-
1
-
-
22144490199
-
An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system
-
DOI 10.1016/j.cell.2005.05.007, PII S0092867405004514
-
Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107-118 (2005). (Pubitemid 40977944)
-
(2005)
Cell
, vol.122
, Issue.1
, pp. 107-118
-
-
Mazmanian, S.K.1
Cui, H.L.2
Tzianabos, A.O.3
Kasper, D.L.4
-
2
-
-
15544369658
-
Hostbacterial mutualism in the human intestine
-
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A. & Gordon, J. I. Hostbacterial mutualism in the human intestine. Science 307, 1915-1920 (2005).
-
(2005)
Science
, vol.307
, pp. 1915-1920
-
-
Bäckhed, F.1
Ley, R.E.2
Sonnenburg, J.L.3
Peterson, D.A.4
Gordon, J.I.5
-
3
-
-
21844444279
-
Periodontal disease and coronary heart disease: A reappraisal of the exposure
-
DOI 10.1161/CIRCULATIONAHA.104.511998
-
Beck, J. D. et al. Periodontal disease and coronary heart disease: a reappraisal of the exposure. Circulation 112, 19-24 (2005). (Pubitemid 40962564)
-
(2005)
Circulation
, vol.112
, Issue.1
, pp. 19-24
-
-
Beck, J.D.1
Eke, P.2
Heiss, G.3
Madianos, P.4
Couper, D.5
Lin, D.6
Moss, K.7
Elter, J.8
Offenbacher, S.9
-
4
-
-
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. U. S. A. 105, 16731-16736 (2008).
-
(2008)
Proc. Natl. Acad. Sci. U. S. A
, vol.105
, pp. 16731-16736
-
-
Sokol, H.1
-
5
-
-
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
-
6
-
-
80051535923
-
The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice
-
Bercik, P. et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology 141, 599-609 (2011).
-
(2011)
Gastroenterology
, vol.141
, pp. 599-609
-
-
Bercik, P.1
-
7
-
-
78149501207
-
Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice
-
Bercik, P. et al. Chronic gastrointestinal inflammation induces anxiety-like behavior and alters central nervous system biochemistry in mice. Gastroenterology 139, 2102-2112 (2010).
-
(2010)
Gastroenterology
, vol.139
, pp. 2102-2112
-
-
Bercik, P.1
-
8
-
-
77957357555
-
The human oral microbiome
-
Dewhirst, F. E. et al. The human oral microbiome. J. Bacteriol. 192, 5002-5017 (2010).
-
(2010)
J. Bacteriol
, vol.192
, pp. 5002-5017
-
-
Dewhirst, F.E.1
-
9
-
-
70449530747
-
Metagenomic study of the oral microbiota by Illumina highthroughput sequencing
-
Lazarevic, V. et al. Metagenomic study of the oral microbiota by Illumina highthroughput sequencing. J. Microbiol. Meth. 79, 266-271 (2009).
-
(2009)
J. Microbiol. Meth
, vol.79
, pp. 266-271
-
-
Lazarevic, V.1
-
10
-
-
34547129847
-
Development of the human infant intestinal microbiota
-
Palmer, C., Bik, E. M., DiGiulio, D. B., Relman, D. A. & Brown, P. O. Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 (2007).
-
(2007)
PLoS Biol
, vol.5
-
-
Palmer, C.1
Bik, E.M.2
Digiulio, D.B.3
Relman, D.A.4
Brown, P.O.5
-
11
-
-
77955386857
-
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
-
Dominguez-Bello, M. G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. U. S. A. 107, 11971-11975 (2010).
-
(2010)
Proc. Natl. Acad. Sci. U. S. A
, vol.107
, pp. 11971-11975
-
-
Dominguez-Bello, M.G.1
-
12
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P. 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.1
-
13
-
-
58149218590
-
Pyrosequencing analysis of the oral microflora of healthy adults
-
Keijser, B. J. F. et al. Pyrosequencing analysis of the oral microflora of healthy adults. J. Dent. Res. 87, 1016-1020 (2008).
-
(2008)
J. Dent. Res
, vol.87
, pp. 1016-1020
-
-
Keijser, B.J.F.1
-
14
-
-
78649686679
-
A pyrosequencing study in twins shows that GImicrobial profiles vary with inflammatory bowel disease phenotypes
-
Willing, B. et al. A pyrosequencing study in twins shows that GImicrobial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844-1854 (2010).
