-
1
-
-
84893741669
-
Anal gas evacuation and colonic microbiota in patients with flatulence: Effect of diet
-
Manichanh, C. et al. Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet. Gut 63, 401-408 (2014).
-
(2014)
Gut
, vol.63
, pp. 401-408
-
-
Manichanh, C.1
-
2
-
-
35348857386
-
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
-
Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104, 13780-13785 (2007).
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 13780-13785
-
-
Frank, D.N.1
-
3
-
-
84944220492
-
Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohns disease
-
Lewis, J. D. et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohns disease. Cell Host Microbe 18, 489-500 (2015).
-
(2015)
Cell Host Microbe
, vol.18
, pp. 489-500
-
-
Lewis, J.D.1
-
4
-
-
33845901507
-
Microbial ecology: Human gut microbes associated with obesity
-
Ley, R. E., Turnbaugh, P. J., Klein, S. and Gordon, J. I. Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022-1023 (2006).
-
(2006)
Nature
, vol.444
, pp. 1022-1023
-
-
Ley, R.E.1
Turnbaugh, P.J.2
Klein, S.3
Gordon, J.I.4
-
5
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006).
-
(2006)
Nature
, vol.444
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
-
6
-
-
84877331372
-
Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis
-
Koeth, R. A. et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Med. 19, 576-585 (2013).
-
(2013)
Nature Med.
, vol.19
, pp. 576-585
-
-
Koeth, R.A.1
-
7
-
-
84863022950
-
Genomic analysis identifies association of Fusobacterium with colorectal carcinoma
-
Kostic, A. D. et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 22, 292-298 (2012).
-
(2012)
Genome Res.
, vol.22
, pp. 292-298
-
-
Kostic, A.D.1
-
8
-
-
84887323708
-
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
-
Scher, J. U. et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2, e01202 (2013).
-
(2013)
ELife
, vol.2
, pp. e01202
-
-
Scher, J.U.1
-
9
-
-
84904411548
-
Correlation between the human fecal microbiota and depression
-
Naseribafrouei, A. et al. Correlation between the human fecal microbiota and depression. Neurogastroenterol. Motil. 26, 1155-1162 (2014).
-
(2014)
Neurogastroenterol. Motil.
, vol.26
, pp. 1155-1162
-
-
Naseribafrouei, A.1
-
10
-
-
84924577956
-
Gut microbiota are related to Parkinsons disease and clinical phenotype
-
Scheperjans, F. et al. Gut microbiota are related to Parkinsons disease and clinical phenotype. Mov. Disord. 30, 350-358 (2015).
-
(2015)
Mov. Disord.
, vol.30
, pp. 350-358
-
-
Scheperjans, F.1
-
11
-
-
84879760435
-
Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children
-
Kang, D. W. et al. Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children. PLoS ONE 8, e68322 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e68322
-
-
Kang, D.W.1
-
12
-
-
84876237691
-
Exploring host-microbiota interactions in animal models and humans
-
Kostic, A. D., Howitt, M. R. and Garrett, W. S. Exploring host-microbiota interactions in animal models and humans. Genes Dev. 27, 701-718 (2013).
-
(2013)
Genes Dev.
, vol.27
, pp. 701-718
-
-
Kostic, A.D.1
Howitt, M.R.2
Garrett, W.S.3
-
13
-
-
84879515171
-
Bacteriophage adhering to mucus provide a non-host-derived immunity
-
Barr, J. J. et al. Bacteriophage adhering to mucus provide a non-host-derived immunity. Proc. Natl Acad. Sci. USA 110, 10771-10776 (2013).
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 10771-10776
-
-
Barr, J.J.1
-
14
-
-
84880439384
-
Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta
-
Haiser, H. J. et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295-298 (2013).
-
(2013)
Science
, vol.341
, pp. 295-298
-
-
Haiser, H.J.1
-
15
-
-
84867192879
-
Intestinal inflammation targets cancer-inducing activity of the microbiota
-
Arthur, J. C. et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338, 120-123 (2012).
-
(2012)
Science
, vol.338
, pp. 120-123
-
-
Arthur, J.C.1
-
16
-
-
80052301430
-
Bayesian community-wide culture-independent microbial source tracking
-
Knights, D. et al. Bayesian community-wide culture-independent microbial source tracking. Nature Methods 8, 761-763 (2011).
-
(2011)
Nature Methods
, vol.8
, pp. 761-763
-
-
Knights, D.1
-
17
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
-
18
-
-
84896092821
-
The treatment-naive microbiome in new-onset Crohns disease
-
Gevers, D. et al. The treatment-naive microbiome in new-onset Crohns disease. Cell Host Microbe 15, 382-392 (2014).
