-
1
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088-5090 (1977
-
(1977)
Proc. Natl Acad. Sci. USA
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
2
-
-
0025366454
-
Genetic diversity in Sargasso Sea bacterioplankton
-
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63 (1990
-
(1990)
Nature
, vol.345
, pp. 60-63
-
-
Giovannoni, S.J.1
Britschgi, T.B.2
Moyer, C.L.3
Field, K.G.4
-
3
-
-
0025366456
-
16S rRNA sequences reveal numerous uncultured inhabitants in a natural community
-
Ward, D. M., Weller, R. & Bateson, M. M. 16S rRNA sequences reveal numerous uncultured inhabitants in a natural community. Nature 345, 63-65 (1990
-
(1990)
Nature
, vol.345
, pp. 63-65
-
-
Ward, D.M.1
Weller, R.2
Bateson, M.M.3
-
4
-
-
0002842298
-
The analysis of natural microbial populations by ribosomal RNA sequences
-
Pace, N. R., Stahl, D. A., Lane, D. J. & Olsen, G. J. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microbial Ecol. 9, 1-55 (1986
-
(1986)
Adv. Microbial Ecol
, vol.9
, pp. 1-55
-
-
Pace, N.R.1
Stahl, D.A.2
Lane, D.J.3
Olsen, G.J.4
-
5
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734-740 (1997
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
6
-
-
84925165888
-
-
Ch. 7 ed. Stackebrandt, E. Springer
-
Neufeld, J. D. & Mohn, W. W. in Molecular Identification, Systematics, and Population Structure of Prokaryotes Ch. 7 (ed. Stackebrandt, E.) (Springer, 2006
-
(2006)
Molecular Identification, Systematics, and Population Structure of Prokaryotes
-
-
Neufeld, J.D.1
Mohn, W.W.2
-
7
-
-
0035487318
-
Counting the uncountable: Statistical approaches to estimating microbial diversity
-
Hughes, J. B., Hellmann, J. J., Ricketts, T. H. & Bohannan, B. J. M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67, 4399-4406 (2001
-
(2001)
Appl. Environ. Microbiol
, vol.67
, pp. 4399-4406
-
-
Hughes, J.B.1
Hellmann, J.J.2
Ricketts, T.H.3
Bohannan, B.J.M.4
-
8
-
-
1142306022
-
Serial analysis of ribosomal sequence tags (SARST): A high-throughput method for profiling complex microbial communities
-
Neufeld, J. D., Yu, Z., Lam, W. & Mohn, W. W. Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities. Environ. Microbiol. 6, 131-144 (2004
-
(2004)
Environ. Microbiol
, vol.6
, pp. 131-144
-
-
Neufeld, J.D.1
Yu, Z.2
Lam, W.3
Mohn, W.W.4
-
9
-
-
34547152047
-
Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities
-
Ashby, M. N., Rine, J., Mongodin, E. F., Nelson, K. E. & Dimster-Denk, D. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl. Environ. Microbiol. 73, 4532-4542 (2007
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 4532-4542
-
-
Ashby, M.N.1
Rine, J.2
Mongodin, E.F.3
Nelson, K.E.4
Dimster-Denk, D.5
-
10
-
-
26844488070
-
Unexpectedly high bacterial diversity in Arctic tundra relative to boreal forest soils revealed with serial analysis of ribosomal sequence tags (SARST)
-
Neufeld, J. D. & Mohn, W. W. Unexpectedly high bacterial diversity in Arctic tundra relative to boreal forest soils revealed with serial analysis of ribosomal sequence tags (SARST). Appl. Environ. Microbiol. 71, 5710-5718 (2005
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 5710-5718
-
-
Neufeld, J.D.1
Mohn, W.W.2
-
11
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored rare biosphere
-
Sogin, M. L. et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc. Natl Acad. Sci. USA 103, 12115-12120 (2006
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
-
13
-
-
33644845577
-
Everything is everywhere, but, the environment selects; What did Baas Becking and Beijerinck really say?
-
De Wit, R. & Bouvier, T. Everything is everywhere, but, the environment selects; what did Baas Becking and Beijerinck really say?. Environ. Microbiol. 8, 755-758 (2006
-
(2006)
Environ. Microbiol
, vol.8
, pp. 755-758
-
-
De Wit, R.1
Bouvier, T.2
-
15
-
-
50949090204
-
Novelty and uniqueness patterns of rare members of the soil biosphere
-
Elshahed, M. S. et al. Novelty and uniqueness patterns of rare members of the soil biosphere. Appl. Environ. Microbiol. 74, 5422-5428 (2008
-
(2008)
Appl. Environ. Microbiol
, vol.74
, pp. 5422-5428
-
-
Elshahed, M.S.1
-
16
-
-
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
-
17
-
-
70449530747
-
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
-
Lazarevic, V. et al. Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. J. Microbiol. Methods 79, 266-271 (2009
-
(2009)
J. Microbiol. Methods
, vol.79
, pp. 266-271
-
-
Lazarevic, V.1
-
18
-
-
79952005915
-
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
-
Caporaso, J. 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 (2010
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 4516-4522
-
-
Caporaso, J.1
-
19
-
-
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 5, e15406 (2010
-
(2010)
PLoS ONE
, vol.5
, pp. e15406
-
-
Gloor, G.1
-
20
-
-
83655191007
-
The rare bacterial biosphere
-
Pedrós-Alió, C. The rare bacterial biosphere. Annu. Rev. Mar. Sci. 4, 449-466 (2012
-
(2012)
Annu. Rev. Mar. Sci
, vol.4
, pp. 449-466
-
-
Pedrós-Alió, C.1
-
21
-
-
76049126745
-
Ecology of the rare microbial biosphere of the Arctic Ocean
-
Galand, P. E., Casamayor, E. O., Kirchman, D. L. & Lovejoy, C. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc. Natl Acad. Sci. USA 106, 22427-22432 (2009
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 22427-22432
-
-
Galand, P.E.1
Casamayor, E.O.2
Kirchman, D.L.3
Lovejoy, C.4
-
22
-
-
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
-
23
-
-
77956096764
-
Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets
-
Gobet, A., Quince, C. & Ramette, A. Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Res. 38, e155 (2010
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e155
-
-
Gobet, A.1
Quince, C.2
Ramette, A.3
-
24
-
-
84878270728
-
Robust estimation of microbial diversity in theory and in practice
-
Haegeman, B. et al. Robust estimation of microbial diversity in theory and in practice. ISME J. 7, 1092-1101 (2013
-
(2013)
ISME J.
, vol.7
, pp. 1092-1101
-
-
Haegeman, B.1
-
25
-
-
84908264764
-
Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity
-
Shade, A. et al. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5, e01371-14 (2014
-
(2014)
Mbio
, vol.5
, pp. e01371-e01314
-
-
Shade, A.1
-
26
-
-
78751575501
-
UniFrac: An effective distance metric for microbial community comparison
-
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169-172 (2010
-
(2010)
ISME J.
