-
1
-
-
1542316379
-
Bacterial contributions to mammalian gut development
-
Hooper LV. 2004. Bacterial contributions to mammalian gut development. Trends Microbiol. 12:129-134. http://dx.doi.org/10.1016/j.tim.2004.01.001.
-
(2004)
Trends Microbiol.
, vol.12
, pp. 129-134
-
-
Hooper, L.V.1
-
2
-
-
2942625911
-
Interactions between commensal intestinal bacteria and the immune system
-
Macpherson AJ, Harris NL. 2004. Interactions between commensal intestinal bacteria and the immune system. Nat. Rev. Immunol. 4:478-485. http://dx.doi.org/10.1038/nri1373.
-
(2004)
Nat. Rev. Immunol.
, vol.4
, pp. 478-485
-
-
Macpherson, A.J.1
Harris, N.L.2
-
3
-
-
70349384799
-
Intestinal microflora and metabolic diseases
-
Serino M, Luche E, Chabo C, Amar J, Burcelin R. 2009. Intestinal microflora and metabolic diseases. Diabetes Metab. 35:262-272. http://dx.doi.org/10.1016/j.diabet.2009.03.003.
-
(2009)
Diabetes Metab.
, vol.35
, pp. 262-272
-
-
Serino, M.1
Luche, E.2
Chabo, C.3
Amar, J.4
Burcelin, R.5
-
4
-
-
84864780633
-
Host responses to the human microbiome
-
Backhed F. 2012. Host responses to the human microbiome. Nutr. Rev. 70(Suppl 1):S14-S17. http://dx.doi.org/10.1111/j.1753-4887.2012.00496.x.
-
(2012)
Nutr. Rev.
, vol.70
, Issue.SUPPL. 1
-
-
Backhed, F.1
-
5
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium,
-
Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214. http: //dx.doi.org/10.1038/nature11234.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
6
-
-
84878699293
-
The role of gut microbiota in the pathogenesis of colorectal cancer
-
Zhu Q, Gao R, Wu W, Qin H. 2013. The role of gut microbiota in the pathogenesis of colorectal cancer. Tumour Biol. 34:1285-1300. http://dx.doi.org/10.1007/s13277-013-0684-4.
-
(2013)
Tumour Biol.
, vol.34
, pp. 1285-1300
-
-
Zhu, Q.1
Gao, R.2
Wu, W.3
Qin, H.4
-
7
-
-
31444449652
-
Molecular analysis of the bacterial microbiota in the human stomach
-
Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA. 2006. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U. S. A. 103:732-737. http://dx.doi.org/10.1073/pnas.0506655103.
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, 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
-
8
-
-
84858591675
-
Evidence of uncultivated bacteria in the adult female bladder
-
Wolfe AJ, Toh E, Shibata N, Rong R, Kenton K, Fitzgerald M, Mueller ER, Schreckenberger P, Dong Q, Nelson DE, Brubaker L. 2012. Evidence of uncultivated bacteria in the adult female bladder. J. Clin. Microbiol. 50:1376-1383. http://dx.doi.org/10.1128/JCM.05852-11.
-
(2012)
J. Clin. Microbiol.
, vol.50
, pp. 1376-1383
-
-
Wolfe, A.J.1
Toh, E.2
Shibata, N.3
Rong, R.4
Kenton, K.5
Fitzgerald, M.6
Mueller, E.R.7
Schreckenberger, P.8
Dong, Q.9
Nelson, D.E.10
Brubaker, L.11
-
9
-
-
84866433160
-
The microbiome of the lung
-
Beck JM, Young VB, Huffnagle GB. 2012. The microbiome of the lung. Transl. Res. 160:258-266. http://dx.doi.org/10.1016/j.trsl.2012.02.005.
-
(2012)
Transl. Res.
, vol.160
, pp. 258-266
-
-
Beck, J.M.1
Young, V.B.2
Huffnagle, G.B.3
-
10
-
-
84863587947
-
Breast, milk and microbes: a complex relationship that does not end with lactation
-
Urbaniak C, Burton JP, Reid G. 2012. Breast, milk and microbes: a complex relationship that does not end with lactation. Womens Health (Lond. Engl.). 8:385-398. http://dx.doi.org/10.2217/whe.12.23.
