-
1
-
-
0022216068
-
Constraints on the coevolution of bacteria and virulent phage: A model, some experiments, and predictions for natural communities
-
Lenski RE, Levin BR (1985) Constraints on the coevolution of bacteria and virulent phage: A model, some experiments, and predictions for natural communities. Am Nat 125: 585-602.
-
(1985)
Am Nat
, vol.125
, pp. 585-602
-
-
Lenski, R.E.1
Levin, B.R.2
-
2
-
-
0033826796
-
Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems
-
Thingstad TF (2000) Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr 45: 1320-1328.
-
(2000)
Limnol Oceanogr
, vol.45
, pp. 1320-1328
-
-
Thingstad, T.F.1
-
3
-
-
0031401197
-
Effect of resource enrichment on a chemostat community of bacteria and bacteriophage
-
Bohannan BJM, Lenski RE (1997) Effect of resource enrichment on a chemostat community of bacteria and bacteriophage. Ecology 78: 2303-2315.
-
(1997)
Ecology
, vol.78
, pp. 2303-2315
-
-
Bohannan, B.J.M.1
Lenski, R.E.2
-
4
-
-
34548692945
-
Cryptic population dynamics: Rapid evolution masks trophic interactions
-
Yoshida T, Ellner SP, Jones LE, Bohannan BJM, Lenski RE, et al. (2007) Cryptic population dynamics: Rapid evolution masks trophic interactions. PLoS Biol 5: 1868-1879.
-
(2007)
PLoS Biol
, vol.5
, pp. 1868-1879
-
-
Yoshida, T.1
Ellner, S.P.2
Jones, L.E.3
Bohannan, B.J.M.4
Lenski, R.E.5
-
5
-
-
0031409490
-
Prey adaptation as a cause of predator-prey cycles
-
Abrams PA, Matsuda H (1997) Prey adaptation as a cause of predator-prey cycles. Evolution 51: 1742-1750.
-
(1997)
Evolution
, vol.51
, pp. 1742-1750
-
-
Abrams, P.A.1
Matsuda, H.2
-
6
-
-
70350180460
-
Explaining microbial population genomics through phage predation
-
Rodriguez-Valera F, Martin-Cuadrado AB, Rodriguez-Brito B, Pašić L, Thingstad TF, et al. (2009) Explaining microbial population genomics through phage predation. Nat Rev Microbiol 7: 828-836.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 828-836
-
-
Rodriguez-Valera, F.1
Martin-Cuadrado, A.B.2
Rodriguez-Brito, B.3
Pašić, L.4
Thingstad, T.F.5
-
7
-
-
0032987301
-
Effect of prey heterogeneity on the response of a model food chain to resource enrichment
-
Bohannan BJM, Lenski RE (1999) Effect of prey heterogeneity on the response of a model food chain to resource enrichment. Am Nat 153: 73-82.
-
(1999)
Am Nat
, vol.153
, pp. 73-82
-
-
Bohannan, B.J.M.1
Lenski, R.E.2
-
8
-
-
0033784827
-
Bacterial growth rate and marine virus-host dynamics
-
Middelboe M (2000) Bacterial growth rate and marine virus-host dynamics. Microb Ecol 40: 114-124.
-
(2000)
Microb Ecol
, vol.40
, pp. 114-124
-
-
Middelboe, M.1
-
9
-
-
77952670727
-
Viral and microbial community dynamics in four aquatic environments
-
Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, et al. (2010) Viral and microbial community dynamics in four aquatic environments. ISME J 4: 739-751.