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
Lladser, M.E.2
Knights, D.3
Stombaugh, J.4
Knight, R.5
-
27
-
-
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
, pp. R50
-
-
Caporaso, J.G.1
-
28
-
-
79952167212
-
Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life
-
Kim, E. et al. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proc. Natl Acad. Sci. USA 108, 1496-1500 (2011
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 1496-1500
-
-
Kim, E.1
-
29
-
-
0036677450
-
Estimating prokaryotic diversity and its limits
-
Curtis, T. P., Sloan, W. T. & Scannell, J. W. Estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99, 10494-10499 (2002
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 10494-10499
-
-
Curtis, T.P.1
Sloan, W.T.2
Scannell, J.W.3
-
30
-
-
2942566096
-
Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology
-
Curtis, T. P. & Sloan, W. T. Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Curr. Opin. Microbiol. 7, 221-226 (2004
-
(2004)
Curr. Opin. Microbiol
, vol.7
, pp. 221-226
-
-
Curtis, T.P.1
Sloan, W.T.2
-
31
-
-
33751226288
-
What is the extent of prokaryotic diversity?. Phil
-
Curtis, T. P. et al. What is the extent of prokaryotic diversity?. Phil. Trans. R. Soc. B 361, 2023-2037 (2006
-
(2006)
Trans. R. Soc
, vol.B361
, pp. 2023-2037
-
-
Curtis, T.P.1
-
32
-
-
34248157603
-
Modeling taxa-abundance distributions in microbial communities using environmental sequence data
-
Sloan, W. T., Woodcock, S., Lunn, M., Head, I. M. & Curtis, T. P. Modeling taxa-abundance distributions in microbial communities using environmental sequence data. Microb. Ecol. 53, 443-455 (2006
-
(2006)
Microb. Ecol
, vol.53
, pp. 443-455
-
-
Sloan, W.T.1
Woodcock, S.2
Lunn, M.3
Head, I.M.4
Curtis, T.P.5
-
33
-
-
46749150088
-
The tragedy of the uncommon: Understanding limitations in the analysis of microbial diversity
-
Bent, S. J. & Forney, L. J. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. ISME J. 2, 689-695 (2008
-
(2008)
ISME J.
, vol.2
, pp. 689-695
-
-
Bent, S.J.1
Forney, L.J.2
-
34
-
-
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
-
35
-
-
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
-
36
-
-
84904903838
-
The microbial contribution to macroecology
-
Barberán, A., Casamayor, E. O. & Fierer, N. The microbial contribution to macroecology. Front. Microbiol. 5, 203 (2014
-
(2014)
Front. Microbiol
, vol.5
, pp. 203
-
-
Barberán, A.1
Casamayor, E.O.2
Fierer, N.3
-
37
-
-
79952751932
-
The generation and maintenance of diversity in microbial communities
-
Fierer, N. & Lennon, J. T. The generation and maintenance of diversity in microbial communities. Am. J. Bot. 98, 439-448 (2011
-
(2011)
Am. J. Bot
, vol.98
, pp. 439-448
-
-
Fierer, N.1
Lennon, J.T.2
-
38
-
-
33846591068
-
Dipping into the rare biosphere
-
Pedrós-Alió, C. Dipping into the rare biosphere. Science 315, 192-193 (2007
-
(2007)
Science
, vol.315
, pp. 192-193
-
-
Pedrós-Alió, C.1
-
39
-
-
84883765148
-
Shifts in the microbial community composition of Gulf Coast beaches following beach oiling
-
Newton, R. J. et al. Shifts in the microbial community composition of Gulf Coast beaches following beach oiling. PLoS ONE 8, e74265 (2013
-
(2013)
PLoS ONE
, vol.8
, pp. e74265
-
-
Newton, R.J.1
-
40
-
-
84889051477
-
Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean
-
Vergin, K. L., Done, B., Carlson, C. A. & Giovannoni, S. J. Spatiotemporal distributions of rare bacterioplankton populations indicate adaptive strategies in the oligotrophic ocean. Aquat. Microb. Ecol. 71, 1-13 (2013
-
(2013)
Aquat. Microb. Ecol.
, vol.71
, pp. 1-13
-
-
Vergin, K.L.1
Done, B.2
Carlson, C.A.3
Giovannoni, S.J.4
-
41
-
-
68549130740
-
Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys
-
Youssef, N. et al. Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl. Environ. Microbiol. 75, 5227-5236 (2009
-
(2009)
Appl. Environ. Microbiol
, vol.75
, pp. 5227-5236
-
-
Youssef, N.1
-
42
-
-
84857121817
-
Diversity and dynamics of rare and of resident bacterial populations in coastal sands
-
Gobet, A. et al. Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J. 6, 542-553 (2011
-
(2011)
ISME J.
, vol.6
, pp. 542-553
-
-
Gobet, A.1
-
43
-
-
68649129020
-
Salt marsh sediment bacteria: Their distribution and response to external nutrient inputs
-
Bowen, J. L., Crump, B. C., Deegan, L. A. & Hobbie, J. E. Salt marsh sediment bacteria: their distribution and response to external nutrient inputs. ISME J. 3, 924-934 (2009
-
(2009)
ISME J.
, vol.3
, pp. 924-934
-
-
Bowen, J.L.1
Crump, B.C.2
Deegan, L.A.3
Hobbie, J.E.4
-
44
-
-
84898791782
-
Patterns of rare and abundant marine microbial eukaryotes
-
Logares, R. et al. Patterns of rare and abundant marine microbial eukaryotes. Curr. Biol. 24, 813-821 (2014
-
(2014)
Curr. Biol
, vol.24
, pp. 813-821
-
-
Logares, R.1
-
45
-
-
84861127065
-
Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone spring, Oklahoma, USA) revealed using a combined pyrosequencing/Sanger approach
-
Youssef, N., Steidley, B. L. & Elshahed, M. S. Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone spring, Oklahoma, USA) revealed using a combined pyrosequencing/Sanger approach. Appl. Environ. Microbiol. 78, 2677-2688 (2012
-
(2012)
Appl. Environ. Microbiol
, vol.78
, pp. 2677-2688
-
-
Youssef, N.1
Steidley, B.L.2
Elshahed, M.S.3
-
46
-
-
84867742872
-
Targeted recovery of novel phylogenetic diversity from next-generation sequence data
-
Lynch, M. D., Bartram, A. K. & Neufeld, J. D. Targeted recovery of novel phylogenetic diversity from next-generation sequence data. ISME J. 6, 2067-2077 (2012
-
(2012)
ISME J.
, vol.6
, pp. 2067-2077
-
-
Lynch, M.D.1
Bartram, A.K.2
Neufeld, J.D.3
-
47
-
-
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. Nature Biotech. 29, 415-420 (2011
-
(2011)
Nature Biotech.
