-
1
-
-
20544444045
-
Diversity of the human intestinal microbial flora
-
1 Eckburg, P.B., Bik, E.M., Bernstein, C.N., et al. Diversity of the human intestinal microbial flora. Science 308:5728 (2005), 1635–1638.
-
(2005)
Science
, vol.308
, Issue.5728
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
-
2
-
-
85016726917
-
Tumour-associated and non-tumour-associated microbiota in colorectal cancer
-
[Epub ahead of print]
-
2 Flemer, B., Lynch, D.B., Brown, J.M., et al. Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut, 2016 [Epub ahead of print].
-
(2016)
Gut
-
-
Flemer, B.1
Lynch, D.B.2
Brown, J.M.3
-
3
-
-
0036300743
-
Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces
-
3 Zoetendal, E.G., von Wright, A., Vilpponen-Salmela, T., et al. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68:7 (2002), 3401–3407.
-
(2002)
Appl Environ Microbiol
, vol.68
, Issue.7
, pp. 3401-3407
-
-
Zoetendal, E.G.1
von Wright, A.2
Vilpponen-Salmela, T.3
-
4
-
-
60549089819
-
Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance
-
4 van Baarlen, P., Troost, F.J., van Hemert, S., et al. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci U S A 106:7 (2009), 2371–2376.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.7
, pp. 2371-2376
-
-
van Baarlen, P.1
Troost, F.J.2
van Hemert, S.3
-
5
-
-
84896092821
-
The treatment-naive microbiome in new-onset Crohn's disease
-
5 Gevers, D., Kugathasan, S., Denson, L.A., et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15:3 (2014), 382–392.
-
(2014)
Cell Host Microbe
, vol.15
, Issue.3
, pp. 382-392
-
-
Gevers, D.1
Kugathasan, S.2
Denson, L.A.3
-
6
-
-
84919884555
-
Microbiota organization is a distinct feature of proximal colorectal cancers
-
6 Dejea, C.M., Wick, E.C., Hechenbleikner, E.M., et al. Microbiota organization is a distinct feature of proximal colorectal cancers. Proc Natl Acad Sci U S A 111:51 (2014), 18321–18326.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, Issue.51
, pp. 18321-18326
-
-
Dejea, C.M.1
Wick, E.C.2
Hechenbleikner, E.M.3
-
7
-
-
84858709310
-
Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
-
7 Bahl, M.I., Bergstrom, A., Licht, T.R., Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 329:2 (2012), 193–197.
-
(2012)
FEMS Microbiol Lett
, vol.329
, Issue.2
, pp. 193-197
-
-
Bahl, M.I.1
Bergstrom, A.2
Licht, T.R.3
-
8
-
-
84899898655
-
Comparison of methods for fecal microbiome biospecimen collection
-
8 Dominianni, C., Wu, J., Hayes, R.B., et al. Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol, 14, 2014, 103.
-
(2014)
BMC Microbiol
, vol.14
, pp. 103
-
-
Dominianni, C.1
Wu, J.2
Hayes, R.B.3
-
9
-
-
84939179628
-
Temporal and technical variability of human gut metagenomes
-
9 Voigt, A.Y., Costea, P.I., Kultima, J.R., et al. Temporal and technical variability of human gut metagenomes. Genome Biol, 16, 2015, 73.
-
(2015)
Genome Biol
, vol.16
, pp. 73
-
-
Voigt, A.Y.1
Costea, P.I.2
Kultima, J.R.3
-
10
-
-
84929119983
-
The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations
-
10 Fouhy, F., Deane, J., Rea, M.C., et al. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One, 10(3), 2015, e0119355.
-
(2015)
PLoS One
, vol.10
, Issue.3
, pp. e0119355
-
-
Fouhy, F.1
Deane, J.2
Rea, M.C.3
-
11
-
-
84996542591
-
Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants
-
11 Hill, C.J., Brown, J.R., Lynch, D.B., et al. Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants. Microbiome, 4(1), 2016, 19.