-
(2010)
ISME J
, vol.4
, pp. 739-751
-
-
Rodriguez-Brito, B.1
Li, L.2
Wegley, L.3
Furlan, M.4
Angly, F.5
-
10
-
-
22144446352
-
Coevolutionary arms races between bacteria and bacteriophage
-
Weitz JS, Hartman H, Levin SA (2005) Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci USA 102: 9535-9540.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 9535-9540
-
-
Weitz, J.S.1
Hartman, H.2
Levin, S.A.3
-
11
-
-
77749309301
-
Trade-offs between competition and defense specialists among unicellular planktonic organisms: The ''Killing the Winner'' hypothesis revisited
-
Winter C, Bouvier T, Weinbauer MG, Thingstad TF (2010) 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)
Microbiol Mol Biol Rev
, vol.74
, pp. 42-57
-
-
Winter, C.1
Bouvier, T.2
Weinbauer, M.G.3
Thingstad, T.F.4
-
12
-
-
68249096294
-
Bacteriophages drive strain diversification in a marine Flavobacterium: Implications for phage resistance and physiological properties
-
Middelboe M, Holmfeldt K, Riemann L, Nybroe O, Haaber J (2009) Bacteriophages drive strain diversification in a marine Flavobacterium: implications for phage resistance and physiological properties. Environ Microbiol 11: 1971-1982.
-
(2009)
Environ Microbiol
, vol.11
, pp. 1971-1982
-
-
Middelboe, M.1
Holmfeldt, K.2
Riemann, L.3
Nybroe, O.4
Haaber, J.5
-
14
-
-
0347933053
-
The effect of spatial heterogeneity and parasites on the evolution of host diversity
-
Brockhurst MA, Rainey PB, Buckling A (2004) The effect of spatial heterogeneity and parasites on the evolution of host diversity. Proc R Soc Lond B Biol Sci 271: 107-111.
-
(2004)
Proc R Soc Lond B Biol Sci
, vol.271
, pp. 107-111
-
-
Brockhurst, M.A.1
Rainey, P.B.2
Buckling, A.3
-
15
-
-
0000123207
-
The paradox of the plankton
-
Hutchinson GE (1961) The paradox of the plankton. Am Nat 95: 137-145.
-
(1961)
Am Nat
, vol.95
, pp. 137-145
-
-
Hutchinson, G.E.1
-
16
-
-
35948993040
-
Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts
-
Holmfeldt K, Middelboe M, Nybroe O, Riemann L (2007) Large variabilities in host strain susceptibility and phage host range govern interactions between lytic marine phages and their Flavobacterium hosts. Applied and Environmental Microbiology 73: 6730-6739.
-
(2007)
Applied and Environmental Microbiology
, vol.73
, pp. 6730-6739
-
-
Holmfeldt, K.1
Middelboe, M.2
Nybroe, O.3
Riemann, L.4
-
17
-
-
34047118522
-
CRISPR provides acquired resistance against viruses in prokaryotes
-
Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, et al. (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
-
(2007)
Science
, vol.315
, pp. 1709-1712
-
-
Barrangou, R.1
Fremaux, C.2
Deveau, H.3
Richards, M.4
Boyaval, P.5
-
18
-
-
57849137502
-
CRISPR interference limits horizontal gene transfer in Staphylococci by Targeting DNA
-
Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in Staphylococci by Targeting DNA. Science 322: 1843-1845.
-
(2008)
Science
, vol.322
, pp. 1843-1845
-
-
Marraffini, L.A.1
Sontheimer, E.J.2
-
19
-
-
23844505202
-
Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin
-
Bolotin A, Quinquis B, Sorokin A, Ehrlich SD (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 151: 2551-2561.
-
(2005)
Microbiology
, vol.151
, pp. 2551-2561
-
-
Bolotin, A.1
Quinquis, B.2
Sorokin, A.3
Ehrlich, S.D.4
-
20
-
-
16444385662
-
Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements
-
Mojica FJM, Di{dotless}́ez-Villasenñor C, Garci{dotless}́a-Marti{dotless}́nez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60: 174-182.
-
(2005)
J Mol Evol
, vol.60
, pp. 174-182
-
-
Mojica, F.J.M.1
Díez-Villasenñor, C.2
García-Martínez, J.3
Soria, E.4
-
21
-
-
15844390228
-
CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies
-
Pourcel C, Salvignol G, Vergnaud G (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 151: 653-663.
-
(2005)
Microbiology
, vol.151
, pp. 653-663
-
-
Pourcel, C.1
Salvignol, G.2
Vergnaud, G.3
-
22
-
-
38949123143
-
Phage response to CRISPR-encoded resistance in Streptococcus thermophilus
-
Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, et al. (2008) Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J Bacteriol 190: 1390-1400.