, vol.29
, pp. 415-420
-
-
Yilmaz, P.1
-
48
-
-
35348968286
-
The human microbiome project
-
Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804-810 (2007
-
(2007)
Nature
, vol.449
, pp. 804-810
-
-
Turnbaugh, P.J.1
-
49
-
-
79959794996
-
The Earth Microbiome Project: Meeting report of the 1st EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6th 2010
-
Gilbert, J. A. et al. The Earth Microbiome Project: meeting report of the 1st EMP meeting on sample selection and acquisition at Argonne National Laboratory October 6th 2010. Stand. Genomic Sci. 3, 249-253 (2010
-
(2010)
Stand. Genomic Sci
, vol.3
, pp. 249-253
-
-
Gilbert, J.A.1
-
50
-
-
73449089058
-
Hypotheses on the role of the protistan rare biosphere in a changing world
-
Caron, D. A. & Countway, P. D. Hypotheses on the role of the protistan rare biosphere in a changing world. Aquat. Microb. Ecol. 57, 227-238 (2009
-
(2009)
Aquat. Microb. Ecol
, vol.57
, pp. 227-238
-
-
Caron, D.A.1
Countway, P.D.2
-
51
-
-
79961239913
-
Activity of abundant and rare bacteria in a coastal ocean
-
Campbell, B. J., Yu, L., Heidelberg, J. F. & Kirchman, D. L. Activity of abundant and rare bacteria in a coastal ocean. Proc. Natl Acad. Sci. USA 108, 12776-12781 (2011
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 12776-12781
-
-
Campbell, B.J.1
Yu, L.2
Heidelberg, J.F.3
Kirchman, D.L.4
-
52
-
-
77950526876
-
Dormancy contributes to the maintenance of microbial diversity
-
Jones, S. E. & Lennon, J. T. Dormancy contributes to the maintenance of microbial diversity. Proc. Natl Acad. Sci. USA 107, 5881-5886 (2010
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 5881-5886
-
-
Jones, S.E.1
Lennon, J.T.2
-
53
-
-
84863984762
-
Unraveling assembly of stream biofilm communities
-
Besemer, K. et al. Unraveling assembly of stream biofilm communities. ISME J. 6, 1459-1468 (2012
-
(2012)
ISME J.
, vol.6
, pp. 1459-1468
-
-
Besemer, K.1
-
54
-
-
84905383347
-
Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams
-
Wilhelm, L. et al. Rare but active taxa contribute to community dynamics of benthic biofilms in glacier-fed streams. Environ. Microbiol. 16, 2514-2524 (2014
-
(2014)
Environ. Microbiol
, vol.16
, pp. 2514-2524
-
-
Wilhelm, L.1
-
55
-
-
0028247937
-
Bacterial viruses in coastal seawater: Lytic rather than lysogenic production
-
Wilcox, R. M. & Fuhrman, J. A. Bacterial viruses in coastal seawater: lytic rather than lysogenic production. Mar. Ecol. Prog. Ser. 114, 35-45 (1994
-
(1994)
Mar. Ecol. Prog. Ser
, vol.114
, pp. 35-45
-
-
Wilcox, R.M.1
Fuhrman, J.A.2
-
56
-
-
77749309301
-
Trade-offs between competition and defense specialists among unicellular planktonic organisms: The killing the winner hypothesis revisited
-
Winter, C., Bouvier, T., Weinbauer, M. G. & Thingstad, T. F. Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited. Microbiol. Mol. Biol. Rev. 74, 42-57 (2010
-
(2010)
Microbiol. Mol. Biol. Rev
, vol.74
, pp. 42-57
-
-
Winter, C.1
Bouvier, T.2
Weinbauer, M.G.3
Thingstad, T.F.4
-
57
-
-
0000123207
-
The paradox of the plankton
-
Hutchinson, G. E. The paradox of the plankton. Am. Nat. 95, 137-145 (1961
-
(1961)
Am. Nat
, vol.95
, pp. 137-145
-
-
Hutchinson, G.E.1
-
58
-
-
0036427039
-
Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria
-
Jürgens, K. & Matz, C. Predation as a shaping force for the phenotypic and genotypic composition of planktonic bacteria. Antonie Van Leeuwenhoek 81, 413-434 (2002
-
(2002)
Antonie Van Leeuwenhoek
, vol.81
, pp. 413-434
-
-
Jürgens, K.1
Matz, C.2
-
59
-
-
21344473000
-
Predation on prokaryotes in the water column and its ecological implications
-
Pernthaler, J. Predation on prokaryotes in the water column and its ecological implications. Nature Rev. Microbiol. 3, 537-546 (2005
-
(2005)
Nature Rev. Microbiol
, vol.3
, pp. 537-546
-
-
Pernthaler, J.1
-
60
-
-
0000344538
-
Herbivores and the number of tree species in tropical forests
-
Janzen, D. H. Herbivores and the number of tree species in tropical forests. Am. Nat. 104, 501-528 (1970
-
(1970)
Am. Nat
, vol.104
, pp. 501-528
-
-
Janzen, D.H.1
-
61
-
-
0003128284
-
-
eds Den Boer, P. J. & Gradwell, G.) Wageningen
-
Connell, J. H. in Dynamics of Populations (eds Den Boer, P. J. & Gradwell, G.) 298-312 (Wageningen, 1971
-
(1971)
Dynamics of Populations
, pp. 298-312
-
-
Connell, J.H.1
-
62
-
-
33846572372
-
The impact of phages on interspecific competition in experimental populations of bacteria
-
Brockhurst, M. A., Fenton, A., Roulston, B. & Rainey, P. B. The impact of phages on interspecific competition in experimental populations of bacteria. BMC Ecol. 6, 19 (2006
-
(2006)
BMC Ecol
, vol.6
, pp. 19
-
-
Brockhurst, M.A.1
Fenton, A.2
Roulston, B.3
Rainey, P.B.4
-
63
-
-
24144447031
-
The contribution of species richness and composition to bacterial services
-
Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L. & Lilley, A. K. The contribution of species richness and composition to bacterial services. Nature 436, 1157-1160 (2005
-
(2005)
Nature
, vol.436
, pp. 1157-1160
-
-
Bell, T.1
Newman, J.A.2
Silverman, B.W.3
Turner, S.L.4
Lilley, A.K.5
-
64
-
-
78651511845
-
Microbial seed banks: The ecological and evolutionary implications of dormancy
-
Lennon, J. T. & Jones, S. E. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nature Rev. Microbiol. 9, 119-130 (2011
-
(2011)
Nature Rev. Microbiol
, vol.9
, pp. 119-130
-
-
Lennon, J.T.1
Jones, S.E.2
-
65
-
-
0036800926
-
The frequency and characteristics of highly thermophilic bacteria in cool soil environments
-
Marchant, R., Banat, I. M., Rahman, T. J. & Berzano, M. The frequency and characteristics of highly thermophilic bacteria in cool soil environments. Environ. Microbiol. 4, 595-602 (2002
-
(2002)
Environ. Microbiol
, vol.4
, pp. 595-602
-
-
Marchant, R.1
Banat, I.M.2
Rahman, T.J.3
Berzano, M.4
-
66
-
-
70349321701
-
A constant flux of diverse thermophilic bacteria into the cold Arctic seabed
-
Hubert, C. et al. A constant flux of diverse thermophilic bacteria into the cold Arctic seabed. Science 325, 1541-1544 (2009
-
(2009)
Science
, vol.325
, pp. 1541-1544
-
-
Hubert, C.1
-
67
-
-
84871372729
-
Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years
-
De Rezende, J. R. et al. Dispersal of thermophilic Desulfotomaculum endospores into Baltic Sea sediments over thousands of years. ISME J. 7, 72-84 (2012
-
(2012)
ISME J.
, vol.7
, pp. 72-84
-
-
De Rezende, J.R.1
-
68
-
-
84901288372
-
Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents
-
Müller, A. L. et al. Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents. ISME J. 8, 1153-1165 (2013
-
(2013)
ISME J.
, vol.8
, pp. 1153-1165
-
-
Müller, A.L.1
-
69
-
-
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
-
70
-
-
84855958621
-
Defining seasonal marine microbial community dynamics
-
Gilbert, J. A. et al. Defining seasonal marine microbial community dynamics. ISME J. 6, 298-308 (2011
-
(2011)
ISME J.
