-
1
-
-
74249119678
-
Obesity and the human microbiome
-
Ley RE. Obesity and the human microbiome. Curr Opin Gastroenterol. 2010;26(1):5-11.
-
(2010)
Curr Opin Gastroenterol.
, vol.26
, Issue.1
, pp. 5-11
-
-
Ley, R.E.1
-
2
-
-
84898809123
-
The microbiome in inflammatory bowel disease: Current status and the future ahead
-
Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology. 2014;146(6):1489-1499.
-
(2014)
Gastroenterology.
, vol.146
, Issue.6
, pp. 1489-1499
-
-
Kostic, A.D.1
Xavier, R.J.2
Gevers, D.3
-
3
-
-
84956777636
-
Epidemiologic studies of the human microbiome and cancer
-
Vogtmann E, Goedert JJ. Epidemiologic studies of the human microbiome and cancer. Br J Cancer. 2016;114(3):237-242.
-
(2016)
Br J Cancer.
, vol.114
, Issue.3
, pp. 237-242
-
-
Vogtmann, E.1
Goedert, J.J.2
-
4
-
-
84924690678
-
Gut microbiome development along the colorectal adenoma-carcinoma sequence
-
Feng Q, Liang S, Jia H, et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat Commun. 2015;6:6528.
-
(2015)
Nat Commun.
, vol.6
, pp. 6528
-
-
Feng, Q.1
Liang, S.2
Jia, H.3
-
5
-
-
84881148921
-
Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults
-
Weir TL, Manter DK, Sheflin AM, et al. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One. 2013;8(8): e70803.
-
(2013)
PLoS One.
, vol.8
, Issue.8
, pp. e70803
-
-
Weir, T.L.1
Manter, D.K.2
Sheflin, A.M.3
-
6
-
-
84880059693
-
Dysbiosis signature of fecal microbiota in colorectal cancer patients
-
Wu N, Yang X, Zhang R, et al. Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb Ecol. 2013; 66(2):462-470.
-
(2013)
Microb Ecol.
, vol.66
, Issue.2
, pp. 462-470
-
-
Wu, N.1
Yang, X.2
Zhang, R.3
-
7
-
-
84924026956
-
Potential of fecal microbiota for early-stage detection of colorectal cancer
-
Zeller G, Tap J, Voigt AY, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol. 2014;10:766.
-
(2014)
Mol Syst Biol.
, vol.10
, pp. 766
-
-
Zeller, G.1
Tap, J.2
Voigt, A.Y.3
-
8
-
-
84891473723
-
Human gut microbiome and risk for colorectal cancer
-
Ahn J, Sinha R, Pei Z, et al. Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst. 2013;105(24): 1907-1911.
-
(2013)
J Natl Cancer Inst.
, vol.105
, Issue.24
, pp. 1907-1911
-
-
Ahn, J.1
Sinha, R.2
Pei, Z.3
-
9
-
-
84942693814
-
Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
-
[published online ahead of print September 25, 2015]
-
Yu J, Feng Q, Wong SH, et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer [published online ahead of print September 25, 2015]. Gut. (doi:10. 1136/gutjnl-2015-309800).
-
Gut.
-
-
Yu, J.1
Feng, Q.2
Wong, S.H.3
-
10
-
-
84957831145
-
Collecting fecal samples for microbiome analyses in epidemiology studies
-
Sinha R, Chen J, Amir A, et al. Collecting fecal samples for microbiome analyses in epidemiology studies. Cancer Epidemiol Biomarkers Prev. 2016;25(2):407-416.
-
(2016)
Cancer Epidemiol Biomarkers Prev.
, vol.25
, Issue.2
, pp. 407-416
-
-
Sinha, R.1
Chen, J.2
Amir, A.3
-
11
-
-
84863981120
-
Ultra-highthroughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso JG, Lauber CL, Walters WA, et al. Ultra-highthroughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621-1624.
-
(2012)
ISME J.
, vol.6
, Issue.8
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
-
12
-
-
79954506754
-
PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers
-
Walters WA, Caporaso JG, Lauber CL, et al. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics. 2011;27(8): 1159-1161.
