-
1
-
-
0032499758
-
Prokaryotes: The unseen majority
-
DOI 10.1073/pnas.95.12.6578
-
Whitman, W.B., Coleman, D.C. & Wiebe, W.J. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95, 6578-6583 (1998). (Pubitemid 28278022)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.12
, pp. 6578-6583
-
-
Whitman, W.B.1
Coleman, D.C.2
Wiebe, W.J.3
-
2
-
-
44449137093
-
The microbial engines that drive earth's biogeochemical cycles
-
DOI 10.1126/science.1153213
-
Falkowski, P.G., Fenchel, T. & Delong, E.F. The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034-1039 (2008). (Pubitemid 351929518)
-
(2008)
Science
, vol.320
, Issue.5879
, pp. 1034-1039
-
-
Falkowski, P.G.1
Fenchel, T.2
Delong, E.F.3
-
3
-
-
79959792587
-
The genomic standards consortium
-
Field, D. et al. The Genomic Standards Consortium. PLoS Biol. 9, e1001088 (2011).
-
(2011)
PLoS Biol.
, vol.9
-
-
Field, D.1
-
5
-
-
84864863043
-
Bioprospecting metagenomics for new glycoside hydrolases
-
Biomass Conversion. (ed. Himmel, M.E.) Humana Press, 2012
-
Gilbert, J.A. et al. Bioprospecting metagenomics for new glycoside hydrolases. in Methods in Molecular Biology vol. 908, Biomass Conversion. (ed. Himmel, M.E.) (Humana Press, 2012).
-
Methods in Molecular Biology
, vol.908
-
-
Gilbert, J.A.1
-
6
-
-
79960176130
-
Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes
-
Jansson, J. Towards "Tera-Terra": Terabase Sequencing of Terrestrial Metagenomes. ASM Microbe 6, 309-315 (2011).
-
(2011)
ASM Microbe
, vol.6
, pp. 309-315
-
-
Jansson, J.1
-
7
-
-
84855770484
-
Sequencing data: A genomic network to monitor Earth
-
Genomic Observatories Network.
-
Davies, N. & Field, D. & Genomic Observatories Network. Sequencing data: A genomic network to monitor Earth. Nature 481, 145 (2012).
-
Nature
, vol.481
, Issue.145
, pp. 2012
-
-
Davies, N.1
Field, D.2
-
8
-
-
1542377296
-
Community structure and metabolism through reconstruction of microbial genomes from the environment
-
DOI 10.1038/nature02340
-
Tyson, G.W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43 (2004). (Pubitemid 38332350)
-
(2004)
Nature
, vol.428
, Issue.6978
, pp. 37-43
-
-
Tyson, G.W.1
Chapman, J.2
Hugenholtz, P.3
Allen, E.E.4
Ram, R.J.5
Richardson, P.M.6
Solovyev, V.V.7
Rubin, E.M.8
Rokhsar, D.S.9
Banfield, J.F.10
-
9
-
-
83555174830
-
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
-
Mackelprang, R. et al. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature 480, 368-371 (2011).
-
(2011)
Nature
, vol.480
, pp. 368-371
-
-
Mackelprang, R.1
-
10
-
-
84865344067
-
Structure, fluctuation and magnitude of a natural grassland soil metagenome
-
published online doi: 10.1038/ismej.2011.197 2 February 2012
-
Delmont, T.O. et al. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. published online, doi: 10.1038/ismej.2011.197 (2 February 2012).
-
ISME J.
-
-
Delmont, T.O.1
-
11
-
-
33947238287
-
The sorcerer II global ocean sampling expedition: Northwest atlantic through eastern tropical pacific
-
Rusch, D.B. et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, e77 (2007).
-
(2007)
PLoS Biol.