-
(2008)
J Bacteriol
, vol.190
, pp. 1390-1400
-
-
Deveau, H.1
Barrangou, R.2
Garneau, J.E.3
Labonté, J.4
Fremaux, C.5
-
23
-
-
32944477673
-
The evolution of adaptive immunity
-
Pancer Z, Cooper MD (2006) The evolution of adaptive immunity. Annu Rev Immunol 24: 497-518.
-
(2006)
Annu Rev Immunol
, vol.24
, pp. 497-518
-
-
Pancer, Z.1
Cooper, M.D.2
-
24
-
-
38949214103
-
Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus
-
Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, et al. (2008) Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol 190: 1401-1412.
-
(2008)
J Bacteriol
, vol.190
, pp. 1401-1412
-
-
Horvath, P.1
Romero, D.A.2
Coûté-Monvoisin, A.C.3
Richards, M.4
Deveau, H.5
-
25
-
-
38149061877
-
Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
-
Tyson GW, Banfield JF (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10: 200-207.
-
(2008)
Environ Microbiol
, vol.10
, pp. 200-207
-
-
Tyson, G.W.1
Banfield, J.F.2
-
26
-
-
58349087246
-
Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes
-
Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D (2009) Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes. PLoS ONE 4: e4169.
-
(2009)
PLoS ONE
, vol.4
-
-
Heidelberg, J.F.1
Nelson, W.C.2
Schoenfeld, T.3
Bhaya, D.4
-
27
-
-
70849124144
-
Variety-the splice of life-in microbial communities
-
Banfield JF, Young M (2009) Variety-the splice of life-in microbial communities. Science 326: 1198-1199.
-
(2009)
Science
, vol.326
, pp. 1198-1199
-
-
Banfield, J.F.1
Young, M.2
-
28
-
-
27844577665
-
Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus
-
Whitaker RJ, Grogan DW, Taylor JW (2005) Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol 22: 2354-2361.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 2354-2361
-
-
Whitaker, R.J.1
Grogan, D.W.2
Taylor, J.W.3
-
30
-
-
34249027580
-
Inference of bacterial microevolution using multilocus sequence data
-
Didelot X, Falush D (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
-
(2007)
Genetics
, vol.175
, pp. 1251-1266
-
-
Didelot, X.1
Falush, D.2
-
31
-
-
0001463548
-
Nonparametric estimation of the number of classes in a population
-
Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11: 265-270.
-
(1984)
Scand J Stat
, vol.11
, pp. 265-270
-
-
Chao, A.1
-
32
-
-
58549120798
-
Viral biogeography revealed by signatures in Sulfolobus islandicus genomes
-
Held NL, Whitaker RJ (2009) Viral biogeography revealed by signatures in Sulfolobus islandicus genomes. Environ Microbiol 11: 457-466.
-
(2009)
Environ Microbiol
, vol.11
, pp. 457-466
-
-
Held, N.L.1
Whitaker, R.J.2
-
33
-
-
66649087973
-
Biogeography of the Sulfolobus islandicus pan-genome
-
Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA 106: 8605-8610.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 8605-8610
-
-
Reno, M.L.1
Held, N.L.2
Fields, C.J.3
Burke, P.V.4
Whitaker, R.J.5
-
34
-
-
0034000319
-
Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria
-
van Embden JDA, van Gorkom T, Kremer K, Jansen R, van der Zeijst BAM, et al. (2000) Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. Journal of Bacteriology 182: 2393-2401.
-
(2000)
Journal of Bacteriology
, vol.182
, pp. 2393-2401
-
-
van Embden, J.D.A.1
van Gorkom, T.2
Kremer, K.3
Jansen, R.4
van der Zeijst, B.A.M.5
-
35
-
-
62949197925
-
CRISPR families of the crenarchaeal genus Sulfolobus: Bidirectional transcription and dynamic properties
-
Lillestol RK, Shah SA, Brugger K, Redder P, Phan H, et al. (2009) CRISPR families of the crenarchaeal genus Sulfolobus: bidirectional transcription and dynamic properties. Mol Microbiol 72: 259-272.