-
(2014)
Cell Host Microbe
, vol.15
, pp. 382-392
-
-
Gevers, D.1
-
19
-
-
77957672841
-
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
-
Kuczynski, J. et al. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nature Methods 7, 813-819 (2010).
-
(2010)
Nature Methods
, vol.7
, pp. 813-819
-
-
Kuczynski, J.1
-
20
-
-
84865733148
-
Inferring correlation networks from genomic survey data
-
Friedman, J. and Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012).
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002687
-
-
Friedman, J.1
Alm, E.J.2
-
21
-
-
84926322943
-
Proportionality: A valid alternative to correlation for relative data
-
Lovell, D., Pawlowsky-Glahn, V., Egozcue, J. J., Marguerat, S. and Bahler, J. Proportionality: a valid alternative to correlation for relative data. PLoS Comput. Biol. 11, e1004075 (2015).
-
(2015)
PLoS Comput. Biol.
, vol.11
, pp. e1004075
-
-
Lovell, D.1
Pawlowsky-Glahn, V.2
Egozcue, J.J.3
Marguerat, S.4
Bahler, J.5
-
22
-
-
80054931117
-
Humanassociated microbial signatures: Examining their predictive value
-
Knights, D., Parfrey, L. W., Zaneveld, J., Lozupone, C. and Knight, R. Humanassociated microbial signatures: examining their predictive value. Cell Host Microbe 10, 292-296 (2011).
-
(2011)
Cell Host Microbe
, vol.10
, pp. 292-296
-
-
Knights, D.1
Parfrey, L.W.2
Zaneveld, J.3
Lozupone, C.4
Knight, R.5
-
23
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
24
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
The Human Microbiome Project Consortium
-
The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
25
-
-
77950904616
-
Forensic identification using skin bacterial communities
-
Fierer, N. et al. Forensic identification using skin bacterial communities. Proc. Natl Acad. Sci. USA 107, 6477-6481 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 6477-6481
-
-
Fierer, N.1
-
26
-
-
84930649544
-
Identifying personal microbiomes using metagenomic codes
-
Franzosa, E. A. et al. Identifying personal microbiomes using metagenomic codes. Proc. Natl Acad. Sci. USA 112, E2930-E2938 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. E2930-E2938
-
-
Franzosa, E.A.1
-
27
-
-
84889649570
-
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data
-
Eren, A. M. et al. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol. Evol. 4, 1111-1119 (2013).
-
(2013)
Methods Ecol. Evol.
, vol.4
, pp. 1111-1119
-
-
Eren, A.M.1
-
28
-
-
85041927917
-
Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation
-
Noecker, C. et al. Metabolic model-based integration of microbiome taxonomic and metabolomic profiles elucidates mechanistic links between ecological and metabolic variation. mSystems 13, http://dx.doi.org/10.1128/mSystems.00013-15 (2015).
-
(2015)
MSystems
, vol.13
-
-
Noecker, C.1
-
29
-
-
84922971911
-
Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract
-
Koenigsknecht, M. J. et al. Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract. Infect. Immun. 83, 934-941 (2015).
-
(2015)
Infect. Immun.
, vol.83
, pp. 934-941
-
-
Koenigsknecht, M.J.1
-
30
-
-
84894118144
-
Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders
-
Hsiao, E. Y. et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 155, 1451-1463 (2013).
-
(2013)
Cell
, vol.155
, pp. 1451-1463
-
-
Hsiao, E.Y.1
-
31
-
-
84944065894
-
The human oral metaproteome reveals potential biomarkers for caries disease
-
Belda-Ferre, P. et al. The human oral metaproteome reveals potential biomarkers for caries disease. Proteomics 15, 3497-3507 (2015).
-
(2015)
Proteomics
, vol.15
, pp. 3497-3507
-
-
Belda-Ferre, P.1
-
32
-
-
78649686679
-
A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes
-
Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844-1854 (2010).
-
(2010)
Gastroenterology
, vol.139
, pp. 1844-1854
-
-
Willing, B.P.1
-
33
-
-
84870322666
-
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohns disease
-
Erickson, A. R. et al. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohns disease. PLoS ONE 7, e49138 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e49138
-
-
Erickson, A.R.1
-
34
-
-
68149099597
-
Metabolomics reveals metabolic biomarkers of Crohns disease
-
Jansson, J. et al. Metabolomics reveals metabolic biomarkers of Crohns disease. PLoS ONE 4, e6386 (2009).
