-
1
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
Huttenhower, C.1
-
2
-
-
84988864262
-
Revised estimates for the number of human and bacteria cells in the body
-
Sender, R., Fuchs, S. & Milo, R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14, e1002533 (2016).
-
(2016)
PLoS Biol.
, vol.14
, pp. e1002533
-
-
Sender, R.1
Fuchs, S.2
Milo, R.3
-
3
-
-
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
-
4
-
-
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
-
5
-
-
84879744885
-
The long-term stability of the human gut microbiota
-
Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
-
(2013)
Science
, vol.341
, pp. 1237439
-
-
Faith, J.J.1
-
6
-
-
84883110880
-
Richness of human gut microbiome correlates with metabolic markers
-
Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
-
(2013)
Nature
, vol.500
, pp. 541-546
-
-
Le-Chatelier, E.1
-
7
-
-
84968918909
-
Population-level analysis of gut microbiome variation
-
Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560-564 (2016).
-
(2016)
Science
, vol.352
, pp. 560-564
-
-
Falony, G.1
-
8
-
-
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
-
9
-
-
84865180569
-
Categorization of the gut microbiota: Enterotypes or gradients?
-
Jeffery, I. B., Claesson, M. J., O'Toole, P. W. & Shanahan, F. Categorization of the gut microbiota: enterotypes or gradients? Nat. Rev. Microbiol. 10, 591-592 (2012).
-
(2012)
Nat. Rev. Microbiol.
, vol.10
, pp. 591-592
-
-
Jeffery, I.B.1
Claesson, M.J.2
O'Toole, P.W.3
Shanahan, F.4
-
10
-
-
84904014790
-
Tipping elements in the human intestinal ecosystem
-
Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M. & de Vos, W. M. Tipping elements in the human intestinal ecosystem. Nat. Commun. 5, 4344 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 4344
-
-
Lahti, L.1
Salojärvi, J.2
Salonen, A.3
Scheffer, M.4
De-Vos, W.M.5
-
11
-
-
0035845511
-
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
-
Sørlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA 98, 10869-10874 (2001).
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 10869-10874
-
-
Sørlie, T.1
-
12
-
-
0037478605
-
Repeated observation of breast tumor subtypes in independent gene expression data sets
-
Sorlie, T. et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA 100, 8418-8423 (2003).
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 8418-8423
-
-
Sorlie, T.1
-
13
-
-
84860589077
-
Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum
-
Yamauchi, M. et al. Assessment of colorectal cancer molecular features along bowel subsites challenges the conception of distinct dichotomy of proximal versus distal colorectum. Gut 61, 847-854 (2012).
-
(2012)
Gut
, vol.61
, pp. 847-854
-
-
Yamauchi, M.1
-
14
-
-
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
-
15
-
-
79952750340
-
Vaginal microbiome of reproductive-age women
-
Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl Acad. Sci. USA 108, 4680-4687 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4680-4687
-
-
Ravel, J.1
-
16
-
-
84873510063
-
A guide to enterotypes across the human body: Meta-analysis of microbial community structures in human microbiome datasets
-
Koren, O. et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput. Biol. 9, e1002863 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002863
-
-
Koren, O.1
-
17
-
-
84900535804
-
Dynamics and associations of microbial community types across the human body
-
Ding, T. & 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
-
18
-
-
84991554351
-
Exploration of bacterial community classes in major human habitats
-
Zhou, Y. et al. Exploration of bacterial community classes in major human habitats. Genome Biol. 15, R66 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R66
-
-
Zhou, Y.1
-
19
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2. Diabetes
-
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2. diabetes. Nature 490, 55-60 (2012).
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
-
20
-
-
33747177087
-
Assembly of the human intestinal microbiota
-
Dethlefsen, L., Eckburg, P. B., Bik, E. M. & Relman, D. A. Assembly of the human intestinal microbiota. Trends Ecol. Evol. 21, 517-523 (2006).
-
(2006)
Trends Ecol. Evol.
, vol.21
, pp. 517-523
-
-
Dethlefsen, L.1
Eckburg, P.B.2
Bik, E.M.3
Relman, D.A.4
-
21
-
-
84871732071
-
Genomic variation landscape of the human gut microbiome
-
Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45-50 (2013).