-
(2012)
Womens Health (Lond. Engl.).
, vol.8
, pp. 385-398
-
-
Urbaniak, C.1
Burton, J.P.2
Reid, G.3
-
11
-
-
0842303407
-
Ultrasound imaging of milk ejection in the breast of lactating women
-
Ramsay DT, Kent JC, Owens RA, Hartmann PE. 2004. Ultrasound imaging of milk ejection in the breast of lactating women. Pediatrics 113: 361-367. http://dx.doi.org/10.1542/peds.113.2.361.
-
(2004)
Pediatrics
, vol.113
, pp. 361-367
-
-
Ramsay, D.T.1
Kent, J.C.2
Owens, R.A.3
Hartmann, P.E.4
-
12
-
-
77957367977
-
Potential role of the intestinal microbiota of the mother in neonatal immune education
-
Donnet-Hughes A, Perez PF, Dore J, Leclerc M, Levenez F, Benyacoub J, Serrant P, Segura-Roggero I, Schiffrin EJ. 2010. Potential role of the intestinal microbiota of the mother in neonatal immune education. Proc. Nutr. Soc. 69:407-415. http://dx.doi.org/10.1017/S0029665110001898.
-
(2010)
Proc. Nutr. Soc.
, vol.69
, pp. 407-415
-
-
Donnet-Hughes, A.1
Perez, P.F.2
Dore, J.3
Leclerc, M.4
Levenez, F.5
Benyacoub, J.6
Serrant, P.7
Segura-Roggero, I.8
Schiffrin, E.J.9
-
13
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461. http://dx.doi.org/10.1093/bioin formatics/btq461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
14
-
-
58149200948
-
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
-
Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed- Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145. http://dx.doi.org/10.1093/nar/gkn879.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
Kulam-Syed-Mohideen, A.S.7
McGarrell, D.M.8
Marsh, T.9
Garrity, G.M.10
Tiedje, J.M.11
-
15
-
-
33746061683
-
Greengenes, a chimerachecked,16S rRNA gene database and workbench compatible with ARB
-
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimerachecked
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
16
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336. http://dx.doi.org/10.1038/nmeth.f.303.
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Pena, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
Huttley, G.A.11
Kelley, S.T.12
Knights, D.13
Koenig, J.E.14
Ley, R.E.15
Lozupone, C.A.16
McDonald, D.17
Muegge, B.D.18
Pirrung, M.19
Reeder, J.20
Sevinsky, J.R.21
Turnbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
17
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price MN, Dehal PS, Arkin AP. 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26:1641-1650. http://dx.doi.org/10.1093/molbev/msp077.
-
(2009)
Mol. Biol. Evol.
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
18
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. http://dx.doi.org/10.1186/1471-2105-5-113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
19
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228- 8235. http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
20
-
-
0037314132
-
Using ecological diversity measures with bacterial communities
-
Hill TC, Walsh KA, Harris JA, Moffett BF. 2003. Using ecological diversity measures with bacterial communities. FEMS Microbiol. Ecol. 43:1-11. http://dx.doi.org/10.1111/j.1574-6941.2003.tb01040.x.
-
(2003)
FEMS Microbiol. Ecol.
, vol.43
, pp. 1-11
-
-
Hill, T.C.1
Walsh, K.A.2
Harris, J.A.3
Moffett, B.F.4
-
21
-
-
84863304598
-
-
R Development Core Team, R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team. 2006. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2006)
R: a language and environment for statistical computing
-
-
-
22
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
23
-
-
84862197046
-
Analyses of the microbial diversity across the human microbiome
-
Li K, Bihan M, Yooseph S, Methe BA. 2012. Analyses of the microbial diversity across the human microbiome. PLoS One 7:e32118. http://dx.doi.org/10.1371/journal.pone.0032118.
-
(2012)
PLoS One
, vol.7
-
-
Li, K.1
Bihan, M.2
Yooseph, S.3
Methe, B.A.4
-
24
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
-
Dethlefsen L, Huse S, Sogin ML, Relman DA. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:e280. http://dx.doi.org/10.1371/journal.pbio.0060280.
-
(2008)
PLoS Biol.
, vol.6
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
25
-
-
77954834323
-
Bacterial diversity in the oral cavity of 10 healthy individuals
-
Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, Nelson KE, Gill SR, Fraser-Liggett CM, Relman DA. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. ISME J. 4:962-974. http://dx.doi.org/10.1038/ismej.2010.30.
