-
1
-
-
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).
-
(1993)
Appl. Environ. Microbiol.
, vol.59
, pp. 695-700
-
-
Muyzer, G.1
De Waal, E.C.2
Uitterlinden, A.G.3
-
2
-
-
0033152336
-
DGGE/TGGE a method for identifying genes from natural ecosystems
-
Myzer, G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol. 2, 317-322 (1999).
-
(1999)
Curr. Opin. Microbiol.
, vol.2
, pp. 317-322
-
-
Myzer, G.1
-
3
-
-
0028028182
-
A Place for DNA-DNA Reassociation and 16S RRNA Sequence Analysis in the Present Species Definition in Bacteriology
-
Stackebrandt, E. & Goebel., B. M. A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44, 846-849 (1994).
-
(1994)
Int. J. Syst. Bacteriol.
, vol.44
, pp. 846-849
-
-
Stackebrandt, E.1
Goebel, B.M.2
-
4
-
-
1642430630
-
An ecological perspective on bacterial biodiversity
-
Horner-Devine, M. H., Carney, K. M. & Bohannan, B. J. M. An ecological perspective on bacterial biodiversity. Proc. R Soc. Land. B 271, 113-122 (2004).
-
(2004)
Proc. R Soc. Land. B
, vol.271
, pp. 113-122
-
-
Horner-Devine, M.H.1
Carney, K.M.2
Bohannan, B.J.M.3
-
5
-
-
44849128805
-
Species divergence and the measurement of microbial diversity
-
Lozupone, C. A. & Knight, R. Species divergence and the measurement of microbial diversity. FEMS Microbiol. Rev. 32, 557-578 (2008).
-
(2008)
FEMS Microbiol. Rev.
, vol.32
, pp. 557-578
-
-
Lozupone, C.A.1
Knight, R.2
-
6
-
-
34547579868
-
Genotypic microbial community profiling: A critical technical review
-
Nocker, A., Burr, M. & Camper, A. K. Genotypic microbial community profiling: a critical technical review. Microbiol. Ecol. 54, 276-289 (2007).
-
(2007)
Microbiol. Ecol.
, vol.54
, pp. 276-289
-
-
Nocker, A.1
Burr, M.2
Camper, A.K.3
-
7
-
-
0034953840
-
Plants and fertilisers as drivers of change in microbial community structure and function in soils
-
O'Donnel, A. G., Seasman, M., Macrae, A., Waite, I. & Davies, J. T. Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant Soil 232, 135-145 (2001).
-
(2001)
Plant Soil
, vol.232
, pp. 135-145
-
-
O'Donnel, A.G.1
Seasman, M.2
MacRae, A.3
Waite, I.4
Davies, J.T.5
-
8
-
-
0034123066
-
Monitoring complex bacterial communities using culture-independent molecular techniques: Application to soil environment
-
Ranjard, L., Poly, F. & Nazaret, S. Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res. Microbiol. 151, 167-177 (2000).
-
(2000)
Res. Microbiol.
, vol.151
, pp. 167-177
-
-
Ranjard, L.1
Poly, F.2
Nazaret, S.3
-
9
-
-
0037052493
-
Prokaryotic diversity-magnitude, dynamics, and controlling factors
-
Torsvik, V., Ovreas, L. & Thingstad, T. F. Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science 296, 1064-1066 (2002).
-
(2002)
Science
, vol.296
, pp. 1064-1066
-
-
Torsvik, V.1
Ovreas, L.2
Thingstad, T.F.3
-
10
-
-
19044401068
-
Community genomics in microbial ecology and evolution
-
Allen, E. E. & Banfield, J. F. Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3, 489-498 (2005).
-
(2005)
Nat. Rev. Microbiol.
, vol.3
, pp. 489-498
-
-
Allen, E.E.1
Banfield, J.F.2
-
11
-
-
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
-
12
-
-
84858376593
-
The impact of the gut microbiota on human health: An integrative view
-
Clemente, J. C., Ursell, L. K., Parfrey, L. W. & Knight, R. The impact of the gut microbiota on human health: an integrative view. Cell 148, 1258-1270 (2012).
-
(2012)
Cell
, vol.148
, pp. 1258-1270
-
-
Clemente, J.C.1
Ursell, L.K.2
Parfrey, L.W.3
Knight, R.4
-
13
-
-
38449088143
-
Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
-
Kurokawa, K. et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14, 169-181 (2007).
-
(2007)
DNA Res.
, vol.14
, pp. 169-181
-
-
Kurokawa, K.1
-
14
-
-
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
-
15
-
-
49649089054
-
Get the most out of your metagenome: Computational analysis of environmental sequence data
-
Raes, J. & Bork, P. Get the most out of your metagenome: computational analysis of environmental sequence data. Nat. Rev. Microbiol. 6, 693-699 (2008).