-
(2009)
PLoS ONE
, vol.4
, pp. e6386
-
-
Jansson, J.1
-
35
-
-
85003054745
-
Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease
-
Michail, S. et al. Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease. FEMS Microbiol. Ecol. 91, 1-9 (2015).
-
(2015)
FEMS Microbiol. Ecol.
, vol.91
, pp. 1-9
-
-
Michail, S.1
-
36
-
-
84949772416
-
Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
-
Forslund, K. et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 528, 262-266 (2015).
-
(2015)
Nature
, vol.528
, pp. 262-266
-
-
Forslund, K.1
-
37
-
-
84883478660
-
Gut microbiota from twins discordant for obesity modulate metabolism in mice
-
Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).
-
(2013)
Science
, vol.341
, pp. 1241214
-
-
Ridaura, V.K.1
-
38
-
-
84886727251
-
Cometabolism of microbes and host: Implications for drug metabolism and drug-induced toxicity
-
Li, H. and Jia, W. Cometabolism of microbes and host: implications for drug metabolism and drug-induced toxicity. Clin. Pharmacol. Ther. 94, 574-581 (2013).
-
(2013)
Clin. Pharmacol. Ther.
, vol.94
, pp. 574-581
-
-
Li, H.1
Jia, W.2
-
39
-
-
0032694577
-
Metabonomics: Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data
-
Nicholson, J. K., Lindon, J. C. and Holmes, E. Metabonomics: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29, 1181-1189 (1999).
-
(1999)
Xenobiotica
, vol.29
, pp. 1181-1189
-
-
Nicholson, J.K.1
Lindon, J.C.2
Holmes, E.3
-
40
-
-
84960387071
-
Emerging applications of metabolomics in drug discovery and precision medicine
-
Wishart, D. S. Emerging applications of metabolomics in drug discovery and precision medicine. Nature Rev. Drug Discov. http://dx.doi.org/10.1038/nrd.2016.32 (2016).
-
(2016)
Nature Rev. Drug Discov.
-
-
Wishart, D.S.1
-
41
-
-
84944230099
-
Illuminating the dark matter in metabolomics
-
da Silva, R. R., Dorrestein, P. C. and Quinn, R. A. Illuminating the dark matter in metabolomics. Proc. Natl Acad. Sci. USA 112, 12549-12550 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. 12549-12550
-
-
Da Silva, R.R.1
Dorrestein, P.C.2
Quinn, R.A.3
-
42
-
-
84923323409
-
Predicting ecosystem emergent properties at multiple scales
-
Gilbert, J. A. and Henry, C. Predicting ecosystem emergent properties at multiple scales. Environ. Microbiol. Rep. 7, 20-22 (2015).
-
(2015)
Environ. Microbiol. Rep.
, vol.7
, pp. 20-22
-
-
Gilbert, J.A.1
Henry, C.2
-
43
-
-
14844363440
-
Pyocyanin production by Pseudomonas aeruginosa induces neutrophil apoptosis and impairs neutrophil-mediated host defenses in vivo
-
Allen, L. et al. Pyocyanin production by Pseudomonas aeruginosa induces neutrophil apoptosis and impairs neutrophil-mediated host defenses in vivo. J. Immunol. 174, 3643-3649 (2005).
-
(2005)
J. Immunol.
, vol.174
, pp. 3643-3649
-
-
Allen, L.1
-
44
-
-
84894090120
-
Biological significance of short-chain fatty acid metabolism by the intestinal microbiome
-
Puertollano, E., Kolida, S. and Yaqoob, P. Biological significance of short-chain fatty acid metabolism by the intestinal microbiome. Curr. Opin. Clin. Nutr. Metab. Care 17, 139-144 (2014).
-
(2014)
Curr. Opin. Clin. Nutr. Metab. Care
, vol.17
, pp. 139-144
-
-
Puertollano, E.1
Kolida, S.2
Yaqoob, P.3
-
45
-
-
84904554933
-
Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters
-
Cimermancic, P. et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421 (2014).
-
(2014)
Cell
, vol.158
, pp. 412-421
-
-
Cimermancic, P.1
-
46
-
-
84908079780
-
A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics
-
Donia, M. S. et al. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell 158, 1402-1414 (2014).
-
(2014)
Cell
, vol.158
, pp. 1402-1414
-
-
Donia, M.S.1
-
47
-
-
0020539371
-
Fermentation in the human large intestine: Evidence and implications for health
-
Cummings, J. H. Fermentation in the human large intestine: evidence and implications for health. Lancet 1, 1206-1209 (1983).