-
(2016)
Microbiome
, vol.4
, Issue.1
, pp. 19
-
-
Hill, C.J.1
Brown, J.R.2
Lynch, D.B.3
-
12
-
-
84947460747
-
Sample storage conditions significantly influence faecal microbiome profiles
-
12 Choo, J.M., Leong, L.E., Rogers, G.B., Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep, 5, 2015, 16350.
-
(2015)
Sci Rep
, vol.5
, pp. 16350
-
-
Choo, J.M.1
Leong, L.E.2
Rogers, G.B.3
-
13
-
-
84893370250
-
Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice
-
13 Faith, J.J., Ahern, P.P., Ridaura, V.K., et al. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med, 6(220), 2014, 220ra211.
-
(2014)
Sci Transl Med
, vol.6
, Issue.220
, pp. 220ra211
-
-
Faith, J.J.1
Ahern, P.P.2
Ridaura, V.K.3
-
14
-
-
84969704060
-
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
-
14 Browne, H.P., Forster, S.C., Anonye, B.O., et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533:7604 (2016), 543–546.
-
(2016)
Nature
, vol.533
, Issue.7604
, pp. 543-546
-
-
Browne, H.P.1
Forster, S.C.2
Anonye, B.O.3
-
15
-
-
84976469315
-
Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling
-
15 Lau, J.T., Whelan, F.J., Herath, I., et al. Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med, 8(1), 2016, 72.
-
(2016)
Genome Med
, vol.8
, Issue.1
, pp. 72
-
-
Lau, J.T.1
Whelan, F.J.2
Herath, I.3
-
16
-
-
84877020842
-
Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut
-
16 Petrof, E.O., Gloor, G.B., Vanner, S.J., et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome, 1(1), 2013, 3.
-
(2013)
Microbiome
, vol.1
, Issue.1
, pp. 3
-
-
Petrof, E.O.1
Gloor, G.B.2
Vanner, S.J.3
-
17
-
-
30944466824
-
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
-
17 Manichanh, C., Rigottier-Gois, L., Bonnaud, E., et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55:2 (2006), 205–211.
-
(2006)
Gut
, vol.55
, Issue.2
, pp. 205-211
-
-
Manichanh, C.1
Rigottier-Gois, L.2
Bonnaud, E.3
-
18
-
-
84960373289
-
Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease
-
18 Quevrain, E., Maubert, M.A., Michon, C., et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease. Gut 65:3 (2016), 415–425.
-
(2016)
Gut
, vol.65
, Issue.3
, pp. 415-425
-
-
Quevrain, E.1
Maubert, M.A.2
Michon, C.3
-
19
-
-
84866738529
-
Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome
-
19 Vrieze, A., Van Nood, E., Holleman, F., et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143:4 (2012), 913–916.e7.
-
(2012)
Gastroenterology
, vol.143
, Issue.4
, pp. 913-916.e7
-
-
Vrieze, A.1
Van Nood, E.2
Holleman, F.3
-
20
-
-
84877249773
-
Medicines from microbiota
-
20 Olle, B., Medicines from microbiota. Nat Biotechnol 31:4 (2013), 309–315.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.4
, pp. 309-315
-
-
Olle, B.1
-
21
-
-
77951977802
-
Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis
-
21 Salonen, A., Nikkila, J., Jalanka-Tuovinen, J., et al. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81:2 (2010), 127–134.
-
(2010)
J Microbiol Methods
, vol.81
, Issue.2
, pp. 127-134
-
-
Salonen, A.1
Nikkila, J.2
Jalanka-Tuovinen, J.3
-
22
-
-
84921532911
-
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
-
22 Wesolowska-Andersen, A., Bahl, M.I., Carvalho, V., et al. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome, 2, 2014, 19.
-
(2014)
Microbiome
, vol.2
, pp. 19
-
-
Wesolowska-Andersen, A.1
Bahl, M.I.2
Carvalho, V.3
-
23
-
-
69249109724
-
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
-
23 Claesson, M.J., O'Sullivan, O., Wang, Q., et al. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One, 4(8), 2009, e6669.