-
(2008)
Nat. Rev. Microbiol.
, vol.6
, pp. 693-699
-
-
Raes, J.1
Bork, P.2
-
16
-
-
33947235074
-
The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
-
Yooseph, S. et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 5, e16 (2007).
-
(2007)
PLoS Biol.
, vol.5
-
-
Yooseph, S.1
-
17
-
-
38549126643
-
KEGG for linking genomes to life and the environment
-
Kanehisa, M. et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36, D480-D484 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Kanehisa, M.1
-
18
-
-
18744374590
-
Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns
-
Fromin, N. et al. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 4, 634-643 (2002).
-
(2002)
Environ. Microbiol.
, vol.4
, pp. 634-643
-
-
Fromin, N.1
-
19
-
-
38549139537
-
IMG/M: A data management and analysis system for metagenomes
-
Markowitz, V. M. et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36, D534-D538 (2008).
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Markowitz, V.M.1
-
20
-
-
80051474525
-
Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria
-
Papalexandratou, Z., Vrancken, G., De Bruyne, K., Vandamme, P. & De Vuyst, L. Spontaneous organic cocoa bean box fermentations in Brazil are characterized by a restricted species diversity of lactic acid bacteria and acetic acid bacteria. Food Microbiol. 28, 1326-1338 (2011).
-
(2011)
Food Microbiol.
, vol.28
, pp. 1326-1338
-
-
Papalexandratou, Z.1
Vrancken, G.2
De Bruyne, K.3
Vandamme, P.4
De Vuyst, L.5
-
21
-
-
84861562148
-
Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity
-
Illeghems, K., De Vuyst, L., Papalexandratou, Z. & Weckx, S. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity. PLoS ONE 7, e38040 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Illeghems, K.1
De Vuyst, L.2
Papalexandratou, Z.3
Weckx, S.4
-
22
-
-
70349898248
-
Analysis of how a biofilm forms on the surface of the aquatic macrophyte Phragmites australis
-
Hiraki, A. et al. Analysis of how a biofilm forms on the surface of the aquatic macrophyte Phragmites australis. Microbes Environ. 24, 265-272 (2009).
-
(2009)
Microbes Environ.
, vol.24
, pp. 265-272
-
-
Hiraki, A.1
-
23
-
-
0028294677
-
Biofilms, the customized microniche
-
Costerton, J. W., Lewandowski, Z., DeBeer, D., Caldwell, D., Korber, D. & James, G. Biofilms, the customized microniche. J. Bacteriol. 176, 2137-2142 (1994).
-
(1994)
J. Bacteriol.
, vol.176
, pp. 2137-2142
-
-
Costerton, J.W.1
Lewandowski, Z.2
Debeer, D.3
Caldwell, D.4
Korber, D.5
James, G.6
-
24
-
-
0036711963
-
Biofilms: Microbial life on surfaces
-
Donlan, R. M. Biofilms: microbial life on surfaces. Emerg. Infect. Dis. 8, 881-890 (2002).
-
(2002)
Emerg. Infect. Dis.
, vol.8
, pp. 881-890
-
-
Donlan, R.M.1
-
25
-
-
70350378677
-
Bacterial interactions in dental biofilm development
-
Hojo, K., Nagaoka, S., Ohshima, T. & Maeda, N. Bacterial interactions in dental biofilm development. J. Dent. Res. 88, 982-990 (2009).
-
(2009)
J. Dent. Res.
, vol.88
, pp. 982-990
-
-
Hojo, K.1
Nagaoka, S.2
Ohshima, T.3
Maeda, N.4
-
26
-
-
0038238087
-
The genomics and proteomics of biofilm formation
-
Sauer, K. The genomics and proteomics of biofilm formation. Genome Biol. 4, 219 (2003).
-
(2003)
Genome Biol.
, vol.4
, pp. 219
-
-
Sauer, K.1
-
27
-
-
0034015354
-
Biofilm, city of microbes
-
Watnick, P. & Kolter, R. Biofilm, city of microbes. J. Bacteriol. 182, 2675-2679 (2000).
-
(2000)
J. Bacteriol.
, vol.182
, pp. 2675-2679
-
-
Watnick, P.1
Kolter, R.2
-
28
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511-518 (2005).
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
29
-
-
79957613599
-
MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
-
30
-
-
0000122573
-
PHYLIP-Phylogeny Inference Package (Version 3.2)
-
Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166 (1989).
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
31
-
-
33750976398
-
MetaGene: Prokaryotic gene finding from environmental genome shotgun sequences
-
Noguchi, H., Park, J. & Takagi, T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res. 34, 5623-5630 (2006).
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 5623-5630
-
-
Noguchi, H.1
Park, J.2
Takagi, T.3
-
32
-
-
34547588704
-
KAAS: An automatic genome annotation and pathway reconstruction server
-
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.4
Kanehisa, M.5
|