-
(2010)
ISME J.
, vol.4
, pp. 962-974
-
-
Bik, E.M.1
Long, C.D.2
Armitage, G.C.3
Loomer, P.4
Emerson, J.5
Mongodin, E.F.6
Nelson, K.E.7
Gill, S.R.8
Fraser-Liggett, C.M.9
Relman, D.A.10
-
26
-
-
79952756960
-
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
-
Dethlefsen L, Relman DA. 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl 1):4554-4561. http://dx.doi.org/10.1073/pnas.1000087107.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.SUPPL. 1
, pp. 4554-4561
-
-
Dethlefsen, L.1
Relman, D.A.2
-
27
-
-
79952750340
-
Vaginal microbiome of reproductiveage women
-
Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. 2011. Vaginal microbiome of reproductiveage women. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl 1):4680-4687. http://dx.doi.org/10.1073/pnas.1002611107.
-
(2011)
Proc. Natl. Acad. Sci. U. S. A.
, vol.108
, Issue.SUPPL. 1
, pp. 4680-4687
-
-
Ravel, J.1
Gajer, P.2
Abdo, Z.3
Schneider, G.M.4
Koenig, S.S.5
McCulle, S.L.6
Karlebach, S.7
Gorle, R.8
Russell, J.9
Tacket, C.O.10
Brotman, R.M.11
Davis, C.C.12
Ault, K.13
Peralta, L.14
Forney, L.J.15
-
28
-
-
65249096027
-
Heterogeneity of vaginal microbial communities within individuals
-
Kim TK, Thomas SM, Ho M, Sharma S, Reich CI, Frank JA, Yeater KM, Biggs DR, Nakamura N, Stumpf R, Leigh SR, Tapping RI, Blanke SR, Slauch JM, Gaskins HR, Weisbaum JS, Olsen GJ, Hoyer LL, Wilson BA.
-
(2009)
J. Clin. Microbiol.
, vol.47
, pp. 1181-1189
-
-
Kim, T.K.1
Thomas, S.M.2
Ho, M.3
Sharma, S.4
Reich, C.I.5
Frank, J.A.6
Yeater, K.M.7
Biggs, D.R.8
Nakamura, N.9
Stumpf, R.10
Leigh, S.R.11
Tapping, R.I.12
Blanke, S.R.13
Slauch, J.M.14
Gaskins, H.R.15
Weisbaum, J.S.16
Olsen, G.J.17
Hoyer, L.L.18
Wilson, B.A.19
-
29
-
-
49449109115
-
Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis
-
Oakley BB, Fiedler TL, Marrazzo JM, Fredricks DN. 2008. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl. Environ. Microbiol. 74:4898-4909. http://dx.doi.org/10.1128/AEM.02884-07.
-
(2008)
Appl. Environ. Microbiol.
, vol.74
, pp. 4898-4909
-
-
Oakley, B.B.1
Fiedler, T.L.2
Marrazzo, J.M.3
Fredricks, D.N.4
-
30
-
-
84897449654
-
Microbial dysbiosis is associated with human breast cancer
-
Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA, Lee DJ. 2014. Microbial dysbiosis is associated with human breast cancer. PLoS One 9:e83744. http://dx.doi.org/10.1371/journal.pone.0083744.
-
(2014)
PLoS One
, vol.9
-
-
Xuan, C.1
Shamonki, J.M.2
Chung, A.3
Dinome, M.L.4
Chung, M.5
Sieling, P.A.6
Lee, D.J.7
-
31
-
-
77957865300
-
Deep sequencing of the vaginal microbiota of women with HIV
-
Hummelen R, Fernandes AD, Macklaim JM, Dickson RJ, Changalucha J, Gloor GB, Reid G. 2010. Deep sequencing of the vaginal microbiota of women with HIV. PLoS One 5:e12078. http://dx.doi.org/10.1371/journal.pone.0012078.
-
(2010)
PLoS One
, vol.5
-
-
Hummelen, R.1
Fernandes, A.D.2
Macklaim, J.M.3
Dickson, R.J.4
Changalucha, J.5
Gloor, G.B.6
Reid, G.7
-
32
-
-
77957357555
-
The human oral microbiome
-
Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. 2010. The human oral microbiome. J. Bacteriol. 192:5002-5017. http://dx.doi.org/10.1128/JB.00542-10.
