-
1
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., et al. (2011). Enterotypes of the human gut microbiome. Nature 473, 174-180. doi: 10.1038/nature09944
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
Raes, J.2
Pelletier, E.3
Le Paslier, D.4
Yamada, T.5
Mende, D.R.6
-
2
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
Caporaso, J. G., Bittinger, K., Bushman, F. D., Desantis, T. Z., Andersen, G. L., and Knight, R. (2010a). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266-267. doi: 10.1093/bioinformatics/btp636
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
Desantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
3
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., et al. (2010b). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. doi: 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
-
4
-
-
84996584385
-
The microbiome of uncontacted Amerindians
-
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., et al. (2015). The microbiome of uncontacted Amerindians. Sci. Adv. 1, e1500183. doi: 10.1126/sciadv.1500183
-
(2015)
Sci. Adv
, vol.1
-
-
Clemente, J.C.1
Pehrsson, E.C.2
Blaser, M.J.3
Sandhu, K.4
Gao, Z.5
Wang, B.6
-
5
-
-
84862286169
-
A framework for human microbiome research
-
Consortium, T. H. M. P. (2012a). A framework for human microbiome research. Nature 486, 215-221. doi: 10.1038/nature11209
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
Consortium, T.H.M.P.1
-
6
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
Consortium, T. H. M. P. (2012b). Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214. doi: 10.1038/nature11234
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
Consortium, T.H.M.P.1
-
7
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., and Knight, R. (2009). Bacterial community variation in human body habitats across space and time. Science 326, 1694-1697. doi: 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
-
8
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461. doi: 10.1093/bioinformatics/btq461
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
9
-
-
84937032044
-
Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups
-
Leung, M. H. Y., Wilkins, D., and Lee, P. K. H. (2015). Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups. Sci. Rep. 5, 11845. doi: 10.1038/srep11845
-
(2015)
Sci. Rep
, vol.5
, pp. 11845
-
-
Leung, M.H.Y.1
Wilkins, D.2
Lee, P.K.H.3
-
10
-
-
84862197046
-
Analyses of the microbial diversity across the human microbiome
-
Li, K., Bihan, M., Yooseph, S., and Methé, B. A. (2012). Analyses of the microbial diversity across the human microbiome. PLoS ONE 7:e32118. doi: 10.1371/journal.pone.0032118
-
(2012)
PLoS ONE
, vol.7
-
-
Li, K.1
Bihan, M.2
Yooseph, S.3
Methé, B.A.4
-
11
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone, C., and Knight, R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71, 8228-8235. doi: 10.1128/AEM.71.12.8228-8235.2005
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
12
-
-
33947269742
-
Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities
-
Lozupone, C. A., Hamady, M., Kelley, S. T., and Knight, R. (2007). Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576-1585. doi: 10.1128/AEM.01996-06
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 1576-1585
-
-
Lozupone, C.A.1
Hamady, M.2
Kelley, S.T.3
Knight, R.4
-
13
-
-
84925708427
-
Subsistence strategies in traditional societies distinguish gut microbiomes
-
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., et al. (2015). Subsistence strategies in traditional societies distinguish gut microbiomes. Nat. Commun. 6, 6505. doi: 10.1038/ncomms7505
-
(2015)
Nat. Commun
, vol.6
, pp. 6505
-
-
Obregon-Tito, A.J.1
Tito, R.Y.2
Metcalf, J.3
Sankaranarayanan, K.4
Clemente, J.C.5
Ursell, L.K.6
-
14
-
-
84908074440
-
Biogeography and individuality shape function in the human skin metagenome
-
Oh, J., Byrd, A. L., Deming, C., Conlan, S., Program, N. C. S., Kong, H. H., et al. (2014). Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59-64. doi: 10.1038/nature13786
-
(2014)
Nature
, vol.514
, pp. 59-64
-
-
Oh, J.1
Byrd, A.L.2
Deming, C.3
Conlan, S.4
Program, N.C.S.5
Kong, H.H.6
-
15
-
-
84902660778
-
Defining dysbiosis and its influence on host immunity and disease
-
Petersen, C., and Round, J. L. (2014). Defining dysbiosis and its influence on host immunity and disease. Cell. Microbiol. 16, 1024-1033. doi: 10.1111/cmi.12308
-
(2014)
Cell. Microbiol
, vol.16
, pp. 1024-1033
-
-
Petersen, C.1
Round, J.L.2
-
16
-
-
70449713952
-
The NIH human microbiome project
-