-
(2013)
Nature
, vol.493
, pp. 45-50
-
-
Schloissnig, S.1
-
22
-
-
84939135810
-
Inter-individual differences in the gene content of human gut bacterial species
-
Zhu, A., Sunagawa, S., Mende, D. R. & Bork, P. Inter-individual differences in the gene content of human gut bacterial species. Genome Biol. 16, 82 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 82
-
-
Zhu, A.1
Sunagawa, S.2
Mende, D.R.3
Bork, P.4
-
23
-
-
80053618114
-
Linking long-term dietary patterns with gut microbial enterotypes
-
Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).
-
(2011)
Science
, vol.334
, pp. 105-108
-
-
Wu, G.D.1
-
24
-
-
84905454882
-
Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue
-
Karlsson, F. H., Nookaew, I. & Nielsen, J. Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue. PLoS Comput. Biol. 10, e1003706 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003706
-
-
Karlsson, F.H.1
Nookaew, I.2
Nielsen, J.3
-
25
-
-
84898646785
-
Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants
-
Bergstrom, A. et al. Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants. Appl. Environ. Microbiol. 80, 2889-2900 (2014).
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 2889-2900
-
-
Bergstrom, A.1
-
26
-
-
84856521514
-
Dirichlet multinomial mixtures: Generative models for microbial metagenomics
-
Holmes, I., Harris, K. & Quince, C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PLoS ONE 7, e30126 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e30126
-
-
Holmes, I.1
Harris, K.2
Quince, C.3
-
27
-
-
84876889703
-
The impact of Crohn's disease genes on healthy human gut microbiota: A pilot study
-
Quince, C. et al. The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study. Gut 62, 952-954 (2013).
-
(2013)
Gut
, vol.62
, pp. 952-954
-
-
Quince, C.1
-
28
-
-
84892992144
-
Microbial enterotypes, inferred by the Prevotella-to-Bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet
-
Roager, H. M., Licht, T. R., Poulsen, S. K., Larsen, T. M. & Bahl, M. I. Microbial enterotypes, inferred by the Prevotella-to-Bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet. Appl. Environ. Microbiol. 80, 1142-1149 (2014).
-
(2014)
Appl. Environ. Microbiol.
, vol.80
, pp. 1142-1149
-
-
Roager, H.M.1
Licht, T.R.2
Poulsen, S.K.3
Larsen, T.M.4
Bahl, M.I.5
-
29
-
-
84865055757
-
Analysis of the gut microbiota in the Old Order Amish and its relation to the metabolic syndrome
-
Zupancic, M. L. et al. Analysis of the gut microbiota in the Old Order Amish and its relation to the metabolic syndrome. PLoS ONE 7, e43052 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e43052
-
-
Zupancic, M.L.1
-
30
-
-
84864722033
-
Gut microbiota composition correlates with diet and health in the elderly
-
Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184 (2012).
-
(2012)
Nature
, vol.488
, pp. 178-184
-
-
Claesson, M.J.1
-
31
-
-
84959557262
-
On the origins and control of community types in the human microbiome
-
Gibson, T. E., Bashan, A., Cao, H.-T., Weiss, S. T. & Liu, Y.-Y. On the origins and control of community types in the human microbiome. PLoS Comput. Biol. 12, e1004688 (2016).
-
(2016)
PLoS Comput. Biol.
, vol.12
, pp. e1004688
-
-
Gibson, T.E.1
Bashan, A.2
Cao, H.-T.3
Weiss, S.T.4
Liu, Y.-Y.5
-
32
-
-
84872687670
-
Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice
-
Hildebrand, F. et al. Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice. Genome Biol. 14, R4 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R4
-
-
Hildebrand, F.1
-
33
-
-
84903722284
-
Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice
-
Wang, J. et al. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proc. Natl Acad. Sci. USA 111, 2703-2710 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 2703-2710
-
-
Wang, J.1
-
34
-
-
84870805463
-
Chimpanzees and humans harbour compositionally similar gut enterotypes
-
Moeller, A. H. et al. Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat. Commun. 3, 1179 (2012).
-
(2012)
Nat. Commun.
, vol.3
, pp. 1179
-
-
Moeller, A.H.1
-
35
-
-
84925300953
-
Stability of the gorilla microbiome despite simian immunodeficiency virus infection
-
Moeller, A. H. et al. Stability of the gorilla microbiome despite simian immunodeficiency virus infection. Mol. Ecol. 24, 690-697 (2015).
-
(2015)
Mol. Ecol.