, vol.6
, pp. 298-308
-
-
Gilbert, J.A.1
-
71
-
-
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
-
72
-
-
76549087358
-
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000 year time scales in hydrothermal chimneys
-
Brazelton, W. J. et al. Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000 year time scales in hydrothermal chimneys. Proc. Natl Acad. Sci. USA 107, 1612-1617 (2010
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 1612-1617
-
-
Brazelton, W.J.1
-
73
-
-
84857065812
-
Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance
-
Sjöstedt, J. et al. Recruitment of members from the rare biosphere of marine bacterioplankton communities after an environmental disturbance. Appl. Environ. Microbiol. 78, 1361-1369 (2012
-
(2012)
Appl. Environ. Microbiol
, vol.78
, pp. 1361-1369
-
-
Sjöstedt, J.1
-
74
-
-
83655192963
-
Progress in understanding harmful algal blooms: Paradigm shifts and new technologies for research, monitoring, and management
-
Anderson, D. M., Cembella, A. D. & Hallegraeff, G. M. Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management. Annu. Rev. Mar. Sci. 4, 143-176 (2012
-
(2012)
Annu. Rev. Mar. Sci
, vol.4
, pp. 143-176
-
-
Anderson, D.M.1
Cembella, A.D.2
Hallegraeff, G.M.3
-
75
-
-
84875249654
-
Evidence for a persistent microbial seed bank throughout the global ocean
-
Gibbons, S. M. et al. Evidence for a persistent microbial seed bank throughout the global ocean. Proc. Natl Acad. Sci. USA 110, 4651-4655 (2013
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 4651-4655
-
-
Gibbons, S.M.1
-
76
-
-
77955263252
-
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts
-
Webster, N. S. et al. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ. Microbiol. 12, 2070-2082 (2010
-
(2010)
Environ. Microbiol
, vol.12
, pp. 2070-2082
-
-
Webster, N.S.1
-
77
-
-
84872914192
-
Sponge-specific bacteria are widespread (but rare) in diverse marine environments
-
Taylor, M. W. et al. "Sponge-specific" bacteria are widespread (but rare) in diverse marine environments. ISME J. 7, 438-443 (2012
-
(2012)
ISME J.
, vol.7
, pp. 438-443
-
-
Taylor, M.W.1
-
78
-
-
84908223133
-
Amphibian skin may select for rare environmental microbes
-
Walke, J. B. et al. Amphibian skin may select for rare environmental microbes. ISME J. 8, 2207-2217 (2014
-
(2014)
ISME J.
, vol.8
, pp. 2207-2217
-
-
Walke, J.B.1
-
79
-
-
84865323947
-
Microbial diversity in Arctic freshwaters is structured by inoculation of microbes from soils
-
Crump, B. C., Amaral-Zettler, L. A. & Kling, G. W. Microbial diversity in Arctic freshwaters is structured by inoculation of microbes from soils. ISME J. 6, 1629-1639 (2012
-
(2012)
ISME J.
, vol.6
, pp. 1629-1639
-
-
Crump, B.C.1
Amaral-Zettler, L.A.2
Kling, G.W.3
-
80
-
-
77953594953
-
The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
-
Kirchman, D. L., Cottrell, M. T. & Lovejoy, C. The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes. Environ. Microbiol. 12, 1132-1143 (2010
-
(2010)
Environ. Microbiol
, vol.12
, pp. 1132-1143
-
-
Kirchman, D.L.1
Cottrell, M.T.2
Lovejoy, C.3
-
81
-
-
84876045220
-
Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters
-
Hugoni, M. et al. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc. Natl Acad. Sci. USA 110, 6004-6009 (2013
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 6004-6009
-
-
Hugoni, M.1
-
82
-
-
84875883112
-
Fundamentals of microbial community resistance and resilience
-
Shade, A. et al. Fundamentals of microbial community resistance and resilience. Front. Microbiol. 3, 417 (2012
-
(2012)
Front. Microbiol
, vol.3
, pp. 417
-
-
Shade, A.1
-
83
-
-
0033574013
-
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis
-
Yachi, S. & Loreau, M. Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc. Natl Acad. Sci. USA 96, 1463-1468 (1999
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 1463-1468
-
-
Yachi, S.1
Loreau, M.2
-
84
-
-
80053650957
-
Resistance, resilience and recovery: Aquatic bacterial dynamics after water column disturbance
-
Shade, A. et al. Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environ. Microbiol. 13, 2752-2767 (2011
-
(2011)
Environ. Microbiol
, vol.13
, pp. 2752-2767
-
-
Shade, A.1
-
85
-
-
2942651148
-
Ecological linkages between aboveground and belowground biota
-
Wardle, D. A. et al. Ecological linkages between aboveground and belowground biota. Science 304, 1629-1633 (2004
-
(2004)
Science
, vol.304
, pp. 1629-1633
-
-
Wardle, D.A.1
-
86
-
-
77956288493
-
Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model
-
Miki, T., Ushio, M., Fukui, S. & Kondoh, M. Functional diversity of microbial decomposers facilitates plant coexistence in a plant-microbe-soil feedback model. Proc. Natl Acad. Sci. USA 107, 14251-14256 (2010
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 14251-14256
-
-
Miki, T.1
Ushio, M.2
Fukui, S.3
Kondoh, M.4
-
87
-
-
4344611656
-
High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean
-
Montoya, J. P. et al. High rates of N2 fixation by unicellular diazotrophs in the oligotrophic Pacific Ocean. Nature 430, 1027-1032 (2004
-
(2004)
Nature
, vol.430
, pp. 1027-1032
-
-
Montoya, J.P.1
-
88
-
-
84863990011
-
Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon
-
Ze, X., Duncan, S. H., Louis, P. & Flint, H. J. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J. 6, 1535-1543 (2012
-
(2012)
ISME J.
, vol.6
, pp. 1535-1543
-
-
Ze, X.1
Duncan, S.H.2
Louis, P.3
Flint, H.J.4
-
89
-
-
84905030166
-
Deciphering microbial interactions and detecting keystone species with co occurrence networks
-
Berry, D. & Widder, S. Deciphering microbial interactions and detecting keystone species with co occurrence networks. Front. Microbiol. 5, 219 (2014
-
(2014)
Front. Microbiol
, vol.5
, pp. 219
-
-
Berry, D.1
Widder, S.2
-
90
-
-
84905396568
-
Demonstrating microbial co occurrence pattern analyses within and between ecosystems
-
Williams, R. J., Howe, A. & Hofmockel, K. Demonstrating microbial co occurrence pattern analyses within and between ecosystems. Front. Microbiol. 5, 358 (2014
-
(2014)
Front. Microbiol
, vol.5
, pp. 358
-
-
Williams, R.J.1
Howe, A.2
Hofmockel, K.3
-
91
-
-
84860511582
-
The Black Queen Hypo thesis: Evolution of dependencies through adaptive gene loss
-
Morris, J. J., Lenski, R. E. & Zinser, E. R. The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036-12 (2012
-
(2012)
Mbio 3
, pp. e00036-12
-
-
Morris, J.J.1
Lenski, R.E.2
Zinser, E.R.3
-
92
-
-
25144486755
-
Molecular diversity and ecology of microbial plankton
-
Giovannoni, S. J. & Stingl, U. Molecular diversity and ecology of microbial plankton. Nature 437, 343-348 (2005
-
(2005)
Nature
, vol.437
, pp. 343-348
-
-
Giovannoni, S.J.1
Stingl, U.2
-
93
-
-
84884221217
-
Microbial community assembly, theory and rare functions
-
Pholchan, M. K., Baptista, J. C., Davenport, R. J., Sloan, W. T. & Curtis, T. P. Microbial community assembly, theory and rare functions. Front. Microbiol. 4, 68 (2013
-
(2013)
Front. Microbiol
, vol.4
, pp. 68
-
-
Pholchan, M.K.1
Baptista, J.C.2
Davenport, R.J.3
Sloan, W.T.4
Curtis, T.P.5
-
94
-
-
84895072762
-
Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm
-
Bartram, A. K. et al. Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS Microbiol. Ecol. 87, 403-415 (2014
-
(2014)
FEMS Microbiol. Ecol
, vol.87
, pp. 403-415
-
-
Bartram, A.K.1
-
95
-
-
78649448174
-
A rare biosphere microorganism contributes to sulfate reduction in a peatland
-
Pester, M., Bittner, N., Deevong, P., Wagner, M. & Loy, A. A rare biosphere microorganism contributes to sulfate reduction in a peatland. ISME J. 4, 1591-1602 (2010
-
(2010)
ISME J.