-
(2010)
Gastroenterology
, vol.139
, pp. 1844-1854
-
-
Willing, B.1
-
15
-
-
79951895603
-
Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease?
-
Wade, W. G. Has the use of molecular methods for the characterization of the human oral microbiome changed our understanding of the role of bacteria in the pathogenesis of periodontal disease? J. Clin. Periodont. 38, 7-16 (2011).
-
(2011)
J. Clin. Periodont
, vol.38
, pp. 7-16
-
-
Wade, W.G.1
-
16
-
-
31444449652
-
Molecular analysis of the bacterial microbiota in the human stomach
-
DOI 10.1073/pnas.0506655103
-
Bik, E. M. et al. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U. S. A. 103, 732-737 (2006). (Pubitemid 43153094)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.3
, pp. 732-737
-
-
Bik, E.M.1
Eckburg, P.B.2
Gill, S.R.3
Nelson, K.E.4
Purdom, E.A.5
Francois, F.6
Perez-Perez, G.7
Blaser, M.J.8
Relman, D.A.9
-
17
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello, E. K. et al. Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697 (2009).
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
-
18
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
Grice, E. A. et al. Topographical and temporal diversity of the human skin microbiome. Science 324, 1190-1192 (2009).
-
(2009)
Science
, vol.324
, pp. 1190-1192
-
-
Grice, E.A.1
-
19
-
-
56649124715
-
The influence of sex, handedness, and washing on the diversity of hand surface bacteria
-
Fierer, N., Hamady, M., Lauber, C. L. & Knight, R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 17994-17999 (2008).
-
(2008)
Proc. Natl. Acad. Sci. U. S. A
, vol.105
, pp. 17994-17999
-
-
Fierer, N.1
Hamady, M.2
Lauber, C.L.3
Knight, R.4
-
20
-
-
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
-
-
Caporaso, J.G.1
-
21
-
-
50949131523
-
Comparative analysis of human gut microbiota by barcoded pyrosequencing
-
Andersson, A. F. et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3, e2836 (2008).
-
(2008)
PLoS ONE
, vol.3
-
-
Andersson, A.F.1
-
22
-
-
79958265126
-
Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads
-
Bartram, A. K., Lynch, M. D. J., Stearns, J. C., Moreno-Hagelsieb, G. & Neufeld, J. D. Generation of multi-million 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads. Appl. Environ. Microbiol. 77, 3846-3852 (2011).
-
(2011)
Appl. Environ. Microbiol
, vol.77
, pp. 3846-3852
-
-
Bartram, A.K.1
Lynch, M.D.J.2
Stearns, J.C.3
Moreno-Hagelsieb, G.4
Neufeld, J.D.5
-
23
-
-
77955251092
-
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
-
Huse, S., Welch, D., Morrison, H. & Sogin, M. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889-1898 (2010).
-
(2010)
Environ. Microbiol
, vol.12
, pp. 1889-1898
-
-
Huse, S.1
Welch, D.2
Morrison, H.3
Sogin, M.4
-
24
-
-
33745634395
-
Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
-
DOI 10.1093/bioinformatics/btl158
-
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658-1659 (2006). (Pubitemid 43985301)
-
(2006)
Bioinformatics
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
25
-
-
78149429458
-
Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products
-
Gloor, G. et al. Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE e15406 (2010).