, vol.24
, pp. 690-697
-
-
Moeller, A.H.1
-
36
-
-
84945433592
-
Early-life establishment of the swine gut microbiome and impact on host phenotypes
-
Mach, N. et al. Early-life establishment of the swine gut microbiome and impact on host phenotypes. Environ. Microbiol. Rep. 7, 554-569 (2015).
-
(2015)
Environ. Microbiol. Rep.
, vol.7
, pp. 554-569
-
-
Mach, N.1
-
37
-
-
84968658925
-
Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits
-
Ramayo-Caldas, Y. et al. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME J. 10, 2973-2977 (2016).
-
(2016)
ISME J.
, vol.10
, pp. 2973-2977
-
-
Ramayo-Caldas, Y.1
-
38
-
-
84938575125
-
Two gut community enterotypes recur in diverse bumblebee species
-
Li, J. et al. Two gut community enterotypes recur in diverse bumblebee species. Curr. Biol. 25, R652-R653 (2015).
-
(2015)
Curr. Biol.
, vol.25
, pp. R652-R653
-
-
Li, J.1
-
39
-
-
84919473614
-
Rapid changes in the gut microbiome during human evolution
-
Moeller, A. H. et al. Rapid changes in the gut microbiome during human evolution. Proc. Natl Acad. Sci. USA 111, 16431-16435 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 16431-16435
-
-
Moeller, A.H.1
-
40
-
-
85026895683
-
The evolution of the host microbiome as an ecosystem on a leash
-
Foster, K. R., Schluter, J., Coyte, K. Z. & Rakoff-Nahoum, S. The evolution of the host microbiome as an ecosystem on a leash. Nature 548, 43-51 (2017).
-
(2017)
Nature
, vol.548
, pp. 43-51
-
-
Foster, K.R.1
Schluter, J.2
Coyte, K.Z.3
Rakoff-Nahoum, S.4
-
41
-
-
0242629042
-
Catastrophic regime shifts in ecosystems: Linking theory to observation
-
Scheffer, M. & Carpenter, S. R. Catastrophic regime shifts in ecosystems: linking theory to observation. Trends Ecol. Evol. 18, 648-656 (2003).
-
(2003)
Trends Ecol. Evol.
, vol.18
, pp. 648-656
-
-
Scheffer, M.1
Carpenter, S.R.2
-
42
-
-
84862173705
-
A core human microbiome as viewed through 16S rRNA sequence clusters
-
Huse, S. M., Ye, Y., Zhou, Y. & Fodor, A. A. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7, e34242 (2012).
-
(2012)
PLoS ONE
, vol.7
, pp. e34242
-
-
Huse, S.M.1
Ye, Y.2
Zhou, Y.3
Fodor, A.A.4
-
43
-
-
84995755353
-
Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle
-
Gorvitovskaia, A., Holmes, S. P. & Huse, S. M. Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome 4, 15 (2016).
-
(2016)
Microbiome
, vol.4
, pp. 15
-
-
Gorvitovskaia, A.1
Holmes, S.P.2
Huse, S.M.3
-
44
-
-
84991204326
-
Species-function relationships shape ecological properties of the human gut microbiome
-
Vieira-Silva, S. et al. Species-function relationships shape ecological properties of the human gut microbiome. Nat. Microbiol. 1, 16088 (2016).
-
(2016)
Nat. Microbiol.
, vol.1
, pp. 16088
-
-
Vieira-Silva, S.1
-
45
-
-
28644450403
-
Determinants of woody cover in African savannas
-
Sankaran, M. et al. Determinants of woody cover in African savannas. Nature 438, 846-849 (2005).
-
(2005)
Nature
, vol.438
, pp. 846-849
-
-
Sankaran, M.1
-
46
-
-
79955920229
-
Tree cover in sub-Saharan Africa: Rainfall and fire constrain forest and savanna as alternative stable states
-
Staver, A. C., Archibald, S. & Levin, S. Tree cover in sub-Saharan Africa: rainfall and fire constrain forest and savanna as alternative stable states. Ecology 92, 1063-1072 (2011).
-
(2011)
Ecology
, vol.92
, pp. 1063-1072
-
-
Staver, A.C.1
Archibald, S.2
Levin, S.3
-
47
-
-
0033982936
-
KEGG: Kyoto encyclopedia of genes and genomes
-
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000).
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
48
-
-
84976905626
-
EggNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
-
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, 286-293 (2016).