-
(1983)
Lancet
, vol.1
, pp. 1206-1209
-
-
Cummings, J.H.1
-
48
-
-
85056037203
-
The impact of the level of the intestinal short chain fatty acids in inflammatory bowel disease patients versus healthy subjects
-
Huda-Faujan, N. et al. The impact of the level of the intestinal short chain fatty acids in inflammatory bowel disease patients versus healthy subjects. Open Biochem. J. 4, 53-58 (2010).
-
(2010)
Open Biochem. J.
, vol.4
, pp. 53-58
-
-
Huda-Faujan, N.1
-
49
-
-
84962195820
-
Intestinal short chain fatty acids and their link with diet and human health
-
Rios-Covian, D. et al. Intestinal short chain fatty acids and their link with diet and human health. Front. Microbiol. 7, 185 (2016).
-
(2016)
Front. Microbiol.
, vol.7
, pp. 185
-
-
Rios-Covian, D.1
-
50
-
-
62649151803
-
Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites
-
Wikoff, W. R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl Acad. Sci. USA 106, 3698-3703 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 3698-3703
-
-
Wikoff, W.R.1
-
51
-
-
84938244327
-
Small molecules from the human microbiota
-
Donia, M. S. and Fischbach, M. A. Small molecules from the human microbiota. Science 349, 1254766 (2015).
-
(2015)
Science
, vol.349
, pp. 1254766
-
-
Donia, M.S.1
Fischbach, M.A.2
-
52
-
-
33747137269
-
Escherichia coli induces DNA double-strand breaks in eukaryotic cells
-
Nougayrede, J. P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848-851 (2006).
-
(2006)
Science
, vol.313
, pp. 848-851
-
-
Nougayrede, J.P.1
-
53
-
-
70350439157
-
Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae
-
Putze, J. et al. Genetic structure and distribution of the colibactin genomic island among members of the family Enterobacteriaceae. Infect. Immun. 77, 4696-4703 (2009).
-
(2009)
Infect. Immun.
, vol.77
, pp. 4696-4703
-
-
Putze, J.1
-
54
-
-
84925500413
-
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
-
Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205-208 (2015).
-
(2015)
Nature
, vol.517
, pp. 205-208
-
-
Buffie, C.G.1
-
55
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol. 31, 814-821 (2013).
-
(2013)
Nature Biotechnol.
, vol.31
, pp. 814-821
-
-
Langille, M.G.1
-
56
-
-
84963891450
-
Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles
-
Allegretti, J. R. et al. Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles. Aliment. Pharmacol. Ther. 43, 1142-1153 (2016).
-
(2016)
Aliment. Pharmacol. Ther.
, vol.43
, pp. 1142-1153
-
-
Allegretti, J.R.1
-
57
-
-
84872535919
-
Xenobiotics shape the physiology and gene expression of the active human gut microbiome
-
Maurice, C. F., Haiser, H. J. and Turnbaugh, P. J. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39-50 (2013).
-
(2013)
Cell
, vol.152
, pp. 39-50
-
-
Maurice, C.F.1
Haiser, H.J.2
Turnbaugh, P.J.3
-
58
-
-
84891848483
-
Understanding and modulating mammalian-microbial communication for improved human health
-
Mani, S., Boelsterli, U. A. and Redinbo, M. R. Understanding and modulating mammalian-microbial communication for improved human health. Annu. Rev. Pharmacol. Toxicol. 54, 559-580 (2014).
-
(2014)
Annu. Rev. Pharmacol. Toxicol.
, vol.54
, pp. 559-580
-
-
Mani, S.1
Boelsterli, U.A.2
Redinbo, M.R.3
-
59
-
-
78149295964
-
Alleviating cancer drug toxicity by inhibiting a bacterial enzyme
-
Wallace, B. D. et al. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 330, 831-835 (2010).
-
(2010)
Science
, vol.330
, pp. 831-835
-
-
Wallace, B.D.1
-
60
-
-
84904012264
-
Pharmacomicrobiomics: The impact of human microbiome variations on systems pharmacology and personalized therapeutics
-
ElRakaiby, M. et al. Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. OMICS 18, 402-414 (2014).