-
(2010)
PLoS ONE
-
-
Gloor, G.1
-
26
-
-
23344442120
-
Obesity alters gut microbial ecology
-
DOI 10.1073/pnas.0504978102
-
Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. U. S. A. 102, 11070-11075 (2005). (Pubitemid 41105994)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.31
, pp. 11070-11075
-
-
Ley, R.E.1
Backhed, F.2
Turnbaugh, P.3
Lozupone, C.A.4
Knight, R.D.5
Gordon, J.I.6
-
27
-
-
20544444045
-
Microbiology: Diversity of the human intestinal microbial flora
-
DOI 10.1126/science.1110591
-
Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635-1638 (2005). (Pubitemid 40807514)
-
(2005)
Science
, vol.308
, Issue.5728
, pp. 1635-1638
-
-
Eckburg, P.B.1
Bik, E.M.2
Bernstein, C.N.3
Purdom, E.4
Dethlefsen, L.5
Sargent, M.6
Gill, S.R.7
Nelson, K.E.8
Relman, D.A.9
-
28
-
-
23744440709
-
A dynamic partnership: Celebrating our gut flora
-
DOI 10.1016/j.anaerobe.2005.05.001, PII S1075996405000685
-
Sears, C. L. A dynamic partnership: celebrating our gut flora. Anaerobe 11, 247-251 (2005). (Pubitemid 41138226)
-
(2005)
Anaerobe
, vol.11
, Issue.5
, pp. 247-251
-
-
Sears, C.L.1
-
29
-
-
77954834323
-
Bacterial diversity in the oral cavity of 10 healthy individuals
-
Bik, E. M. et al. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J 4, 962-974 (2010).
-
(2010)
ISME J
, vol.4
, pp. 962-974
-
-
Bik, E.M.1
-
30
-
-
84859776493
-
The oral metagenome in health and disease
-
In press
-
Belda-Ferre, P. et al. The oral metagenome in health and disease. ISME J In press (2011).
-
(2011)
ISME J
-
-
Belda-Ferre, P.1
-
31
-
-
77958056493
-
Analysis of oral microbiota in children with dental caries by PCRDGGE and barcoded pyrosequencing
-
Ling, Z. et al. Analysis of oral microbiota in children with dental caries by PCRDGGE and barcoded pyrosequencing. Microb. Ecol. 60, 677-690 (2010).
-
(2010)
Microb. Ecol
, vol.60
, pp. 677-690
-
-
Ling, Z.1
-
32
-
-
77956266605
-
The noncolonic microbiome: Does it really matter?
-
Lawson, R. D. & Coyle, W. J. The noncolonic microbiome: does it really matter? Curr. Gastroenterol. Rep. 12, 259-262 (2010).
-
(2010)
Curr. Gastroenterol. Rep
, vol.12
, pp. 259-262
-
-
Lawson, R.D.1
Coyle, W.J.2
-
33
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
-
Kunin, V., Engelbrektson, A., Ochman, H. & Hugenholtz, P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12, 118-123 (2010).
-
(2010)
Environ. Microbiol
, vol.12
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
34
-
-
0037425743
-
Gut flora in health and disease
-
DOI 10.1016/S0140-6736(03)12489-0
-
Guarner, F. & Malagelada, J. R. Gut flora in health and disease. The Lancet 361, 512-519 (2003). (Pubitemid 36173720)
-
(2003)
Lancet
, vol.361
, Issue.9356
, pp. 512-519
-
-
Guarner, F.1
Malagelada, J.-R.2
-
35
-
-
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
-
36
-
-
79959299471
-
In search of an uncultured human-associated TM7 bacterium in the environment
-
Dinis, J. M. et al. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS ONE 6, e21280 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Dinis, J.M.1
-
37
-
-
0034992657
-
Bacterial diversity in human subgingival plaque
-
DOI 10.1128/JB.183.12.3770-3783.2001
-
Paster, B. J. et al. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183, 3770-3783 (2001). (Pubitemid 32510445)
-
(2001)
Journal of Bacteriology
, vol.183
, Issue.12
, pp. 3770-3783
-
-
Paster, B.J.1
Boches, S.K.2
Galvin, J.L.3
Ericson, R.E.4
Lau, C.N.5
Levanos, V.A.6
Sahasrabudhe, A.7
Dewhirst, F.E.8
-
38
-
-
12244254440
-
Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients
-
DOI 10.1128/JCM.41.2.558-563.2003
-
Kazor, C. E. et al. Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J. Clin. Microbiol. 41, 558-563 (2003). (Pubitemid 36184161)
-
(2003)
Journal of Clinical Microbiology
, vol.41
, Issue.2
, pp. 558-563
-
-
Kazor, C.E.1
Mitchell, P.M.2
Lee, A.M.3
Stokes, L.N.4
Loesche, W.J.5
Dewhirst, F.E.6
Paster, B.J.7
-
39
-
-
0038050412
-
New bacterial species associated with chronic periodontitis
-
Kumar, P. S. et al. New bacterial species associated with chronic periodontitis. J. Dent. Res. 82, 338-344 (2003). (Pubitemid 41756823)
-
(2003)
Journal of Dental Research
, vol.82
, Issue.5
, pp. 338-344
-
-
Kumar, P.S.1
Griffen, A.L.2
Barton, J.A.3
Paster, B.J.4
Moeschberger, M.L.5
Leys, E.J.6
-
40
-
-
1642488364
-
Bacterial biota in the human distal esophagus
-
DOI 10.1073/pnas.0306398101
-
Pei, Z. et al. Bacterial biota in the human distal esophagus. Proc. Natl. Acad. Sci. U. S. A. 101, 4250-4255 (2004). (Pubitemid 38405915)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.12
, pp. 4250-4255
-
-
Pei, Z.1
Bini, E.J.2
Yang, L.3
Zhou, M.4
Francois, F.5
Blaser, M.J.6
-
41
-
-
57749194898
-
Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease
-
Kuehbacher, T. et al. Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J. Med. Microbiol. 57, 1569-1576 (2008).