-
(2010)
J. Bacteriol.
, vol.192
, pp. 5002-5017
-
-
Dewhirst, F.E.1
Chen, T.2
Izard, J.3
Paster, B.J.4
Tanner, A.C.5
Yu, W.H.6
Lakshmanan, A.7
Wade, W.G.8
-
33
-
-
84873708523
-
The oral microbiome in health and disease
-
Wade WG. 2013. The oral microbiome in health and disease. Pharmacol. Res. 69:137-143. http://dx.doi.org/10.1016/j.phrs.2012.11.006.
-
(2013)
Pharmacol. Res.
, vol.69
, pp. 137-143
-
-
Wade, W.G.1
-
34
-
-
66349083859
-
Topographical and temporal diversity of the human skin microbiome
-
Comparative Sequencing Program NISC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA
-
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Comparative Sequencing Program NISC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA. 2009. Topographical and temporal diversity of the human skin microbiome. Science 324:1190-1192. http://dx.doi.org/10.1126/science.1171700.
-
(2009)
Science
, vol.324
, pp. 1190-1192
-
-
Grice, E.A.1
Kong, H.H.2
Conlan, S.3
Deming, C.B.4
Davis, J.5
Young, A.C.6
-
35
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697. http://dx.doi.org/10.1126/science.1177486.
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
Knight, R.6
-
36
-
-
84875367117
-
Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon
-
El Aidy S, Derrien M, Merrifield CA, Levenez F, Dore J, Boekschoten MV, Dekker J, Holmes E, Zoetendal EG, van Baarlen P, Claus SP, Kleerebezem M. 2013. Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon. ISME J. 7:743-755. http://dx.doi.org/10.1038/ismej.2012.142.
-
(2013)
ISME J.
, vol.7
, pp. 743-755
-
-
El Aidy, S.1
Derrien, M.2
Merrifield, C.A.3
Levenez, F.4
Dore, J.5
Boekschoten, M.V.6
Dekker, J.7
Holmes, E.8
Zoetendal, E.G.9
van Baarlen, P.10
Claus, S.P.11
Kleerebezem, M.12
-
37
-
-
78649887273
-
Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models
-
Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F, Clarke SF, O'Toole PW, Quigley EM, Stanton C, Ross PR, O'Doherty RM, Shanahan F. 2010. Composition and energy harvesting capacity of the gut microbiota: relationship to diet, obesity and time in mouse models. Gut 59:1635-1642. http://dx.doi.org/10.1136/gut.2010.215665.
-
(2010)
Gut
, vol.59
, pp. 1635-1642
-
-
Murphy, E.F.1
Cotter, P.D.2
Healy, S.3
Marques, T.M.4
O'sullivan, O.5
Fouhy, F.6
Clarke, S.F.7
O'Toole, P.W.8
Quigley, E.M.9
Stanton, C.10
Ross, P.R.11
O'Doherty, R.M.12
Shanahan, F.13
-
38
-
-
84878007093
-
Human milk metagenome: a functional capacity analysis
-
Ward TL, Hosid S, Ioshikhes I, Altosaar I. 2013. Human milk metagenome: a functional capacity analysis. BMC Microbiol. 13:116. http://dx.doi.org/10.1186/1471-2180-13-116.
-
(2013)
BMC Microbiol.
, vol.13
, pp. 116
-
-
Ward, T.L.1
Hosid, S.2
Ioshikhes, I.3
Altosaar, I.4
-
39
-
-
0025812956
-
Urothelial hyperplasia and neoplasia III. Detection of nitrosamine production with different bacterial genera in chronic urinary tract infections of rats
-
Davis CP, Cohen MS, Hackett RL, Anderson MD, Warren MM. 1991. Urothelial hyperplasia and neoplasia. III. Detection of nitrosamine production with different bacterial genera in chronic urinary tract infections of rats. J. Urol. 145:875-880.
-
(1991)
J. Urol.
, vol.145
, pp. 875-880
-
-
Davis, C.P.1
Cohen, M.S.2
Hackett, R.L.3
Anderson, M.D.4
Warren, M.M.5
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