, vol.4
, pp. 1591-1602
-
-
Pester, M.1
Bittner, N.2
Deevong, P.3
Wagner, M.4
Loy, A.5
-
96
-
-
34948835698
-
Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism
-
Neufeld, J. D. et al. Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism. ISME J. 1, 480-491 (2007
-
(2007)
ISME J.
, vol.1
, pp. 480-491
-
-
Neufeld, J.D.1
-
97
-
-
77956095351
-
Big sulfur bacteria
-
Jørgensen, B. B. Big sulfur bacteria. ISME J. 4, 1083-1084 (2010
-
(2010)
ISME J.
, vol.4
, pp. 1083-1084
-
-
Jørgensen, B.B.1
-
98
-
-
0033067617
-
Thioploca spp.: Filamentous sulfur bacteria with nitrate vacuoles
-
Jørgensen, B. B. & Gallardo, V. A. Thioploca spp.: filamentous sulfur bacteria with nitrate vacuoles. FEMS Microbiol. Ecol. 28, 301-313 (1999
-
(1999)
FEMS Microbiol. Ecol
, vol.28
, pp. 301-313
-
-
Jørgensen, B.B.1
Gallardo, V.A.2
-
99
-
-
0033574742
-
Dense populations of a giant sulfur bacterium in Namibian shelf sediments
-
Schulz, H. et al. Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284, 493-495 (1999
-
(1999)
Science
, vol.284
, pp. 493-495
-
-
Schulz, H.1
-
100
-
-
77955237433
-
Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 N
-
Jørgensen, B. B., Dunker, R., Grünke, S. & Røy, H. Filamentous sulfur bacteria, Beggiatoa spp., in arctic marine sediments (Svalbard, 79 N). FEMS Microbiol. Ecol. 73, 500-513 (2010
-
(2010)
FEMS Microbiol. Ecol
, vol.73
, pp. 500-513
-
-
Jørgensen, B.B.1
Dunker, R.2
Grünke, S.3
Røy, H.4
-
101
-
-
77949899455
-
Reduction of rare soil microbes modifies plant-herbivore interactions
-
Hol, W. H. G. et al. Reduction of rare soil microbes modifies plant-herbivore interactions. Ecol. Lett. 13, 292-301 (2010
-
(2010)
Ecol. Lett
, vol.13
, pp. 292-301
-
-
Hol, W.H.G.1
-
102
-
-
84904687373
-
Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression
-
Fisher, C. K. & Mehta, P. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression. PLoS ONE 9, e102451 (2014
-
(2014)
PLoS ONE
, vol.9
, pp. e102451
-
-
Fisher, C.K.1
Mehta, P.2
-
103
-
-
69549129476
-
The rare biosphere: A reality check
-
Reeder, J. & Knight, R. The rare biosphere: a reality check. Nature Methods 6, 636-637 (2009
-
(2009)
Nature Methods
, vol.6
, pp. 636-637
-
-
Reeder, J.1
Knight, R.2
-
104
-
-
33745038020
-
Much more than a prized and local fungal delicacy
-
Mello, A., Murat, C. & Bonfante, P. Truffles: much more than a prized and local fungal delicacy. FEMS Microbiol. Lett. 260, 1-8 (2006
-
(2006)
FEMS Microbiol. Lett
, vol.260
, pp. 1-8
-
-
Mello, A.1
Murat, C.2
Truffles, B.P.3
-
105
-
-
84881138595
-
Insights into the phylogeny and coding potential of microbial dark matter
-
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013
-
(2013)
Nature
, vol.499
, pp. 431-437
-
-
Rinke, C.1
-
106
-
-
79952806659
-
Stalking the fourth domain in metagenomic data: Searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees
-
Wu, D. et al. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS ONE 6, e18011 (2011
-
(2011)
PLoS ONE
, vol.6
, pp. e18011
-
-
Wu, D.1
-
107
-
-
84960449500
-
Norwegian deep-water coral reefs: Cultivation and molecular analysis of planktonic microbial communities
-
Jensen, S., Lynch, M. D. J., Ray, J. L., Neufeld, J. D. & Hovland, M. Norwegian deep-water coral reefs: cultivation and molecular analysis of planktonic microbial communities. Environ. Microbiol. http://dx. doi.org/10.1111/1462-2920.12531 (2014
-
(2014)
Environ. Microbiol
-
-
Jensen, S.1
Lynch, M.D.J.2
Ray, J.L.3
Neufeld, J.D.4
Hovland, M.5
-
108
-
-
0031662188
-
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity
-
Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774 (1998
-
(1998)
J. Bacteriol
, vol.180
, pp. 4765-4774
-
-
Hugenholtz, P.1
Goebel, B.M.2
Pace, N.R.3
-
109
-
-
79955025122
-
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
-
Goodman, A. L. et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108, 6252-6257 (2011
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 6252-6257
-
-
Goodman, A.L.1
-
110
-
-
0030765047
-
Dominant marine bacterioplankton species found among colony-forming bacteria
-
Pinhassi, J., Zweifel, U. L. & Hagstroëm, A. Dominant marine bacterioplankton species found among colony-forming bacteria. Appl. Environ. Microbiol. 63, 3359-3366 (1997
-
(1997)
Appl. Environ. Microbiol
, vol.63
, pp. 3359-3366
-
-
Pinhassi, J.1
Zweifel, U.L.2
Hagstroëm, A.3
-
111
-
-
0037180507
-
Cultivating the uncultured
-
Zengler, K. et al. Cultivating the uncultured. Proc. Natl Acad. Sci. USA 99, 15681-15686 (2002
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 15681-15686
-
-
Zengler, K.1
-
112
-
-
2142687113
-
Laboratory cultivation of widespread and previously uncultured soil bacteria
-
Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69, 7210-7215 (2003
-
(2003)
Appl. Environ. Microbiol
, vol.69
, pp. 7210-7215
-
-
Joseph, S.J.1
Hugenholtz, P.2
Sangwan, P.3
Osborne, C.A.4
Janssen, P.H.5
-
113
-
-
0038265180
-
Cultivation of recalcitrant microbes: Cells are alive, well and revealing their secrets in the 21st century laboratory
-
Leadbetter, J. R. Cultivation of recalcitrant microbes: cells are alive, well and revealing their secrets in the 21st century laboratory. Curr. Opin. Microbiol. 6, 274-281 (2003
-
(2003)
Curr. Opin. Microbiol
, vol.6
, pp. 274-281
-
-
Leadbetter, J.R.1
-
114
-
-
34249112197
-
Cultivation gives context to the microbial ecologist
-
Nichols, D. Cultivation gives context to the microbial ecologist. FEMS Microbiol. Ecol. 60, 351-357 (2007
-
(2007)
FEMS Microbiol. Ecol
, vol.60
, pp. 351-357
-
-
Nichols, D.1