, vol.5
-
-
Rusch, D.B.1
-
12
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's inferior
-
DOI 10.1126/science.1120250
-
DeLong, E.F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496-503 (2006). (Pubitemid 43157723)
-
(2006)
Science
, vol.311
, Issue.5760
, pp. 496-503
-
-
DeLong, E.F.1
Preston, C.M.2
Mincer, T.3
Rich, V.4
Hallam, S.J.5
Frigaard, N.-U.6
Martinez, A.7
Sullivan, M.B.8
Edwards, R.9
Brito, B.R.10
Chisholm, S.W.11
Karl, D.M.12
-
13
-
-
78649732106
-
The taxonomic and functional diversity of microbes at a temperate coastal site: A 'multi-omic' study of seasonal and diel temporal variation
-
Gilbert, J.A. et al. The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation. PLoS ONE 5, e15545 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Gilbert, J.A.1
-
14
-
-
36549000721
-
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
-
DOI 10.1038/nature06269
-
Warnecke, F. et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450, 560-565 (2007). (Pubitemid 350190243)
-
(2007)
Nature
, vol.450
, Issue.7169
, pp. 560-565
-
-
Warnecke, F.1
Luginbuhl, P.2
Ivanova, N.3
Ghassemian, M.4
Richardson, T.H.5
Stege, J.T.6
Cayouette, M.7
McHardy, A.C.8
Djordjevic, G.9
Aboushadi, N.10
Sorek, R.11
Tringe, S.G.12
Podar, M.13
Martin, H.G.14
Kunin, V.15
Dalevi, D.16
Madejska, J.17
Kirton, E.18
Platt, D.19
Szeto, E.20
Salamov, A.21
Barry, K.22
Mikhailova, N.23
Kyrpides, N.C.24
Matson, E.G.25
Ottesen, E.A.26
Zhang, X.27
Hernandez, M.28
Murillo, C.29
Acosta, L.G.30
Rigoutsos, I.31
Tamayo, G.32
Green, B.D.33
Chang, C.34
Rubin, E.M.35
Mathur, E.J.36
Robertson, D.E.37
Hugenholtz, P.38
Leadbetter, J.R.39
more..
-
15
-
-
79251587455
-
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
-
Hess, M. et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331, 463-467 (2011).
-
(2011)
Science
, vol.331
, pp. 463-467
-
-
Hess, M.1
-
16
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
DOI 10.1126/science.1124234
-
Gill, S.R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006). (Pubitemid 43839542)
-
(2006)
Science
, vol.312
, Issue.5778
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
DeBoy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
Samuel, B.S.6
Gordon, J.I.7
Relman, D.A.8
Fraser-Liggett, C.M.9
Nelson, K.E.10
-
17
-
-
33845874101
-
An obesity-associated gut microbiome with increased capacity for energy harvest
-
DOI 10.1038/nature05414, PII NATURE05414
-
Turnbaugh, P.J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006). (Pubitemid 46018515)
-
(2006)
Nature
, vol.444
, Issue.7122
, pp. 1027-1031
-
-
Turnbaugh, P.J.1
Ley, R.E.2
Mahowald, M.A.3
Magrini, V.4
Mardis, E.R.5
Gordon, J.I.6
-
18
-
-
81855194370
-
Metagenomic mining for microbiologists
-
Delmont, T.O. et al. Metagenomic mining for microbiologists. ISME J. 5, 1837-1843 (2011).
-
(2011)
ISME J.
, vol.5
, pp. 1837-1843
-
-
Delmont, T.O.1
-
19
-
-
41649109613
-
Functional metagenomic profiling of nine biomes
-
DOI 10.1038/nature06810, PII NATURE06810
-
Dinsdale, E.A. et al. Functional metagenomic profiling of nine biomes. Nature 452, 629-632 (2008). (Pubitemid 351483360)
-
(2008)
Nature
, vol.452
, Issue.7187
, pp. 629-632
-
-
Dinsdale, E.A.1
Edwards, R.A.2
Hall, D.3
Angly, F.4
Breitbart, M.5
Brulc, J.M.6
Furlan, M.7
Desnues, C.8
Haynes, M.9
Li, L.10
McDaniel, L.11
Moran, M.A.12
Nelson, K.E.13
Nilsson, C.14
Olson, R.15
Paul, J.16
Brito, B.R.17
Ruan, Y.18
Swan, B.K.19
Stevens, R.20
Valentine, D.L.21
Thurber, R.V.22
Wegley, L.23
White, B.A.24
Rohwer, F.25
more..
-
20
-
-
20244376755
-
Comparative metagenomics of microbial communities
-
DOI 10.1126/science.1107851
-
Tringe, S.G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005). (Pubitemid 40570586)
-
(2005)
Science
, vol.308
, Issue.5721
, pp. 554-557
-
-
Tringe, S.G.1
Von Mering, C.2
Kobayashi, A.3
Salamov, A.A.4
Chen, K.5
Chang, H.W.6
Podar, M.7
Short, J.M.8
Mathur, E.J.9
Detter, J.C.10
Bork, P.11
Hugenholtz, P.12
Rubin, E.M.13
-
21
-
-
78049434937
-
Replicate or lie
-
Prosser, J.I. Replicate or lie. Environ. Microbiol. 12, 1806-1810 (2010).