-
(2016)
Nucleic Acids Res.
, vol.44
, pp. 286-293
-
-
Huerta-Cepas, J.1
-
49
-
-
84879456755
-
Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans
-
Ou, J. et al. Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am. J. Clin. Nutr. 98, 111-120 (2013).
-
(2013)
Am. J. Clin. Nutr.
, vol.98
, pp. 111-120
-
-
Ou, J.1
-
50
-
-
84923372539
-
Diversity in gut bacterial community of school-age children in Asia
-
Nakayama, J. et al. Diversity in gut bacterial community of school-age children in Asia. Sci. Rep. 5, 8397 (2015).
-
(2015)
Sci. Rep.
, vol.5
, pp. 8397
-
-
Nakayama, J.1
-
51
-
-
84873875156
-
Gut microbiomes of Malawian twin pairs discordant for Kwashiorkor
-
Smith, M. I. et al. Gut microbiomes of Malawian twin pairs discordant for Kwashiorkor. Science 339, 548-554 (2013).
-
(2013)
Science
, vol.339
, pp. 548-554
-
-
Smith, M.I.1
-
52
-
-
77957075815
-
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
-
De Filippo, C. et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl Acad. Sci. USA 107, 14691-14696 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 14691-14696
-
-
De-Filippo, C.1
-
53
-
-
84892828465
-
Diet rapidly and reproducibly alters the human gut microbiome
-
David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563 (2014).
-
(2014)
Nature
, vol.505
, pp. 559-563
-
-
David, L.A.1
-
54
-
-
78149466996
-
Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: Insights into their environmental niche
-
Purushe, J. et al. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb. Ecol. 60, 721-729 (2010).
-
(2010)
Microb. Ecol.
, vol.60
, pp. 721-729
-
-
Purushe, J.1
-
55
-
-
58149200943
-
The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics
-
Cantarel, B. L. et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233-D238 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D233-D238
-
-
Cantarel, B.L.1
-
56
-
-
85016946769
-
Microbial nutrient niches in the gut
-
Pereira, F. C. & Berry, D. Microbial nutrient niches in the gut. Environ. Microbiol. 19, 1366-1378 (2017).
-
(2017)
Environ. Microbiol.
, vol.19
, pp. 1366-1378
-
-
Pereira, F.C.1
Berry, D.2
-
57
-
-
84952942226
-
Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates
-
Vandeputte, D. et al. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65, 57-62 (2016).
-
(2016)
Gut
, vol.65
, pp. 57-62
-
-
Vandeputte, D.1
-
58
-
-
84983651716
-
Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut
-
Roager, H. M. et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat. Microbiol. 1, 16093 (2016).
-
(2016)
Nat. Microbiol.
, vol.1
, pp. 16093
-
-
Roager, H.M.1
-
59
-
-
79957574938
-
Moving pictures of the human microbiome
-
Caporaso, J. G. et al. Moving pictures of the human microbiome. Genome Biol. 12, R50 (2011).
-
(2011)
Genome Biol.
, vol.12
, pp. R50
-
-
Caporaso, J.G.1
-
60
-
-
85014146143
-
Two dynamic regimes in the human gut microbiome
-
Gibbons, S. M., Kearney, S. M., Smillie, C. S. & Alm, E. J. Two dynamic regimes in the human gut microbiome. PLoS Comput. Biol. 13, e1005364 (2017).
-
(2017)
PLoS Comput. Biol.
, vol.13
, pp. e1005364
-
-
Gibbons, S.M.1
Kearney, S.M.2
Smillie, C.S.3
Alm, E.J.4
-
61
-
-
84939179628
-
Temporal and technical variability of human gut metagenomes
-
Voigt, A. Y. et al. Temporal and technical variability of human gut metagenomes. Genome Biol. 16, 73 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 73
-
-
Voigt, A.Y.1
-
62
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
Dethlefsen, L. & Relman, D. A. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA 108, 4554-4561 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
63
-
-
84873019302
-
Duodenal infusion of donor feces for recurrent Clostridium difficile
-
Van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368, 407-415 (2013).
-
(2013)
N. Engl. J. Med.
, vol.368
, pp. 407-415
-
-
Van-Nood, E.1
-
64
-
-
84949491459
-
Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella
-
Kovatcheva-Datchary, P. et al. Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metab. 22, 971-982 (2015).
-
(2015)
Cell Metab.