-
(2009)
Mol Microbiol
, vol.72
, pp. 259-272
-
-
Lillestol, R.K.1
Shah, S.A.2
Brugger, K.3
Redder, P.4
Phan, H.5
-
36
-
-
44449133775
-
Virus population dynamics and acquired virus resistance in natural microbial communities
-
Andersson AF, Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 1047-1050.
-
(2008)
Science
, vol.320
, pp. 1047-1050
-
-
Andersson, A.F.1
Banfield, J.F.2
-
37
-
-
0029662733
-
Host-parasite coexistence: The role of spatial refuges in stabilizing bacteria-phage interactions
-
Schrag SJ, Mittler JE (1996) Host-parasite coexistence: The role of spatial refuges in stabilizing bacteria-phage interactions. Am Nat 148: 348-377.
-
(1996)
Am Nat
, vol.148
, pp. 348-377
-
-
Schrag, S.J.1
Mittler, J.E.2
-
38
-
-
24044488634
-
The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa
-
Brockhurst MA, Buckling A, Rainey PB (2005) The effect of a bacteriophage on diversification of the opportunistic bacterial pathogen, Pseudomonas aeruginosa. Proc R Soc Lond B Biol Sci 272: 1385-1391.
-
(2005)
Proc R Soc Lond B Biol Sci
, vol.272
, pp. 1385-1391
-
-
Brockhurst, M.A.1
Buckling, A.2
Rainey, P.B.3
-
39
-
-
2542583245
-
The fate of competing beneficial mutations in an asexual population
-
Gerrish PJ, Lenski RE (1998) The fate of competing beneficial mutations in an asexual population. Genetica 103: 127-144.
-
(1998)
Genetica
, vol.103
, pp. 127-144
-
-
Gerrish, P.J.1
Lenski, R.E.2
-
40
-
-
0037398083
-
Mechanisms of coexistence of a bacteria and a bacteriophage in a spatially homogeneous environment
-
Lythgoe KA, Chao L (2003) Mechanisms of coexistence of a bacteria and a bacteriophage in a spatially homogeneous environment. Ecol Lett 6: 326-334.
-
(2003)
Ecol Lett
, vol.6
, pp. 326-334
-
-
Lythgoe, K.A.1
Chao, L.2
-
41
-
-
67650492062
-
A unique virus release mechanism in the Archaea
-
Bize A, Karlsson EA, Ekefjärd K, Quax TEF, Pina M, et al. (2009) A unique virus release mechanism in the Archaea. Proc Natl Acad Sci USA 106: 11306-11311.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11306-11311
-
-
Bize, A.1
Karlsson, E.A.2
Ekefjärd, K.3
Quax, T.E.F.4
Pina, M.5
-
42
-
-
27144541842
-
Viruses of hyperthermophilic Crenarchaea
-
Prangishvili D, Garrett RA (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13: 535-542.
-
(2005)
Trends Microbiol
, vol.13
, pp. 535-542
-
-
Prangishvili, D.1
Garrett, R.A.2
-
43
-
-
0042242559
-
Geographic barriers isolate endemic populations of hyperthermophilic archaea
-
Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976-978.
-
(2003)
Science
, vol.301
, pp. 976-978
-
-
Whitaker, R.J.1
Grogan, D.W.2
Taylor, J.W.3
-
44
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
46
-
-
0004248459
-
Phylogenetic Analysis Using Parsimony
-
SunderlandMassachusetts: Sinauer Associates
-
Swofford DL (2003) PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods).Version 4. SunderlandMassachusetts: Sinauer Associates.
-
(2003)
-
-
Swofford, D.L.1
-
47
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368-376.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
48
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
-
49
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
-
50
-
-
34250662138
-
The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
-
Grissa I, Vergnaud G, Pourcel C (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. Bmc Bioinformatics 8: 172.
-
(2007)
Bmc Bioinformatics
, vol.8
, pp. 172
-
-
Grissa, I.1
Vergnaud, G.2
Pourcel, C.3
|