-
(2010)
Environ. Microbiol.
, vol.12
, pp. 1806-1810
-
-
Prosser, J.I.1
-
22
-
-
84855958621
-
Defining seasonal marine microbial community dynamics
-
Gilbert, J.A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298-308 (2012).
-
(2012)
ISME J.
, vol.6
, pp. 298-308
-
-
Gilbert, J.A.1
-
23
-
-
79952005915
-
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
-
Caporaso, J.G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA 108 (suppl. 1), 4516-4522 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, Issue.SUPPL. 1
, pp. 4516-4522
-
-
Caporaso, J.G.1
-
24
-
-
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
-
25
-
-
84855931244
-
Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea
-
Parsons, R.J., Breitbart, M., Lomas, M.W. & Carlson, C.A. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J. 6, 273-284 (2012).
-
(2012)
ISME J.
, vol.6
, pp. 273-284
-
-
Parsons, R.J.1
Breitbart, M.2
Lomas, M.W.3
Carlson, C.A.4
-
26
-
-
79955742866
-
Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria
-
Farnelid, H. et al. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria. PLoS ONE 6, e19223 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Farnelid, H.1
-
27
-
-
84856456747
-
From genomics to metagenomics
-
Desai, N., Antonopoulos, D., Gilbert, J.A., Glass, E.M. & Meyer, F. From genomics to metagenomics. Curr. Opin. Biotechnol. 23, 72-76 (2012).
-
(2012)
Curr. Opin. Biotechnol.
, vol.23
, pp. 72-76
-
-
Desai, N.1
Antonopoulos, D.2
Gilbert, J.A.3
Glass, E.M.4
Meyer, F.5
-
28
-
-
47549119041
-
Methanogenic archaea: Ecologically relevant differences in energy conservation
-
Thauer, R.K., Kaster, A.K., Seedorf, H., Buckel, W. & Hedderich, R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6, 579-591 (2008).
-
(2008)
Nat. Rev. Microbiol.
, vol.6
, pp. 579-591
-
-
Thauer, R.K.1
Kaster, A.K.2
Seedorf, H.3
Buckel, W.4
Hedderich, R.5
-
29
-
-
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
-
30
-
-
84861990785
-
Predicting bacterial community assemblages using an artificial neural network approach
-
advance online publication doi:10.1038/nmeth.1975 15 April 2012
-
Larsen, P., Field, D. & Gilbert, J.A. Predicting bacterial community assemblages using an artificial neural network approach. Nat. Methods advance online publication, doi:10.1038/nmeth.1975 (15 April 2012).
-
Nat. Methods
-
-
Larsen, P.1
Field, D.2
Gilbert, J.A.3
-
31
-
-
84861347511
-
The Western English Channel contains a persistent microbial seed bank
-
Caporaso, J.G., Paszkiewicz, K., Field, D., Knight, R. & Gilbert, J.A. The Western English Channel contains a persistent microbial seed bank. ISME J. 6, 1089-1093 (2012).
-
(2012)
ISME J.
, vol.6
, pp. 1089-1093
-
-
Caporaso, J.G.1
Paszkiewicz, K.2
Field, D.3
Knight, R.4
Gilbert, J.A.5
-
32
-
-
65249149643
-
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla
-
Mahowald, M.A. et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc. Natl. Acad. Sci. USA 106, 5859-5864 (2009).
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 5859-5864
-
-
Mahowald, M.A.1
-
33
-
-
71249091315
-
The seasonal structure of microbial communities in the Western English Channel
-
Gilbert, J.A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132-3139 (2009).
-
(2009)
Environ. Microbiol.
, vol.11
, pp. 3132-3139
-
-
Gilbert, J.A.1
-
34
-
-
85027927719
-
Enterotypes of the human gut microbiome
-
Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
-
(2011)
Nature
, vol.473
, pp. 174-180
-
-
Arumugam, M.1
-
35
-
-
80053618114
-
Linking long-term dietary patterns with gut microbial enterotypes
-
Wu, G.D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).
-
(2011)
Science
, vol.334
, pp. 105-108
-
-
Wu, G.D.1
-
36
-
-
77955874456
-
Direct sequencing of the human microbiome readily reveals community differences
-
Kuczynski, J. et al. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol. 11, 210 (2010).
-
Genome Biol.