-
115
-
-
80053637866
-
Chthonomonas calidirosea gen nov., sp. Nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10
-
Lee, K. C. Y. et al. Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10. Int. J. Syst. Evol. Microbiol. 61, 2482-2490 (2011
-
(2011)
Int. J. Syst. Evol. Microbiol
, vol.61
, pp. 2482-2490
-
-
Lee, K.C.Y.1
-
116
-
-
43549113806
-
Scratching the surface of the rare biosphere with ribosomal sequence tag primers
-
Neufeld, J. D., Li, J. & Mohn, W. W. Scratching the surface of the rare biosphere with ribosomal sequence tag primers. FEMS Microbiol. Lett. 283, 146-153 (2008
-
(2008)
FEMS Microbiol. Lett
, vol.283
, pp. 146-153
-
-
Neufeld, J.D.1
Li, J.2
Mohn, W.W.3
-
117
-
-
0035146134
-
Novel bacterial lineages at the (sub) division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms
-
Derakshani, M., Lukow, T. & Liesack, W. Novel bacterial lineages at the (sub) division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67, 623-631 (2001
-
(2001)
Appl. Environ. Microbiol
, vol.67
, pp. 623-631
-
-
Derakshani, M.1
Lukow, T.2
Liesack, W.3
-
118
-
-
84856087315
-
Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses
-
Nakai, R. et al. Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses. Polar Biol. 35, 425-433 (2012
-
(2012)
Polar Biol
, vol.35
, pp. 425-433
-
-
Nakai, R.1
-
119
-
-
84860146462
-
An early-branching microbialite cyanobacterium forms intracellular carbonates
-
Couradeau, E. et al. An early-branching microbialite cyanobacterium forms intracellular carbonates. Science 336, 459-462 (2012
-
(2012)
Science
, vol.336
, pp. 459-462
-
-
Couradeau, E.1
-
120
-
-
84885143535
-
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria
-
Di Rienzi, S. C. et al. The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. eLife 2, e01102 (2013
-
(2013)
ELife
, vol.2
, pp. e01102
-
-
Di Rienzi, S.C.1
-
121
-
-
77951498638
-
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
-
Engelbrektson, A. et al. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4, 642-647 (2010
-
(2010)
ISME J.
, vol.4
, pp. 642-647
-
-
Engelbrektson, A.1
-
122
-
-
84906330281
-
Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles
-
Kennedy, K., Hall, M. W., Lynch, M. D. J., Moreno Hagelsieb, G. & Neufeld, J. D. Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles. Appl. Environ. Microbiol. 80, 5717-5722 (2014
-
(2014)
Appl. Environ. Microbiol
, vol.80
, pp. 5717-5722
-
-
Kennedy, K.1
Hall, M.W.2
Lynch, M.D.J.3
Moreno Hagelsieb, G.4
Neufeld, J.D.5
-
123
-
-
84865060813
-
PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets
-
Pinto, A. J. & Raskin, L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS ONE 7, e43093 (2012
-
(2012)
PLoS ONE
, vol.7
, pp. e43093
-
-
Pinto, A.J.1
Raskin, L.2
-
124
-
-
84862276328
-
Human Microbiome Project Consortium. Structure function and diversity of the healthy human microbiome
-
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
125
-
-
34248211629
-
Finding the needles in the metagenome haystack
-
Kowalchuk, G. A., Speksnijder, A. G. C. L., Zhang, K., Goodman, R. M. & Veen, J. A. Finding the needles in the metagenome haystack. Microb. Ecol. 53, 475-485 (2007
-
(2007)
Microb. Ecol
, vol.53
, pp. 475-485
-
-
Kowalchuk, G.A.1
Speksnijder, A.G.C.L.2
Zhang, K.3
Goodman, R.M.4
Veen, J.A.5
-
126
-
-
84879678051
-
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
-
Albertsen, M. et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotech. 31, 533-538 (2013
-
(2013)
Nature Biotech
, vol.31
, pp. 533-538
-
-
Albertsen, M.1
-
127
-
-
84871125786
-
Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data
-
Frisli, T., Haverkamp, T., Jakobsen, K., Stenseth, N. C. & Rudi, K. Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data. J. Appl. Microbiol. 114, 141-151 (2013
-
(2013)
J. Appl. Microbiol
, vol.114
, pp. 141-151
-
-
Frisli, T.1
Haverkamp, T.2
Jakobsen, K.3
Stenseth, N.C.4
Rudi, K.5
-
128
-
-
23944525404
-
Computational improvements reveal great bacterial diversity and high metal toxicity in soil
-
Gans, J., Wolinsky, M. & Dunbar, J. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387-1390 (2005
-
(2005)
Science
, vol.309
, pp. 1387-1390
-
-
Gans, J.1
Wolinsky, M.2
Dunbar, J.3
-
129
-
-
33746639717
-
Toward a census of bacteria in soil
-
Schloss, P. D. & Handelsman, J. Toward a census of bacteria in soil. PLoS Comput. Biol. 2, 786-793 (2006
-
(2006)
PLoS Comput. Biol
, vol.2
, pp. 786-793
-
-
Schloss, P.D.1
Handelsman, J.2
-
130
-
-
34547540925
-
Dissecting biological dark matter with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
-
Marcy, Y. et al. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889-11894 (2007
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 11889-11894
-
-
Marcy, Y.1
-
131
-
-
34249701816
-
Targeted access to the genomes of low-abundance organisms in complex microbial communities
-
Podar, M. et al. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73, 3205-3214 (2007
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 3205-3214
-
-
Podar, M.1
-
132
-
-
0033140334
-
Rrna probe-based cell fishing of bacteria
-
Stoffels, M., Ludwig, W. & Schleifer, K. H. rRNA probe-based cell fishing of bacteria. Environ. Microbiol. 1, 259-271 (1999
-
(1999)
Environ. Microbiol
, vol.1
, pp. 259-271
-
-
Stoffels, M.1
Ludwig, W.2
Schleifer, K.H.3
-
133
-
-
40249095175
-
Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology
-
Binga, E. K., Lasken, R. S. & Neufeld, J. D. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2, 233-241 (2008
-
(2008)
ISME J.