-
(2014)
OMICS
, vol.18
, pp. 402-414
-
-
ElRakaiby, M.1
-
61
-
-
70149096873
-
Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism
-
Clayton, T. A., Baker, D., Lindon, J. C., Everett, J. R. and Nicholson, J. K. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc. Natl Acad. Sci. USA 106, 14728-14733 (2009). This study provided the first link between the toxicity of a drug (in this case, acetaminophen, a widely used analgesic) and microbial metabolism.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 14728-14733
-
-
Clayton, T.A.1
Baker, D.2
Lindon, J.C.3
Everett, J.R.4
Nicholson, J.K.5
-
62
-
-
70149092771
-
Drugs, bugs, and personalized medicine: Pharmacometabonomics enters the ring
-
Wilson, I. D. Drugs, bugs, and personalized medicine: pharmacometabonomics enters the ring. Proc. Natl Acad. Sci. USA 106, 14187-14188 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 14187-14188
-
-
Wilson, I.D.1
-
63
-
-
85041651856
-
From sample to multi-omics conclusions in under 48 hours
-
Quinn, R. A. et al. From sample to multi-omics conclusions in under 48 hours. mSystems http://dx.doi.org/10.1128/mSystems.00038-16 (2016).
-
(2016)
MSystems
-
-
Quinn, R.A.1
-
64
-
-
84907190237
-
Longitudinal analysis of microbial interaction between humans and the indoor environment
-
Lax, S. et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345, 1048-1052 (2014).
-
(2014)
Science
, vol.345
, pp. 1048-1052
-
-
Lax, S.1
-
65
-
-
84920721220
-
Ecological succession and viability of human-associated microbiota on restroom surfaces
-
Gibbons, S. M. et al. Ecological succession and viability of human-associated microbiota on restroom surfaces. Appl. Environ. Microbiol. 81, 765-773 (2015).
-
(2015)
Appl. Environ. Microbiol.
, vol.81
, pp. 765-773
-
-
Gibbons, S.M.1
-
66
-
-
84941368240
-
Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples
-
Korem, T. et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science 349, 1101-1106 (2015).
-
(2015)
Science
, vol.349
, pp. 1101-1106
-
-
Korem, T.1
-
67
-
-
84934284959
-
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
-
Quick, J. et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 114
-
-
Quick, J.1
-
68
-
-
84978619185
-
Partial restoration of the microbiota of cesareanborn infants via vaginal microbial transfer
-
Dominguez-Bello, M. G. et al. Partial restoration of the microbiota of cesareanborn infants via vaginal microbial transfer. Nature Med. 22, 250-253 (2016).
-
(2016)
Nature Med.
, vol.22
, pp. 250-253
-
-
Dominguez-Bello, M.G.1
-
69
-
-
84947461438
-
Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development
-
Goyal, M. S., Venkatesh, S., Milbrandt, J., Gordon, J. I. and Raichle, M. E. Feeding the brain and nurturing the mind: linking nutrition and the gut microbiota to brain development. Proc. Natl Acad. Sci. USA 112, 14105-14112 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. 14105-14112
-
-
Goyal, M.S.1
Venkatesh, S.2
Milbrandt, J.3
Gordon, J.I.4
Raichle, M.E.5
-
70
-
-
84961406580
-
Tools for the microbiome: Nano and beyond
-
Biteen, J. S. et al. Tools for the microbiome: nano and beyond. ACS Nano 10, 6-37 (2016).
-
(2016)
ACS Nano
, vol.10
, pp. 6-37
-
-
Biteen, J.S.1
-
71
-
-
84929997716
-
Determinants of community structure in the global plankton interactome
-
Lima-Mendez, G. et al. Determinants of community structure in the global plankton interactome. Science 348, 1262073 (2015).
-
(2015)
Science
, vol.348
, pp. 1262073
-
-
Lima-Mendez, G.1
-
72
-
-
84953226740
-
Network analysis suggests a potentially evil alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities
-
Sam Ma, Z. et al. Network analysis suggests a potentially evil alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities. Sci. Rep. 5, 8275 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 8275
-
-
Sam Ma, Z.1
-
73
-
-
84929297936
-
Dynamics and stabilization of the human gut microbiome during the first year of life
-
erratum 17, 852 (2015)
-
Backhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690-703 (2015); erratum 17, 852 (2015).
-
(2015)
Cell Host Microbe
, vol.17
, pp. 690-703
-
-
Backhed, F.1
-
74
-
-
84907686349
-
The Integrative Human Microbiome Project: Dynamic analysis of microbiome-host omics profiles during periods of human health and disease
-
The Integrative HMP (iHMP) Research Network Consortium
-
The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 16, 276-289 (2014).
