain fatty acid production, " Proceedings of the Nutrition Society, vol. 62, no. 1, pp. 67-72, 2003.
-
(2003)
Proceedings of the Nutrition Society
, vol.62
, Issue.1
, pp. 67-72
-
-
Macfarlane, S.1
Macfarlane, G.T.2
-
67
-
-
84883139076
-
The role of short-chainfatty acids in the interplay between diet, gut microbiota, and host energy metabolism
-
G. Den Besten, K. Van Eunen, A. K. Groen, K. Venema, D.-J. Reijngoud, andB. M. Bakker, "The role of short-chainfatty acids in the interplay between diet, gut microbiota, and host energy metabolism, " Journal of Lipid Research, vol. 54, no. 9, pp. 2325-2340, 2013.
-
(2013)
Journal of Lipid Research
, vol.54
, Issue.9
, pp. 2325-2340
-
-
Den Besten, G.1
Van Eunen, K.2
Groen, A.K.3
Venema, K.4
Reijngoud, D.-J.5
Bakker, B.M.6
-
68
-
-
8144224956
-
Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product
-
S. H. Duncan, P. Louis, and H. J. Flint, "Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product, " Applied and Environmental Microbiology, vol. 70, no. 10, pp. 5810-5817, 2004.
-
(2004)
Applied and Environmental Microbiology
, vol.70
, Issue.10
, pp. 5810-5817
-
-
Duncan, S.H.1
Louis, P.2
Flint, H.J.3
-
69
-
-
35448960761
-
Impact of pH on lactate formation and utilization by human fecal microbial communities
-
A. Belenguer, S. H. Duncan, G. Holtrop, S. E. Anderson, G. E. Lobley, and H. J. Flint, "Impact of pH on lactate formation and utilization by human fecal microbial communities, " Applied and EnvironmentalMicrobiology, vol. 73, no. 20, pp. 6526-6533, 2007.
-
(2007)
Applied and EnvironmentalMicrobiology
, vol.73
, Issue.20
, pp. 6526-6533
-
-
Belenguer, A.1
Duncan, S.H.2
Holtrop, G.3
Erson, S.E.4
Lobley, G.E.5
Flint, H.J.6
-
70
-
-
14944368136
-
The acetate switch
-
A. J. Wolfe, "The acetate switch, " Microbiology and Molecular Biology Reviews, vol. 69, no. 1, pp. 12-50, 2005.
-
(2005)
Microbiology and Molecular Biology Reviews
, vol.69
, Issue.1
, pp. 12-50
-
-
Wolfe, A.J.1
-
71
-
-
0036793753
-
Acetate utilization and butyryl coenzyme A (CoA): Acetate-CoA transferase in butyrate-producing bacteria from the human large intestine
-
S. H. Duncan, A. Barcenilla, C. S. Stewart, S. E. Pryde, and H. J. Flint, "Acetate utilization and butyryl coenzyme A (CoA): Acetate-CoA transferase in butyrate-producing bacteria from the human large intestine, " Applied and Environmental Microbiology, vol. 68, no. 10, pp. 5186-5190, 2002.
-
(2002)
Applied and Environmental Microbiology
, vol.68
, Issue.10
, pp. 5186-5190
-
-
Duncan, S.H.1
Barcenilla, A.2
Stewart, C.S.3
Pryde, S.E.4
Flint, H.J.5
-
72
-
-
0034021744
-
Molecular ecological analysis of the succession and diversity of sulfatereducing bacteria in the mouse gastrointestinal tract
-
B. Deplancke, K. R. Hristova, H. A. Oakley et al., "Molecular ecological analysis of the succession and diversity of sulfatereducing bacteria in the mouse gastrointestinal tract, " Applied and Environmental Microbiology, vol. 66, no. 5, pp. 2166-2174, 2000.
-
(2000)
Applied and Environmental Microbiology
, vol.66
, Issue.5
, pp. 2166-2174
-
-
Deplancke, B.1
Hristova, K.R.2
Oakley, H.A.3
-
73
-
-
0000253782
-
Physiological ecology of methanogens
-
J. G. Ferry, Ed., Chapman Hall Routledge, New York, NY, USA
-
S. H. Zinder, "Physiological ecology of methanogens, " in Methanogenesis, J. G. Ferry, Ed., pp. 128-206, Chapman Hall Routledge, New York, NY, USA, 1993.
-
(1993)
Methanogenesis
, pp. 128-206
-
-
Zinder, S.H.1
-
74
-
-
45749140542
-
Structure of the archaeal community of the rumen
-
P. H. Janssen and M. Kirs, "Structure of the archaeal community of the rumen, " Applied and EnvironmentalMicrobiology, vol. 74, no. 12, pp. 3619-3625, 2008.
-
(2008)
Applied and EnvironmentalMicrobiology
, vol.74
, Issue.12
, pp. 3619-3625
-
-
Janssen, P.H.1
Kirs, M.2
-
75
-
-
0001891324
-
Proteolysis and amino acid fermentation
-
G. R. Gibson and G. T. Macfarlane, Eds., CRC Press, Boca Raton, Fla, USA
-
S. Macfarlane andG. T. Macfarlane, "Proteolysis and amino acid fermentation, " in Human Colonic Bacteria: Role in Nutrition, Physiology and Pathology, G. R. Gibson and G. T. Macfarlane, Eds., pp. 75-100, CRC Press, Boca Raton, Fla, USA, 1995.
-
(1995)
Human Colonic Bacteria: Role in Nutrition, Physiology and Pathology
, pp. 75-100
-
-
Macfarlane, S.1
Macfarlane, G.T.2
-
76
-
-
0023186954
-
Protein origin of the volatile fatty acids isobutyrate and isovalerate in human stool
-
E. J. Zarling and M. A. Ruchim, "Protein origin of the volatile fatty acids isobutyrate and isovalerate in human stool, " The Journal of Laboratory and Clinical Medicine, vol. 109, no. 5, pp. 566-570, 1987.
-
(1987)
The Journal of Laboratory and Clinical Medicine
, vol.109
, Issue.5
, pp. 566-570
-
-
Zarling, E.J.1
Ruchim, M.A.2
|