, vol.2
, pp. 233-241
-
-
Binga, E.K.1
Lasken, R.S.2
Neufeld, J.D.3
-
134
-
-
34248577608
-
DNA stable-isotope probing
-
Neufeld, J. D. et al. DNA stable-isotope probing. Nature Protoc. 2, 860-866 (2007
-
(2007)
Nature Protoc
, vol.2
, pp. 860-866
-
-
Neufeld, J.D.1
-
135
-
-
84908291385
-
Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities
-
Verastegui, Y. et al. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities. mBio 5, e01157-14 (2014
-
(2014)
Mbio
, vol.5
, pp. e01157-e01214
-
-
Verastegui, Y.1
-
136
-
-
23744483488
-
Suicide polymerase endonuclease restriction, a novel technique for enhancing PCR amplification of minor DNA templates
-
Green, S. J. & Minz, D. Suicide polymerase endonuclease restriction, a novel technique for enhancing PCR amplification of minor DNA templates. Appl. Environ. Microbiol. 71, 4721-4727 (2005
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 4721-4727
-
-
Green, S.J.1
Minz, D.2
-
137
-
-
84855949949
-
Using network analysis to explore co occurrence patterns in soil microbial communities
-
Barberán, A., Bates, S. T., Casamayor, E. O. & Fierer, N. Using network analysis to explore co occurrence patterns in soil microbial communities. ISME J. 6, 343-351 (2011
-
(2011)
ISME J.
, vol.6
, pp. 343-351
-
-
Barberán, A.1
Bates, S.T.2
Casamayor, E.O.3
Fierer, N.4
-
138
-
-
0031284508
-
Species assemblages and indicator species: The need for a flexible asymmetrical approach
-
Dufrêne, M. & Legendre, P. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Monogr. 67, 345-366 (1997
-
(1997)
Ecol. Monogr
, vol.67
, pp. 345-366
-
-
Dufrêne, M.1
Legendre, P.2
-
139
-
-
84876122754
-
The future is now: Single-cell genomics of bacteria and archaea
-
Blainey, P. C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407-427 (2013
-
(2013)
FEMS Microbiol. Rev
, vol.37
, pp. 407-427
-
-
Blainey, P.C.1
-
140
-
-
84865720868
-
Culturing captures members of the soil rare biosphere
-
Shade, A. et al. Culturing captures members of the soil rare biosphere. Environ. Microbiol. 14, 2247-2252 (2012
-
(2012)
Environ. Microbiol
, vol.14
, pp. 2247-2252
-
-
Shade, A.1
-
141
-
-
0000594195
-
Evolution and measurement of species diversity
-
Whittaker, R. H. Evolution and measurement of species diversity. Taxon 21, 213-251 (1972
-
(1972)
Taxon
, vol.21
, pp. 213-251
-
-
Whittaker, R.H.1
-
143
-
-
35348949524
-
Neutral assembly of bacterial communities
-
Woodcock, S. et al. Neutral assembly of bacterial communities. FEMS Microbiol. Ecol. 62, 171-180 (2007
-
(2007)
FEMS Microbiol. Ecol
, vol.62
, pp. 171-180
-
-
Woodcock, S.1
-
144
-
-
21744447099
-
The co distribution of species in relation to the neutral theory of community ecology
-
Bell, G. The co distribution of species in relation to the neutral theory of community ecology. Ecology 86, 1757-1770 (2005
-
(2005)
Ecology
, vol.86
, pp. 1757-1770
-
-
Bell, G.1
-
145
-
-
77957270949
-
Combined niche and neutral effects in a microbial wastewater treatment community
-
Ofi?eru, I. D. et al. Combined niche and neutral effects in a microbial wastewater treatment community. Proc. Natl Acad. Sci. USA 107, 15345-15350 (2010
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 15345-15350
-
-
Ofieru, I.D.1
-
146
-
-
84880919285
-
Phylogenetic beta diversity in bacterial assemblages across ecosystems: Deterministic versus stochastic processes
-
Wang, J. et al. Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes. ISME J. 7, 1310-1321 (2013
-
(2013)
ISME J.
, vol.7
, pp. 1310-1321
-
-
Wang, J.1
-
147
-
-
84856746382
-
Macroecology of unicellular organisms - Patterns and processes
-
Soininen, J. Macroecology of unicellular organisms - patterns and processes. Environ. Microbiol. Rep. 4, 10-22 (2012
-
(2012)
Environ. Microbiol. Rep
, vol.4
, pp. 10-22
-
-
Soininen, J.1
-
148
-
-
33747174849
-
Spatial scaling of microbial biodiversity
-
Green, J. & Bohannan, B. J. M. Spatial scaling of microbial biodiversity. Trends Ecol. Evol. 21, 501-507 (2006
-
(2006)
Trends Ecol. Evol
, vol.21
, pp. 501-507
-
-
Green, J.1
Bohannan, B.J.M.2
-
150
-
-
84902141062
-
Commonness and rarity in the marine biosphere
-
Connolly, S. R. et al. Commonness and rarity in the marine biosphere. Proc. Natl Acad. Sci. USA 111, 8524-8529 (2014
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 8524-8529
-
-
Connolly, S.R.1
-
151
-
-
34548536276
-
Species abundance distributions: Moving beyond single prediction theories to integration within an ecological framework
-
McGill, B. J. et al. Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework. Ecol. Lett. 10, 995-1015 (2007
-
(2007)
Ecol. Lett
, vol.10
, pp. 995-1015
-
-
McGill, B.J.1
-
152
-
-
0029789623
-
A quantitative map of nucleotide substitution rates in bacterial rRNA
-
Van de Peer, Y., Chapelle, S. & De Wachter, R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 24, 3381-3391 (1996
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 3381-3391
-
-
Van De Peer, Y.1
Chapelle, S.2
De Wachter, R.3
-
153
-
-
34548293679
-
Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Nave Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261-5267 (2007
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
154
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium
-
Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
155
-
-
37349073351
-
Microbial communities in nature: A postgenomic perspective
-
Klein, D. Microbial communities in nature: a postgenomic perspective. Microbe 2, 591-595 (2007
-
(2007)
Microbe
, vol.2
, pp. 591-595
-
-
Klein, D.1
-
156
-
-
34548546604
-
Cycling of extracellular DNA in the soil environment
-
Levy-Booth, D. J. et al. Cycling of extracellular DNA in the soil environment. Soil Biol. Biochem. 39, 2977-2991 (2007
-
(2007)
Soil Biol. Biochem
, vol.39
, pp. 2977-2991
-
-
Levy-Booth, D.J.1
-
157
-
-
0037390078
-
Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5? Nuclease PCR
-
Nogva, H. K., Dromtorp, S., Nissen, H. & Rudi, K. Ethidium monoazide for DNA-based differentiation of viable and dead bacteria by 5? nuclease PCR. Biotechniques 34, 804-813 (2003
-
(2003)
Biotechniques
, vol.34
, pp. 804-813
-
-
Nogva, H.K.1
Dromtorp, S.2
Nissen, H.3
Rudi, K.4
-
158
-
-
13544254304
-
Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples
-
Rudi, K., Moen, B., Drømtorp, S. M. & Holck, A. L. Use of ethidium monoazide and PCR in combination for quantification of viable and dead cells in complex samples. Appl. Environ. Microbiol. 71, 1018-1024 (2005
-
(2005)
Appl. Environ. Microbiol
, vol.71
, pp. 1018-1024
-
-
Rudi, K.1
Moen, B.2
Drømtorp, S.M.3
Holck, A.L.4
-
159
-
-
33748746842
-
Comparison of propidium monoazide with ethidium monoazide for differentiation of live versus dead bacteria by selective removal of DNA from dead cells
-