-
(2014)
Cell Host Microbe
, vol.16
, pp. 276-289
-
-
-
75
-
-
84991526597
-
EMPeror: A tool for visualizing high-throughput microbial community data
-
Vazquez-Baeza, Y., Pirrung, M., Gonzalez, A. and Knight, R. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2, 16 (2013).
-
(2013)
Gigascience
, vol.2
, pp. 16
-
-
Vazquez-Baeza, Y.1
Pirrung, M.2
Gonzalez, A.3
Knight, R.4
-
76
-
-
84931355745
-
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection
-
Weingarden, A. et al. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection. Microbiome 3, 10 (2015).
-
(2015)
Microbiome
, vol.3
, pp. 10
-
-
Weingarden, A.1
-
77
-
-
79952763661
-
Succession of microbial consortia in the developing infant gut microbiome
-
Koenig, J. E. et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl Acad. Sci. USA 108 (suppl. 1), 4578-4585 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4578-4585
-
-
Koenig, J.E.1
-
78
-
-
84883864245
-
Meta-analyses of studies of the human microbiota
-
Lozupone, C. A. et al. Meta-analyses of studies of the human microbiota. Genome Res. 23, 1704-1714 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 1704-1714
-
-
Lozupone, C.A.1
-
79
-
-
84965187800
-
Temporal variability is a personalized feature of the human microbiome
-
Flores, G. E. et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol. 15, 531 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 531
-
-
Flores, G.E.1
-
80
-
-
84908264764
-
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity
-
Shade, A. et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5, e01371-14 (2014).
-
(2014)
MBio
, vol.5
, pp. e01371-e01414
-
-
Shade, A.1
-
81
-
-
84941005620
-
Temporal and spatial variation of the human microbiota during pregnancy
-
DiGiulio, D. B. et al. Temporal and spatial variation of the human microbiota during pregnancy. Proc. Natl Acad. Sci. USA 112, 11060-11065 (2015).
-
(2015)
Proc. Natl Acad. Sci. USA
, vol.112
, pp. 11060-11065
-
-
DiGiulio, D.B.1
-
82
-
-
84864614787
-
Host remodeling of the gut microbiome and metabolic changes during pregnancy
-
Koren, O. et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150, 470-480 (2012).
-
(2012)
Cell
, vol.150
, pp. 470-480
-
-
Koren, O.1
-
83
-
-
84898859680
-
Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide
-
Wang, Z. et al. Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide. Eur. Heart J. 35, 904-910 (2014).
-
(2014)
Eur. Heart J.
, vol.35
, pp. 904-910
-
-
Wang, Z.1
-
84
-
-
84947812071
-
Personalized nutrition by prediction of glycemic responses
-
Zeevi, D. et al. Personalized nutrition by prediction of glycemic responses. Cell 163, 1079-1094 (2015).
-
(2015)
Cell
, vol.163
, pp. 1079-1094
-
-
Zeevi, D.1
-
85
-
-
84941271231
-
Prediction of early childhood caries via spatial-temporal variations of oral microbiota
-
Teng, F. et al. Prediction of early childhood caries via spatial-temporal variations of oral microbiota. Cell Host Microbe 18, 296-306 (2015).
-
(2015)
Cell Host Microbe
, vol.18
, pp. 296-306
-
-
Teng, F.1
-
86
-
-
84906942512
-
Predictive modeling of gingivitis severity and susceptibility via oral microbiota
-
Huang, S. et al. Predictive modeling of gingivitis severity and susceptibility via oral microbiota. ISME J. 8, 1768-1780 (2014).
-
(2014)
ISME J.
, vol.8
, pp. 1768-1780
-
-
Huang, S.1
-
87
-
-
84938817346
-
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment
-
Zhang, X. et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nature Med. 21, 895-905 (2015).
-
(2015)
Nature Med.
, vol.21
, pp. 895-905
-
-
Zhang, X.1
-
88
-
-
84900535804
-
Dynamics and associations of microbial community types across the human body
-
Ding, T. and Schloss, P. D. Dynamics and associations of microbial community types across the human body. Nature 509, 357-360 (2014).
-
(2014)
Nature
, vol.509
, pp. 357-360
-
-
Ding, T.1
Schloss, P.D.2
-
89
-
-
84883057637
-
Dietary intervention impact on gut microbial gene richness
-
Cotillard, A. et al. Dietary intervention impact on gut microbial gene richness. Nature 500, 585-588 (2013).