-
(2011)
Bioinformatics.
, vol.27
, Issue.8
, pp. 1159-1161
-
-
Walters, W.A.1
Caporaso, J.G.2
Lauber, C.L.3
-
13
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335-336.
-
(2010)
Nat Methods.
, vol.7
, Issue.5
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
-
14
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7): 5069-5072.
-
(2006)
Appl Environ Microbiol.
, vol.72
, Issue.7
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
-
15
-
-
58149200948
-
The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
-
Database issue
-
Cole JR, Wang Q, Cardenas E, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37(Database issue): D141-D145.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D141-D145
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
-
16
-
-
84876427223
-
Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data
-
McMurdie PJ, Holmes S. phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217.
-
(2013)
PLoS One.
, vol.8
, Issue.4
, pp. e61217
-
-
McMurdie, P.J.1
Holmes, S.2
-
17
-
-
84865082160
-
Associating microbiome composition with environmental covariates using generalized UniFrac distances
-
Chen J, Bittinger K, Charlson ES, et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics. 2012;28(16):2106-2113.
-
(2012)
Bioinformatics.
, vol.28
, Issue.16
, pp. 2106-2113
-
-
Chen, J.1
Bittinger, K.2
Charlson, E.S.3
-
18
-
-
84864344549
-
Storage conditions of intestinal microbiota matter in metagenomic analysis
-
Cardona S, Eck A, Cassellas M, et al. Storage conditions of intestinal microbiota matter in metagenomic analysis. BMC Microbiol. 2012;12:158.
-
(2012)
BMC Microbiol.
, vol.12
, pp. 158
-
-
Cardona, S.1
Eck, A.2
Cassellas, M.3
-
19
-
-
84867177603
-
Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage
-
Carroll IM, Ringel-Kulka T, Siddle JP, et al. Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage. PLoS One. 2012;7(10):e46953.
-
(2012)
PLoS One.
, vol.7
, Issue.10
, pp. e46953
-
-
Carroll, I.M.1
Ringel-Kulka, T.2
Siddle, J.P.3
-
20
-
-
84947460747
-
Sample storage conditions significantly influence faecal microbiome profiles
-
Choo JM, Leong LE, Rogers GB. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep. 2015;5:16350.
-
(2015)
Sci Rep.
, vol.5
, pp. 16350
-
-
Choo, J.M.1
Leong, L.E.2
Rogers, G.B.3
-
21
-
-
84899898655
-
Comparison of methods for fecal microbiome biospecimen collection
-
Dominianni C, Wu J, Hayes RB, et al. Comparison of methods for fecal microbiome biospecimen collection. BMC Microbiol. 2014;14:103.
-
(2014)
BMC Microbiol.
, vol.14
, pp. 103
-
-
Dominianni, C.1
Wu, J.2
Hayes, R.B.3
-
22
-
-
84965141050
-
Collection media and delayed freezing effects on microbial composition of human stool
-
Flores R, Shi J, Yu G, et al. Collection media and delayed freezing effects on microbial composition of human stool. Microbiome. 2015;3:33.
-
(2015)
Microbiome.
, vol.3
, pp. 33
-
-
Flores, R.1
Shi, J.2
Yu, G.3
-
23
-
-
84901847186
-
Relating the metatranscriptome and metagenome of the human gut
-
Franzosa EA, Morgan XC, Segata N, et al. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA. 2014;111(22):E2329-E2338.
-
(2014)
Proc Natl Acad Sci USA.
, vol.111
, Issue.22
, pp. E2329-E2338
-
-
Franzosa, E.A.1
Morgan, X.C.2
Segata, N.3
-
24
-
-
84941985499
-
Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool
-
Gorzelak MA, Gill SK, Tasnim N, et al. Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool. PLoS One. 2015;10(8):e0134802.
-
(2015)
PLoS One.
, vol.10
, Issue.8
, pp. e0134802
-
-
Gorzelak, M.A.1
Gill, S.K.2
Tasnim, N.3
-
25
-
-
77951941062
-
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples
-
Lauber CL, Zhou N, Gordon JI, et al. Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. FEMS Microbiol Lett. 2010;307(1):80-86.