-
(2009)
PLoS One
, vol.4
, Issue.8
, pp. e6669
-
-
Claesson, M.J.1
O'Sullivan, O.2
Wang, Q.3
-
24
-
-
78650453707
-
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
-
24 Claesson, M.J., Wang, Q., O'Sullivan, O., et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res, 38(22), 2010, e200.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.22
, pp. e200
-
-
Claesson, M.J.1
Wang, Q.2
O'Sullivan, O.3
-
25
-
-
84986538850
-
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
-
25 Gohl, D.M., Vangay, P., Garbe, J., et al. Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies. Nat Biotechnol 34:9 (2016), 942–949.
-
(2016)
Nat Biotechnol
, vol.34
, Issue.9
, pp. 942-949
-
-
Gohl, D.M.1
Vangay, P.2
Garbe, J.3
-
26
-
-
85041651856
-
From sample to Multi-Omics conclusions in under 48 Hours
-
e00038-16
-
26 Quinn, R.A., Navas-Molina, J.A., Hyde, E.R., et al. From sample to Multi-Omics conclusions in under 48 Hours. mSystems, 1(2), 2016 e00038-16.
-
(2016)
mSystems
, vol.1
, Issue.2
-
-
Quinn, R.A.1
Navas-Molina, J.A.2
Hyde, E.R.3
-
27
-
-
84884127512
-
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
-
27 Langille, M.G., Zaneveld, J., Caporaso, J.G., et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:9 (2013), 814–821.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.9
, pp. 814-821
-
-
Langille, M.G.1
Zaneveld, J.2
Caporaso, J.G.3
-
28
-
-
84942895870
-
Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
-
28 Sun, Z., Harris, H.M., McCann, A., et al. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun, 6, 2015, 8322.
-
(2015)
Nat Commun
, vol.6
, pp. 8322
-
-
Sun, Z.1
Harris, H.M.2
McCann, A.3
-
29
-
-
84867192879
-
Intestinal inflammation targets cancer-inducing activity of the microbiota
-
29 Arthur, J.C., Perez-Chanona, E., Muhlbauer, M., et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science 338:6103 (2012), 120–123.
-
(2012)
Science
, vol.338
, Issue.6103
, pp. 120-123
-
-
Arthur, J.C.1
Perez-Chanona, E.2
Muhlbauer, M.3
-
30
-
-
84862286169
-
A framework for human microbiome research
-
30 Consortium HMP. A framework for human microbiome research. Nature 486:7402 (2012), 215–221.
-
(2012)
Nature
, vol.486
, Issue.7402
, pp. 215-221
-
-
-
31
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
31 Qin, J., Li, R., Raes, J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:7285 (2010), 59–65.
-
(2010)
Nature
, vol.464
, Issue.7285
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
-
32
-
-
84924026956
-
Potential of fecal microbiota for early-stage detection of colorectal cancer
-
32 Zeller, G., Tap, J., Voigt, A.Y., et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol, 10, 2014, 766.
-
(2014)
Mol Syst Biol
, vol.10
, pp. 766
-
-
Zeller, G.1
Tap, J.2
Voigt, A.Y.3
-
33
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
33 DeSantis, T.Z., Hugenholtz, P., Larsen, N., et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:7 (2006), 5069–5072.
-
(2006)
Appl Environ Microbiol
, vol.72
, Issue.7
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
-
34
-
-
84891787231
-
Ribosomal Database Project: data and tools for high throughput rRNA analysis
-
34 Cole, J.R., Wang, Q., Fish, J.A., et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:Database issue (2014), D633–D642.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.Database issue
, pp. D633-D642
-
-
Cole, J.R.1
Wang, Q.2
Fish, J.A.3
-
35
-
-
70149090063
-
R: A language and environment for statistical computing
-
R Foundation for Statistical Computing Vienna (Austria)
-
35 R Development Core Team, R: A language and environment for statistical computing. 2013, R Foundation for Statistical Computing, Vienna (Austria).