-
(2013)
Nature
, vol.500
, pp. 585-588
-
-
Cotillard, A.1
-
90
-
-
84908348194
-
Meta-analyses of human gut microbes associated with obesity and IBD
-
Walters, W. A., Xu, Z. and Knight, R. Meta-analyses of human gut microbes associated with obesity and IBD. FEBS Lett. 588, 4223-4233 (2014).
-
(2014)
FEBS Lett.
, vol.588
, pp. 4223-4233
-
-
Walters, W.A.1
Xu, Z.2
Knight, R.3
-
91
-
-
84937611678
-
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis
-
Kang, D., Shi, B., Erfe, M. C., Craft, N. and Li, H. Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Sci. Transl. Med. 7, 293ra103 (2015).
-
(2015)
Sci. Transl. Med.
, vol.7
, pp. 293ra103
-
-
Kang, D.1
Shi, B.2
Erfe, M.C.3
Craft, N.4
Li, H.5
-
92
-
-
84949675208
-
The microbiome quality control project: Baseline study design and future directions
-
Sinha, R., Abnet, C. C., White, O., Knight, R. and Huttenhower, C. The microbiome quality control project: baseline study design and future directions. Genome Biol. 16, 276 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 276
-
-
Sinha, R.1
Abnet, C.C.2
White, O.3
Knight, R.4
Huttenhower, C.5
-
93
-
-
84957831145
-
Collecting fecal samples for microbiome analyses in epidemiology studies
-
Sinha, R. et al. Collecting fecal samples for microbiome analyses in epidemiology studies. Cancer Epidemiol. Biomarkers Prev. 25, 407-416 (2016).
-
(2016)
Cancer Epidemiol. Biomarkers Prev.
, vol.25
, pp. 407-416
-
-
Sinha, R.1
-
94
-
-
55949124035
-
Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients
-
Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA 105, 16731-16736 (2008).
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
-
95
-
-
84872592295
-
Fecal microbiota composition differs between children with -cell autoimmunity and those without
-
de Goffau, M. C. et al. Fecal microbiota composition differs between children with -cell autoimmunity and those without. Diabetes 62, 1238-1244 (2013).
-
(2013)
Diabetes
, vol.62
, pp. 1238-1244
-
-
De Goffau, M.C.1
-
96
-
-
78650616947
-
Toward defining the autoimmune microbiome for type 1 diabetes
-
Giongo, A. et al. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. 5, 82-91 (2011).
-
(2011)
ISME J.
, vol.5
, pp. 82-91
-
-
Giongo, A.1
-
97
-
-
84922941772
-
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes
-
Kostic, A. D. et al. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe 17, 260-273 (2015).
-
(2015)
Cell Host Microbe
, vol.17
, pp. 260-273
-
-
Kostic, A.D.1
-
98
-
-
84867054370
-
Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis
-
Scher, J. U. et al. Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis. Arthritis Rheum. 64, 3083-3094 (2012).
-
(2012)
Arthritis Rheum.
, vol.64
, pp. 3083-3094
-
-
Scher, J.U.1
-
99
-
-
79952758083
-
Human oral, gut, and plaque microbiota in patients with atherosclerosis
-
Koren, O. et al. Human oral, gut, and plaque microbiota in patients with atherosclerosis. Proc. Natl Acad. Sci. USA 108 (suppl. 1), 4592-4598 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4592-4598
-
-
Koren, O.1
-
100
-
-
85006192445
-
Dysbiosis of gut microbiota with reduced trimethylamine-N-oxide level in patients with large-artery atherosclerotic stroke or transient ischemic attack
-
Yin, J. et al. Dysbiosis of gut microbiota with reduced trimethylamine-N-oxide level in patients with large-artery atherosclerotic stroke or transient ischemic attack. J. Am. Heart Assoc. 4, e002699 (2015).
-
(2015)
J. Am. Heart Assoc.
, vol.4
, pp. e002699
-
-
Yin, J.1
-
101
-
-
84925862053
-
Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease
-
Tang, W. H. et al. Gut microbiota-dependent trimethylamine N-oxide (TMAO) pathway contributes to both development of renal insufficiency and mortality risk in chronic kidney disease. Circ. Res. 116, 448-455 (2015).
-
(2015)
Circ. Res.
, vol.116
, pp. 448-455
-
-
Tang, W.H.1
-
102
-
-
84969261931
-
A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO) a gut microbial metabolite of dietary meat and fat
-
Xu, R., Wang, Q. and Li, L. A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat. BMC Genomics 16 (suppl. 7), S4 (2015).
-
(2015)
BMC Genomics
, vol.16
, pp. S4
-
-
Xu, R.1
Wang, Q.2
Li, L.3
-
103
-
-
84876563088
-
Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk
-
Tang, W. H. et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N. Engl. J. Med. 368, 1575-1584 (2013).