-
(2008)
J. Med. Microbiol
, vol.57
, pp. 1569-1576
-
-
Kuehbacher, T.1
-
42
-
-
35348852708
-
Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis
-
DOI 10.1128/JCM.01272-07
-
Fredricks, D. N., Fiedler, T. L., Thomas, K. K., Oakley, B. B. & Marrazzo, J. M. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. J. Clin. Microbiol. 45, 3270-3276 (2007). (Pubitemid 47585650)
-
(2007)
Journal of Clinical Microbiology
, vol.45
, Issue.10
, pp. 3270-3276
-
-
Fredricks, D.N.1
Fiedler, T.L.2
Thomas, K.K.3
Oakley, B.B.4
Marrazzo, J.M.5
-
43
-
-
33847305053
-
Molecular analysis of human forearm superficial skin bacterial biota
-
DOI 10.1073/pnas.0607077104
-
Gao, Z., Tseng, C.-h., Pei, Z. & Blaser, M. J. Molecular analysis of human forearm superficial skin bacterial biota. Proc. Natl. Acad. Sci. U. S. A. 104, 2927-2932 (2007). (Pubitemid 46327980)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.8
, pp. 2927-2932
-
-
Gao, Z.1
Tseng, C.-H.2
Pei, Z.3
Blaser, M.J.4
-
44
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere"
-
DOI 10.1073/pnas.0605127103
-
Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored "rare biosphere" Proc. Natl. Acad. Sci. U. S. A. 103, 12115-12120 (2006). (Pubitemid 44215820)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.32
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, S.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
45
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
DOI 10.1128/AEM.00062-07
-
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Na?̈ve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007). (Pubitemid 47326658)
-
(2007)
Applied and Environmental Microbiology
, vol.73
, Issue.16
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
46
-
-
0003416694
-
-
(eds E. Stackebrandt & M. Goodfellow) (John Wiley & Sons, Inc)
-
Lane, D. J. in Nucleic acid techniques in bacterial systematics. (eds E. Stackebrandt & M. Goodfellow) 115-175 (John Wiley & Sons, Inc, 1991).
-
(1991)
Nucleic Acid Techniques in Bacterial Systematics
, pp. 115-175
-
-
Lane, D.J.1
-
47
-
-
0027460328
-
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
-
Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59, 695-700 (1993). (Pubitemid 23072343)
-
(1993)
Applied and Environmental Microbiology
, vol.59
, Issue.3
, pp. 695-700
-
-
Muyzer, G.1
De Waal, E.C.2
Uitterlinden, A.G.3
-
48
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
51
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72, 5069-5072 (2006).
-
(2006)
Appl. Environ. Microbiol
, vol.72
, pp. 5069-5072
-
-
Desantis, T.Z.1
-
52
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
53
-
-
67649327176
-
FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641-1650 (2009).
-
(2009)
Mol. Biol. Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
54
-
-
84859761611
-
-
v1 3. 1. Institute of Evolutionary Biology, University of Edinburgh
-
Rambaut, A. & Drummond, A. FigTree v1. 3. 1. Institute of Evolutionary Biology, University of Edinburgh (2010).
-
(2010)
Fig Tree
-
-
Rambaut, A.1
Drummond, A.2
|