, vol.22
, pp. 971-982
-
-
Kovatcheva-Datchary, P.1
-
65
-
-
33845901507
-
Human gut microbes associated with obesity
-
Ley, R. E., Turnbaugh, P. J., Klein, S. & Gordon, J. I. 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
-
66
-
-
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
-
67
-
-
84956873905
-
Bidirectional interactions between indomethacin and the murine intestinal microbiota
-
Liang, X. et al. Bidirectional interactions between indomethacin and the murine intestinal microbiota. eLife 4, e08973 (2015).
-
(2015)
ELife
, vol.4
, pp. e08973
-
-
Liang, X.1
-
68
-
-
84961226156
-
The microbial pharmacists within us: A metagenomic view of xenobiotic metabolism
-
Spanogiannopoulos, P., Bess, E. N., Carmody, R. N. & Turnbaugh, P. J. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism. Nat. Rev. Microbiol. 14, 273-287 (2016).
-
(2016)
Nat. Rev. Microbiol.
, vol.14
, pp. 273-287
-
-
Spanogiannopoulos, P.1
Bess, E.N.2
Carmody, R.N.3
Turnbaugh, P.J.4
-
69
-
-
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
-
70
-
-
84873296091
-
Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH
-
Zhu, L. et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH. Hepatology 57, 601-609 (2013).
-
(2013)
Hepatology
, vol.57
, pp. 601-609
-
-
Zhu, L.1
-
71
-
-
84924026956
-
Potential of fecal microbiota for early-stage detection of colorectal cancer
-
Zeller, G. et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol. Syst. Biol. 10, 766 (2014).
-
(2014)
Mol. Syst. Biol.
, vol.10
, pp. 766
-
-
Zeller, G.1
-
72
-
-
79551571717
-
Microbial dysbiosis in colorectal cancer (CRC) patients
-
Sobhani, I. et al. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS ONE 6, e16393 (2011).
-
(2011)
PLoS ONE
, vol.6
, pp. e16393
-
-
Sobhani, I.1
-
73
-
-
77949886724
-
Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children
-
De Palma, G. et al. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. Microbiology 10, 63 (2010).
-
(2010)
Microbiology
, vol.10
, pp. 63
-
-
De-Palma, G.1
-
74
-
-
78049522796
-
Long-term impacts of antibiotic exposure on the human intestinal microbiota
-
Jernberg, C., Löfmark, S., Edlund, C. & Jansson, J. K. Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156, 3216-3223 (2010).
-
(2010)
Microbiology
, vol.156
, pp. 3216-3223
-
-
Jernberg, C.1
Löfmark, S.2
Edlund, C.3
Jansson, J.K.4
-
75
-
-
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
-
76
-
-
77949393654
-
Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults
-
Larsen, N. et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 5, e9085 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e9085
-
-
Larsen, N.1
-
77
-
-
84883855720
-
Alterations in the gut microbiota associated with HIV-1 infection
-
Lozupone, C. A. et al. Alterations in the gut microbiota associated with HIV-1 infection. Cell Host Microbe 14, 329-339 (2013).
-
(2013)
Cell Host Microbe
, vol.14
, pp. 329-339
-
-
Lozupone, C.A.1
-
78
-
-
84957063177
-
Gut microbiota linked to sexual preference and HIV infection
-
Noguera-Julian, M. et al. Gut microbiota linked to sexual preference and HIV infection. EBioMedicine 5, 135-146 (2016).
-
(2016)
EBioMedicine
, vol.5
, pp. 135-146
-
-
Noguera-Julian, M.1
-
79
-
-
84871814687
-
Symptomatic atherosclerosis is associated with an altered gut metagenome
-
Karlsson, F. H. et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat. Commun. 3, 1245 (2012).
-
(2012)
Nat. Commun.
, vol.3
, pp. 1245
-
-
Karlsson, F.H.1
-
80
-
-
84908067044
-
Rethinking 'enterotypes'
-
Knights, D. et al. Rethinking 'enterotypes'. Cell Host Microbe 16, 433-437 (2014).
-
(2014)
Cell Host Microbe
, vol.16
, pp. 433-437
-
-
Knights, D.1
-
81
-
-
84904012195
-
Microbiome data distinguish patients with Clostridium difficile infection and non-C. Difficile-associated diarrhea from healthy controls
-
Schubert, A. M. et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. mBio 5, e01021-14 (2014).