-
(2010)
FEMS Microbiol Lett.
, vol.307
, Issue.1
, pp. 80-86
-
-
Lauber, C.L.1
Zhou, N.2
Gordon, J.I.3
-
26
-
-
38049080602
-
Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces
-
Nechvatal JM, Ram JL, Basson MD, et al. Fecal collection, ambient preservation, and DNA extraction for PCR amplification of bacterial and human markers from human feces. J Microbiol Methods. 2008;72(2):124-132.
-
(2008)
J Microbiol Methods.
, vol.72
, Issue.2
, pp. 124-132
-
-
Nechvatal, J.M.1
Ram, J.L.2
Basson, M.D.3
-
27
-
-
9944245052
-
In vitro alterations of intestinal bacterial microbiota in fecal samples during storage
-
Ott SJ, Musfeldt M, Timmis KN, et al. In vitro alterations of intestinal bacterial microbiota in fecal samples during storage. Diagn Microbiol Infect Dis. 2004;50(4):237-245.
-
(2004)
Diagn Microbiol Infect Dis.
, vol.50
, Issue.4
, pp. 237-245
-
-
Ott, S.J.1
Musfeldt, M.2
Timmis, K.N.3
-
28
-
-
85056036546
-
Influence of fecal sample storage on bacterial community diversity
-
Roesch LF, Casella G, Simell O, et al. Influence of fecal sample storage on bacterial community diversity. Open Microbiol J. 2009;3:40-46.
-
(2009)
Open Microbiol J.
, vol.3
, pp. 40-46
-
-
Roesch, L.F.1
Casella, G.2
Simell, O.3
-
29
-
-
84935022171
-
The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects
-
Tedjo DI, Jonkers DM, Savelkoul PH, et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PLoS One. 2015;10(5): e0126685.
-
(2015)
PLoS One.
, vol.10
, Issue.5
, pp. e0126685
-
-
Tedjo, D.I.1
Jonkers, D.M.2
Savelkoul, P.H.3
-
30
-
-
84939179628
-
Temporal and technical variability of human gut metagenomes
-
Voigt AY, Costea PI, Kultima JR, et al. Temporal and technical variability of human gut metagenomes. Genome Biol. 2015;16:73.
-
(2015)
Genome Biol.
, vol.16
, pp. 73
-
-
Voigt, A.Y.1
Costea, P.I.2
Kultima, J.R.3
-
31
-
-
77955067191
-
Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
-
Wu GD, Lewis JD, Hoffmann C, et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010;10:206.
-
(2010)
BMC Microbiol.
, vol.10
, pp. 206
-
-
Wu, G.D.1
Lewis, J.D.2
Hoffmann, C.3
-
32
-
-
84982224114
-
Preservation methods differ in fecal microbiome stability, affecting suitability for field studies
-
Song SJ, Amir A, Metcalf JL, et al. Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems. 2016;1(3):e00021-00016.
-
(2016)
MSystems.
, vol.1
, Issue.3
, pp. e00021-00016
-
-
Song, S.J.1
Amir, A.2
Metcalf, J.L.3
-
33
-
-
84995801941
-
DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model
-
Baxter NT, Koumpouras CC, Rogers MA, et al. DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model. Microbiome. 2016;4(1):59.
-
(2016)
Microbiome.
, vol.4
, Issue.1
, pp. 59
-
-
Baxter, N.T.1
Koumpouras, C.C.2
Rogers, M.A.3
-
35
-
-
84858709310
-
Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
-
Bahl MI, Bergström A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett. 2012;329(2):193-197.
-
(2012)
FEMS Microbiol Lett.
, vol.329
, Issue.2
, pp. 193-197
-
-
Bahl, M.I.1
Bergström, A.2
Licht, T.R.3
-
36
-
-
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. 2012;486(7402):207-214.
-
(2012)
Nature.
, vol.486
, Issue.7402
, pp. 207-214
-
-
|