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 1575-1584
-
-
Tang, W.H.1
-
104
-
-
84959922537
-
Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk
-
Zhu, W. et al. Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk. Cell 165, 111-124 (2016).
-
(2016)
Cell
, vol.165
, pp. 111-124
-
-
Zhu, W.1
-
105
-
-
84864520051
-
Modeling an autism risk factor in mice leads to permanent immune dysregulation
-
Hsiao, E. Y., McBride, S. W., Chow, J., Mazmanian, S. K. and Patterson, P. H. Modeling an autism risk factor in mice leads to permanent immune dysregulation. Proc. Natl Acad. Sci. USA 109, 12776-12781 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 12776-12781
-
-
Hsiao, E.Y.1
McBride, S.W.2
Chow, J.3
Mazmanian, S.K.4
Patterson, P.H.5
-
106
-
-
54549106898
-
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
-
Liu, Z., DeSantis, T. Z., Andersen, G. L. and Knight, R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36, e120 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e120
-
-
Liu, Z.1
DeSantis, T.Z.2
Andersen, G.L.3
Knight, R.4
-
107
-
-
80052722544
-
Meeting report: The terabase metagenomics workshop and the vision of an Earth microbiome project
-
Gilbert, J. A. et al. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand. Genomic Sci. 3, 243-248 (2010).
-
(2010)
Stand. Genomic Sci.
, vol.3
, pp. 243-248
-
-
Gilbert, J.A.1
-
108
-
-
29144464937
-
UniFrac: A new phylogenetic method for comparing microbial communities
-
Lozupone, C. and Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235 (2005).
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
109
-
-
84949604733
-
Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome
-
Quinn, R. A. et al. Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. ISME J. 10, 1483-98 (2015).
-
(2015)
ISME J.
, vol.10
, pp. 1483-1498
-
-
Quinn, R.A.1
-
110
-
-
84898546855
-
Bile acids and the gut microbiome
-
Ridlon, J. M., Kang, D. J., Hylemon, P. B. and Bajaj, J. S. Bile acids and the gut microbiome. Curr. Opin. Gastroenterol. 30, 332-338 (2014).
-
(2014)
Curr. Opin. Gastroenterol.
, vol.30
, pp. 332-338
-
-
Ridlon, J.M.1
Kang, D.J.2
Hylemon, P.B.3
Bajaj, J.S.4
-
111
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006).
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
-
112
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
113
-
-
35348968286
-
The human microbiome project
-
Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804-810 (2007).
-
(2007)
Nature
, vol.449
, pp. 804-810
-
-
Turnbaugh, P.J.1
-
114
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White, J. R., Nagarajan, N. and Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol. 5, e1000352 (2009).
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. e1000352
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
115
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. and Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
116
-
-
84946878517
-
Analysis of composition of microbiomes: A novel method for studying microbial composition
-
Mandal, S. et al. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb. Ecol. Health Dis. 26, 27663 (2015).
-
(2015)
Microb. Ecol. Health Dis.
, vol.26
, pp. 27663
-
-
Mandal, S.1
-
117
-
-
79251625980
-
Supervised classification of human microbiota
-
Knights, D., Costello, E. K. and Knight, R. Supervised classification of human microbiota. FEMS Microbiol. Rev. 35, 343-359 (2011).
-
(2011)
FEMS Microbiol. Rev.
, vol.35
, pp. 343-359
-
-
Knights, D.1
Costello, E.K.2
Knight, R.3
-
118
-
-
23344442120
-
Obesity alters gut microbial ecology
-
Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070-11075 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 11070-11075
-
-
Ley, R.E.1
-
119
-
-
77950250064
-
Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5
-
Vijay-Kumar, M. et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328, 228-231 (2010).
-
(2010)
Science
, vol.328
, pp. 228-231
-
-
Vijay-Kumar, M.1
-
120
-
-
84872156123
-
Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice
-
Parks, B. W. et al. Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice. Cell Metab. 17, 141-152 (2013).
-
(2013)
Cell Metab.
, vol.17
, pp. 141-152
-
-
Parks, B.W.1
-
121
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227 (2012).
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
-
122
-
-
84910096224
-
Human genetics shape the gut microbiome
-
Goodrich, J. K. et al. Human genetics shape the gut microbiome. Cell 159, 789-799 (2014).
-
(2014)
Cell
, vol.159
, pp. 789-799
-
-
Goodrich, J.K.1
|