, vol.11
, Issue.210
, pp. 2010
-
-
Kuczynski, J.1
-
37
-
-
79959794996
-
The earth microbiome project: meeting report of the "1 EMP meeting on sample selection and acquisition" at argonne national laboratory october 6 2010
-
Gilbert, J.A. et al. The Earth Microbiome Project: meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. Stand. Genomic Sci. 3, 249-253 (2010).
-
(2010)
Stand. Genomic Sci.
, vol.3
, pp. 249-253
-
-
Gilbert, J.A.1
-
38
-
-
80053281919
-
Open science is a research accelerator
-
Woelfle, M., Olliaro, P. & Todd, M.H. Open science is a research accelerator. Nat. Chem. 3, 745-748 (2011).
-
(2011)
Nat. Chem.
, vol.3
, pp. 745-748
-
-
Woelfle, M.1
Olliaro, P.2
Todd, M.H.3
-
39
-
-
79955749319
-
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
-
Yilmaz, P. et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol. 29, 415-420 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 415-420
-
-
Yilmaz, P.1
-
41
-
-
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
-
42
-
-
53549118607
-
The metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes
-
Meyer, F. et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9, 386 (2008).
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 386
-
-
Meyer, F.1
-
43
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
Wu, D. et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060 (2009).
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
-
44
-
-
84861898310
-
IMG: The Integrated Microbial Genomes database and comparative analysis system
-
Markowitz, V.M. et al. IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res. 40, D115-D122 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Markowitz, V.M.1
-
45
-
-
84862024797
-
IMG/M: The integrated metagenome data management and comparative analysis system
-
Markowitz, V.M. et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40, D123-D129 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Markowitz, V.M.1
-
46
-
-
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
-
47
-
-
46249085739
-
Evolution of mammals and their gut microbes
-
DOI 10.1126/science.1155725
-
Ley, R.E. et al. Evolution of mammals and their gut microbes. Science 320, 1647-1651 (2008). (Pubitemid 351931256)
-
(2008)
Science
, vol.320
, Issue.5883
, pp. 1647-1651
-
-
Ley, R.E.1
Hamady, M.2
Lozupone, C.3
Turnbaugh, P.J.4
Ramey, R.R.5
Bircher, J.S.6
Schlegel, M.L.7
Tucker, T.A.8
Schrenzel, M.D.9
Knight, R.10
Gordon, J.I.11
-
48
-
-
77950904616
-
Forensic identification using skin bacterial communities
-
Fierer, N. et al. Forensic identification using skin bacterial communities. Proc. Natl. Acad. Sci. USA 107, 6477-6481 (2010).
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 6477-6481
-
-
Fierer, N.1
-
49
-
-
80052540333
-
Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems
-
Zinger, L. et al. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6, e24570 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Zinger, L.1
-
50
-
-
79956301905
-
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans
-
Muegge, B.D. et al. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974 (2011).
-
(2011)
Science
, vol.332
, pp. 970-974
-
-
Muegge, B.D.1
-
51
-
-
79952757721
-
Composition, variability, and temporal stability of the intestinal microbiota of the elderly
-
Claesson, M.J. et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl. Acad. Sci. USA 108 (suppl. 1), 4586-4591 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, Issue.SUPPL. 1
, pp. 4586-4591
-
-
Claesson, M.J.1
-
52
-
-
35348857386
-
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases
-
DOI 10.1073/pnas.0706625104
-
Frank, D.N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104, 13780-13785 (2007). (Pubitemid 350003397)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.34
, pp. 13780-13785
-
-
Frank, D.N.1
St. Amand, A.L.2
Feldman, R.A.3
Boedeker, E.C.4
Harpaz, N.5
Pace, N.R.6
-
53
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P.J. 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.J.1
-
54
-
-
77954627922
-
Viruses in the faecal microbiota of monozygotic twins and their mothers
-
Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338 (2010).
-
(2010)
Nature
, vol.466
, pp. 334-338
-
-
Reyes, A.1
-
55
-
-
79952750340
-
Vaginal microbiome of reproductive-age women
-
Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. USA 108 (suppl. 1), 4680-4687 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, Issue.SUPPL. 1
, pp. 4680-4687
-
-
Ravel, J.1
-
56
-
-
79951813515
-
Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest
-
Rasche, F. et al. Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME J. 5, 389-402 (2011).
-
(2011)
ISME J.
, vol.5
, pp. 389-402
-
-
Rasche, F.1
|