-
(2013)
-
-
R Development Core Team1
-
36
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
36 Schloss, P.D., Westcott, S.L., Ryabin, T., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:23 (2009), 7537–7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, Issue.23
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
37
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
37 Caporaso, J.G., Kuczynski, J., Stombaugh, J., et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:5 (2010), 335–336.
-
(2010)
Nat Methods
, vol.7
, Issue.5
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
38
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
38 Edgar, R.C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:19 (2010), 2460–2461.
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2460-2461
-
-
Edgar, R.C.1
-
39
-
-
84969871954
-
DADA2: High-resolution sample inference from Illumina amplicon data
-
39 Callahan, B.J., McMurdie, P.J., Rosen, M.J., et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:7 (2016), 581–583.
-
(2016)
Nat Methods
, vol.13
, Issue.7
, pp. 581-583
-
-
Callahan, B.J.1
McMurdie, P.J.2
Rosen, M.J.3
-
40
-
-
84863105536
-
Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease
-
40 Papa, E., Docktor, M., Smillie, C., et al. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One, 7(6), 2012, e39242.
-
(2012)
PLoS One
, vol.7
, Issue.6
, pp. e39242
-
-
Papa, E.1
Docktor, M.2
Smillie, C.3
-
41
-
-
84963525850
-
Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions
-
41 Baxter, N.T., Ruffin, M.T., Rogers, M.A., et al. Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions. Genome Med, 8(1), 2016, 37.
-
(2016)
Genome Med
, vol.8
, Issue.1
, pp. 37
-
-
Baxter, N.T.1
Ruffin, M.T.2
Rogers, M.A.3
-
42
-
-
84910116215
-
The Human Gut Microbiome as a Screening Tool for Colorectal Cancer
-
42 Zackular, J.P., Rogers, M.A., Ruffin, M.T., et al. The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. Cancer Prev Res (Phila) 7:11 (2014), 1112–1121.
-
(2014)
Cancer Prev Res (Phila)
, vol.7
, Issue.11
, pp. 1112-1121
-
-
Zackular, J.P.1
Rogers, M.A.2
Ruffin, M.T.3
-
43
-
-
84946144999
-
Gut mucosal microbiome across stages of colorectal carcinogenesis
-
43 Nakatsu, G., Li, X., Zhou, H., et al. Gut mucosal microbiome across stages of colorectal carcinogenesis. Nat Commun, 6, 2015, 8727.
-
(2015)
Nat Commun
, vol.6
, pp. 8727
-
-
Nakatsu, G.1
Li, X.2
Zhou, H.3
-
44
-
-
84942693814
-
Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
-
[Epub ahead of print]
-
44 Yu, J., Feng, Q., Wong, S.H., et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut, 2015 [Epub ahead of print].
-
(2015)
Gut
-
-
Yu, J.1
Feng, Q.2
Wong, S.H.3
-
45
-
-
84883110880
-
Richness of human gut microbiome correlates with metabolic markers
-
45 Le Chatelier, E., Nielsen, T., Qin, J., et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500:7464 (2013), 541–546.
-
(2013)
Nature
, vol.500
, Issue.7464
, pp. 541-546
-
-
Le Chatelier, E.1
Nielsen, T.2
Qin, J.3
-
46
-
-
84978081339
-
Human gut microbes impact host serum metabolome and insulin sensitivity
-
46 Pedersen, H.K., Gudmundsdottir, V., Nielsen, H.B., et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature 535:7612 (2016), 376–381.
-
(2016)
Nature
, vol.535
, Issue.7612
, pp. 376-381
-
-
Pedersen, H.K.1
Gudmundsdottir, V.2
Nielsen, H.B.3
-
47
-
-
84861578319
-
An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota
-
47 Jeffery, I.B., O'Toole, P.W., Ohman, L., et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 61 (2012), 997–1006.
-
(2012)
Gut
, vol.61
, pp. 997-1006
-
-
Jeffery, I.B.1
O'Toole, P.W.2
Ohman, L.3
|