Peterson, J., Garges, S., Giovanni, M., Mcinnes, P., Wang, L., Schloss, J. A., et al. (2009). The NIH human microbiome project. Genome Res. 19, 2317-2323. doi: 10.1101/gr.096651.109
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
Giovanni, M.3
Mcinnes, P.4
Wang, L.5
Schloss, J.A.6
-
17
-
-
84891123514
-
Emerging insights on intestinal dysbiosis during bacterial infections
-
Pham, T. A. N., and Lawley, T. D. (2014). Emerging insights on intestinal dysbiosis during bacterial infections. Curr. Opin. Microbiol. 17, 67-74. doi: 10.1016/j.mib.2013.12.002
-
(2014)
Curr. Opin. Microbiol
, vol.17
, pp. 67-74
-
-
Pham, T.A.N.1
Lawley, T.D.2
-
18
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M. N., Dehal, P. S., and Arkin, A. P. (2009). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641-1650. doi: 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
-
19
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65. doi: 10.1038/nature08821
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
Manichanh, C.6
-
20
-
-
84903398286
-
The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils
-
Rascovan, N., Carbonetto, B., Revale, S., Reinert, M., Alvarez, R., Godeas, A., et al. (2013). The PAMPA datasets: a metagenomic survey of microbial communities in Argentinean pampean soils. Microbiome 1, 21. doi: 10.1186/2049-2618-1-21
-
(2013)
Microbiome
, vol.1
, pp. 21
-
-
Rascovan, N.1
Carbonetto, B.2
Revale, S.3
Reinert, M.4
Alvarez, R.5
Godeas, A.6
-
21
-
-
84942645768
-
The human microbiome and the future practice of medicine
-
Relman, D. A. (2015). The human microbiome and the future practice of medicine. JAMA 314, 1127-1128. doi: 10.1001/jama.2015.10700
-
(2015)
JAMA
, vol.314
, pp. 1127-1128
-
-
Relman, D.A.1
-
22
-
-
84938484058
-
16S gut community of the Cameron County Hispanic Cohort
-
Ross, M., Muzny, D., Mccormick, J., Gibbs, R., Fisher-Hoch, S., and Petrosino, J. (2015). 16S gut community of the Cameron County Hispanic Cohort. Microbiome 3, 1-11. doi: 10.1186/s40168-015-0072-y
-
(2015)
Microbiome
, vol.3
, pp. 1-11
-
-
Ross, M.1
Muzny, D.2
Mccormick, J.3
Gibbs, R.4
Fisher-Hoch, S.5
Petrosino, J.6
-
23
-
-
84923080032
-
Gut microbiome of the Hadza hunter-gatherers
-
Schnorr, S. L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., et al. (2014). Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654. doi: 10.1038/ncomms4654
-
(2014)
Nat. Commun
, vol.5
, pp. 3654
-
-
Schnorr, S.L.1
Candela, M.2
Rampelli, S.3
Centanni, M.4
Consolandi, C.5
Basaglia, G.6
-
24
-
-
84894182162
-
Opportunities and challenges for gut microbiome studies in the Indian population
-
Shetty, S., Marathe, N., and Shouche, Y. (2013). Opportunities and challenges for gut microbiome studies in the Indian population. Microbiome 1, 24. doi: 10.1186/2049-2618-1-24
-
(2013)
Microbiome
, vol.1
, pp. 24
-
-
Shetty, S.1
Marathe, N.2
Shouche, Y.3
-
25
-
-
84927516569
-
Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences
-
Wagner Mackenzie, B., Waite, D. W., and Taylor, M. W. (2015). Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences. Front. Microbiol. 6:130. doi: 10.3389/fmicb.2015.00130
-
(2015)
Front. Microbiol
, vol.6
, pp. 130
-
-
Wagner Mackenzie, B.1
Waite, D.W.2
Taylor, M.W.3
-
26
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G. M., Tiedje, J. M., and Cole, J. R. (2007). Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267. doi: 10.1128/AEM.00062-07
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
27
-
-
84862141704
-
Human gut microbiome viewed across age and geography
-
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., et al. (2012). Human gut microbiome viewed across age and geography. Nature 486, 222-227. doi: 10.1038/nature11053
-
(2012)
Nature
, vol.486
, pp. 222-227
-
-
Yatsunenko, T.1
Rey, F.E.2
Manary, M.J.3
Trehan, I.4
Dominguez-Bello, M.G.5
Contreras, M.6
-
28
-
-
84907165154
-
Acquiring and maintaining a normal oral microbiome: current perspective
-
Zaura, E., Nicu, E. A., Krom, B. P., and Keijser, B. J. F. (2014). Acquiring and maintaining a normal oral microbiome: current perspective. Front. Cell. Infect. Microbiol. 4:85. doi: 10.3389/fcimb.2014.00085
-
(2014)
Front. Cell. Infect. Microbiol
, vol.4
, pp. 85
-
-
Zaura, E.1
Nicu, E.A.2
Krom, B.P.3
Keijser, B.J.F.4
-
29
-
-
84872154220
-
Biogeography of the ecosystems of the healthy human body
-
Zhou, Y., Gao, H., Mihindukulasuriya, K., La Rosa, P., Wylie, K., Vishnivetskaya, T., et al. (2013). Biogeography of the ecosystems of the healthy human body. Genome Biol. 14, R1. doi: 10.1186/gb-2013-14-1-r1
-
(2013)
Genome Biol
, vol.14
, pp. R1
-
-
Zhou, Y.1
Gao, H.2
Mihindukulasuriya, K.3
La Rosa, P.4
Wylie, K.5
Vishnivetskaya, T.6
|