-
(2014)
MBio
, vol.5
, pp. e01021-e01114
-
-
Schubert, A.M.1
-
82
-
-
84871784819
-
Association of all-cause mortality with overweight and obesity using standard body mass index categories: A systematic review and meta-analysis
-
Flegal, K. M., Kit, B. K., Orpana, H. & Graubard, B. I. Association of all-cause mortality with overweight and obesity using standard body mass index categories: a systematic review and meta-analysis. JAMA 309, 71-82 (2013).
-
(2013)
JAMA
, vol.309
, pp. 71-82
-
-
Flegal, K.M.1
Kit, B.K.2
Orpana, H.3
Graubard, B.I.4
-
83
-
-
77955067191
-
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
-
Wu, G. D. et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. Microbiology 10, 206 (2010).
-
(2010)
Microbiology
, vol.10
, pp. 206
-
-
Wu, G.D.1
-
84
-
-
85034013111
-
Uncovering the horseshoe effect in microbial analyses
-
Morton, J. T. et al. Uncovering the horseshoe effect in microbial analyses. mSystems 2, e00166-16 (2017).
-
(2017)
MSystems
, vol.2
, pp. e00166-e00216
-
-
Morton, J.T.1
-
85
-
-
85033585402
-
Towards standards for human fecal sample processing in metagenomic studies
-
Costea, P. et al. Towards standards for human fecal sample processing in metagenomic studies. Nat. Biotechnol. 35, 1069-1076 (2017).
-
(2017)
Nat. Biotechnol.
, vol.35
, pp. 1069-1076
-
-
Costea, P.1
-
86
-
-
85033445586
-
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
-
Sinha, R. et al. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat. Biotechnol. 35, 1077-1086 (2017).
-
(2017)
Nat. Biotechnol.
, vol.35
, pp. 1077-1086
-
-
Sinha, R.1
-
87
-
-
84890204819
-
Metagenomic analysis of the dynamic changes in the gut microbiome of the participants of the MARS-500 experiment, simulating long term space flight
-
Mardanov, A. V. et al. Metagenomic analysis of the dynamic changes in the gut microbiome of the participants of the MARS-500 experiment, simulating long term space flight. Acta Naturae 5, 116-125 (2013).
-
(2013)
Acta Naturae
, vol.5
, pp. 116-125
-
-
Mardanov, A.V.1
-
88
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811-814 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
-
89
-
-
84905454882
-
Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue
-
Karlsson, F. H., Nookaew, I. & Nielsen, J. Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue. PLoS Comput. Biol. 10, e1003706 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003706
-
-
Karlsson, F.H.1
Nookaew, I.2
Nielsen, J.3
-
90
-
-
84864945803
-
Rapid identification of high-confidence taxonomic assignments for metagenomic data
-
MacDonald, N. J., Parks, D. H. & Beiko, R. G. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res. 40, e111 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e111
-
-
MacDonald, N.J.1
Parks, D.H.2
Beiko, R.G.3
-
91
-
-
84901056709
-
Mongolians core gut microbiota and its correlation with seasonal dietary changes
-
Zhang, J. et al. Mongolians core gut microbiota and its correlation with seasonal dietary changes. Sci. Rep. 4, 5001 (2014).
-
(2014)
Sci. Rep.
, vol.4
, pp. 5001
-
-
Zhang, J.1
-
92
-
-
79960289551
-
Evaluation of intestinal microbiotas of healthy Japanese adults and effect of antibiotics using the 16S ribosomal RNA gene based clone library method
-
Morotomi, N. et al. Evaluation of intestinal microbiotas of healthy japanese adults and effect of antibiotics using the 16S ribosomal RNA gene based clone library method. Biol. Pharm. Bull. 34, 1011-1020 (2011).
-
(2011)
Biol. Pharm. Bull.
, vol.34
, pp. 1011-1020
-
-
Morotomi, N.1
-
93
-
-
84876584775
-
Impact of oral typhoid vaccination on the human gut microbiota and correlations with S. Typhi-specific immunological responses
-
Eloe-Fadrosh, E. A. et al. Impact of oral typhoid vaccination on the human gut microbiota and correlations with S. typhi-specific immunological responses. PLoS ONE 4, e62026 (2013).
-
(2013)
PLoS ONE
, vol.4
, pp. e62026
-
-
Eloe-Fadrosh, E.A.1
|