Nocker, A., Cheung, C. Y. & Camper, A. K. Comparison of propidium monoazide with ethidium monoazide for differentiation of live versus dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods 67, 310-320 (2006
-
(2006)
J. Microbiol. Methods
, vol.67
, pp. 310-320
-
-
Nocker, A.1
Cheung, C.Y.2
Camper, A.K.3
-
160
-
-
37349080565
-
Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells
-
Pan, Y. & Breidt, F. Enumeration of viable Listeria monocytogenes cells by real-time PCR with propidium monoazide and ethidium monoazide in the presence of dead cells. Appl. Environ. Microbiol. 73, 8028-8031 (2007
-
(2007)
Appl. Environ. Microbiol
, vol.73
, pp. 8028-8031
-
-
Pan, Y.1
Breidt, F.2
-
161
-
-
77956881490
-
Soil microbial abundance and diversity along a low precipitation gradient
-
Bachar, A. et al. Soil microbial abundance and diversity along a low precipitation gradient. Microb. Ecol. 60, 453-461 (2010
-
(2010)
Microb. Ecol
, vol.60
, pp. 453-461
-
-
Bachar, A.1
-
162
-
-
42349085540
-
Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide
-
Wagner, A. O., Malin, C., Knapp, B. A. & Illmer, P. Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Appl. Environ. Microbiol. 74, 2537-2539 (2008
-
(2008)
Appl. Environ. Microbiol
, vol.74
, pp. 2537-2539
-
-
Wagner, A.O.1
Malin, C.2
Knapp, B.A.3
Illmer, P.4
-
163
-
-
34249908634
-
Insufficient differentiation of live and dead Campylobacter jejuni and Listeria monocytogenes cells by ethidium monoazide (EMA) compromises EMA/real-time PCR
-
Flekna, G. et al. Insufficient differentiation of live and dead Campylobacter jejuni and Listeria monocytogenes cells by ethidium monoazide (EMA) compromises EMA/real-time PCR. Res. Microbiol. 158, 405-412 (2007
-
(2007)
Res. Microbiol
, vol.158
, pp. 405-412
-
-
Flekna, G.1
-
164
-
-
64849090618
-
Unsuitable distinction between viable and dead Staphylococcus aureus and Staphylococcus epidermidis by ethidium bromide monoazide
-
Kobayashi, H., Oethinger, M., Tuohy, M., Hall, G. & Bauer, T. Unsuitable distinction between viable and dead Staphylococcus aureus and Staphylococcus epidermidis by ethidium bromide monoazide. Lett. Appl. Microbiol. 48, 633-638 (2009
-
(2009)
Lett. Appl. Microbiol
, vol.48
, pp. 633-638
-
-
Kobayashi, H.1
Oethinger, M.2
Tuohy, M.3
Hall, G.4
Bauer, T.5
-
165
-
-
0037401010
-
Molecular methods for the assessment of bacterial viability
-
Keer, J. & Birch, L. Molecular methods for the assessment of bacterial viability. J. Microbiol. Methods 53, 175-183 (2003
-
(2003)
J. Microbiol. Methods
, vol.53
, pp. 175-183
-
-
Keer, J.1
Birch, L.2
-
166
-
-
84886725824
-
Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses
-
Blazewicz, S. J., Barnard, R. L., Daly, R. A. & Firestone, M. K. Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME J. 7, 2061-2068 (2013
-
(2013)
ISME J.
, vol.7
, pp. 2061-2068
-
-
Blazewicz, S.J.1
Barnard, R.L.2
Daly, R.A.3
Firestone, M.K.4
-
167
-
-
84904569753
-
Conducting a microbiome study
-
Goodrich, J. K. et al. Conducting a microbiome study. Cell 158, 250-262 (2014
-
(2014)
Cell
, vol.158
, pp. 250-262
-
-
Goodrich, J.K.1
-
168
-
-
84876117081
-
Effects of OTU clustering and PCR artifacts on microbial diversity estimates
-
Patin, N. V., Kunin, V., Lidström, U. & Ashby, M. N. Effects of OTU clustering and PCR artifacts on microbial diversity estimates. Microb. Ecol. 65, 709-719 (2013
-
(2013)
Microb. Ecol
, vol.65
, pp. 709-719
-
-
Patin, N.V.1
Kunin, V.2
Lidström, U.3
Ashby, M.N.4
-
169
-
-
83355173006
-
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
-
Schloss, P. D., Gevers, D. & Westcott, S. L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6, e27310 (2011
-
(2011)
PLoS ONE
, vol.6
, pp. e27310
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
-
170
-
-
84866065801
-
Groundtruthing next-gen sequencing for microbial ecology - Biases and errors in community structure estimates from PCR amplicon pyrosequencing
-
Lee, C. K. et al. Groundtruthing next-gen sequencing for microbial ecology - biases and errors in community structure estimates from PCR amplicon pyrosequencing. PLoS ONE 7, e44224 (2012
-
(2012)
PLoS ONE
, vol.7
, pp. e44224
-
-
Lee, C.K.1
-
171
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
172
-
-
5044240973
-
Bellerophon: A program to detect chimeric sequences in multiple sequence alignments
-
Huber, T., Faulkner, G. & Hugenholtz, P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319 (2004
-
(2004)
Bioinformatics
, vol.20
, pp. 2317-2319
-
-
Huber, T.1
Faulkner, G.2
Hugenholtz, P.3
-
173
-
-
79251565226
-
Removing noise from pyrosequenced amplicons
-
Quince, C., Lanzen, A., Davenport, R. J. & Turnbaugh, P. J. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12, 38 (2011
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
174
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince, C. et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 6, 639-641 (2009
-
(2009)
Nature Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
-
175
-
-
78650453707
-
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
-
Claesson, M. J. et al. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 38, e200 (2010
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e200
-
-
Claesson, M.J.1
-
176
-
-
84879138105
-
A filtering method to generate high quality short reads using Illumina paired-end technology
-
Eren, A. M., Vineis, J. H., Morrison, H. G. & Sogin, M. L. A filtering method to generate high quality short reads using Illumina paired-end technology. PLoS ONE 8, e66643 (2013
-
(2013)
PLoS ONE
, vol.8
, pp. e66643
-
-
Eren, A.M.1
Vineis, J.H.2
Morrison, H.G.3
Sogin, M.L.4
-
177
-
-
84876500108
-
Secondary structure improves OTU assignments of 16S rRNA gene sequences
-
Schloss, P. D. Secondary structure improves OTU assignments of 16S rRNA gene sequences. ISME J. 7, 457-460 (2013
-
(2013)
ISME J.
, vol.7
, pp. 457-460
-
-
Schloss, P.D.1
-
178
-
-
65549111754
-
Infernal 1.0: Inference of RNA alignments
-
Nawrocki, E. P., Kolbe, D. L. & Eddy, S. R. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335-1337 (2009
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
Kolbe, D.L.2
Eddy, S.R.3
-
179
-
-
84864134721
-
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
-
Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829 (2012
-
(2012)
Bioinformatics
, vol.28
, pp. 1823-1829
-
-
Pruesse, E.1
Peplies, J.2
Glöckner, F.O.3
-
180
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
Cannone, J. J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 1-31 (2002
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 1-31
-
-
Cannone, J.J.1
-
181
-
-
84921613578
-
Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production
-
Doxey, A. C. et al. Aquatic metagenomes implicate Thaumarchaeota in global cobalamin production. ISME J. 9, 461-471 (2015
-
(2015)
ISME J.
, vol.9
, pp. 461-471
-
-
Doxey, A.C.1
|