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Volumn 14, Issue 7, 2016, Pages 461-471

Advancing microbial sciences by individual-based modelling

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE BEHAVIOR; AMMONIA OXIDIZING BACTERIUM; ANABAENA FLOS-AQUAE; BACTERIAL CELL; BACTERIOPHAGE; BIOFILM; BIOLOGICAL MODEL; CHEMOSTAT; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; COMMUNITY DYNAMICS; FRESHWATER ENVIRONMENT; GENE EXPRESSION; GROWTH RATE; INDIVIDUAL BASED MODEL; INDIVIDUALITY; MICROBIAL COMMUNITY; MICROBIOLOGY; MICROELECTRODE; MIXED CELL CULTURE; MOLECULAR EVOLUTION; NATURAL SELECTION; NITRITE OXIDIZING BACTERIUM; NONHUMAN; ORGANISMAL INTERACTION; POPULATION DENSITY; PRIORITY JOURNAL; REVIEW; SUBSTRATE CONCENTRATION; SYNECHOCOCCUS; BACTERIAL PHENOMENA AND FUNCTIONS; EVOLUTION; MICROBIAL CONSORTIUM; SINGLE CELL ANALYSIS;

EID: 84973474463     PISSN: 17401526     EISSN: 17401534     Source Type: Journal    
DOI: 10.1038/nrmicro.2016.62     Document Type: Review
Times cited : (168)

References (93)
  • 1
    • 4544370545 scopus 로고    scopus 로고
    • Single-cell microbiology: Tools, technologies, and applications
    • Brehm-Stecher, B. F., & Johnson, E. A. Single-cell microbiology: tools, technologies, and applications. Microbiol. Mol. Biol. Rev. 68, 538-559 (2004
    • (2004) Microbiol. Mol. Biol. Rev , vol.68 , pp. 538-559
    • Brehm-Stecher, B.F.1    Johnson, E.A.2
  • 2
    • 21644441288 scopus 로고    scopus 로고
    • Long-Term monitoring of bacteria undergoing programmed population control in a microchemostat
    • Balagaddé, F. K., You, L., Hansen, C. L., Arnold, F. H., & Quake, S. R. Long-Term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 309, 137-140 (2005
    • (2005) Science , vol.309 , pp. 137-140
    • Balagaddé, F.K.1    You, L.2    Hansen, C.L.3    Arnold, F.H.4    Quake, S.R.5
  • 3
    • 24044453695 scopus 로고    scopus 로고
    • A microfluidic chemostat for experiments with bacterial and yeast cells
    • Groisman, A., et al. A microfluidic chemostat for experiments with bacterial and yeast cells. Nat. Methods 2, 685-689 (2005
    • (2005) Nat. Methods , vol.2 , pp. 685-689
    • Groisman, A.1
  • 5
    • 70349531263 scopus 로고    scopus 로고
    • Single-cell ecophysiology of microbes as revealed by raman microspectroscopy or secondary ion mass spectrometry imaging
    • Wagner, M. Single-cell ecophysiology of microbes as revealed by raman microspectroscopy or secondary ion mass spectrometry imaging. Annu. Rev. Microbiol. 63, 411-429 (2009
    • (2009) Annu. Rev. Microbiol , vol.63 , pp. 411-429
    • Wagner, M.1
  • 6
    • 71449095855 scopus 로고    scopus 로고
    • Central role of the cell in microbial ecology
    • Zengler, K. Central role of the cell in microbial ecology. Microbiol. Mol. Biol. Rev. 73, 712-729 (2009
    • (2009) Microbiol. Mol. Biol. Rev , vol.73 , pp. 712-729
    • Zengler, K.1
  • 7
    • 79959855149 scopus 로고    scopus 로고
    • Probing individual environmental bacteria for viruses by using microfluidic digital PCR
    • Tadmor, A. D., Ottesen, E. A., Leadbetter, J. R., & Phillips, R. Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Science 333, 58-62 (2011
    • (2011) Science , vol.333 , pp. 58-62
    • Tadmor, A.D.1    Ottesen, E.A.2    Leadbetter, J.R.3    Phillips, R.4
  • 8
    • 84856716159 scopus 로고    scopus 로고
    • Detecting metabolic activities in single cells, with emphasis on nanoSIMS
    • Musat, N., Foster, R., Vagner, T., Adam, B., & Kuypers, M. M. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol. Rev. 36, 486-511 (2012
    • (2012) FEMS Microbiol. Rev , vol.36 , pp. 486-511
    • Musat, N.1    Foster, R.2    Vagner, T.3    Adam, B.4    Kuypers, M.M.5
  • 9
    • 84884640242 scopus 로고    scopus 로고
    • A chemostat array enables the spatio-Temporal analysis of the yeast proteome
    • Dénervaud, N., et al. A chemostat array enables the spatio-Temporal analysis of the yeast proteome. Proc. Natl Acad. Sci. USA 110, 15842-15847 (2013
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 15842-15847
    • Dénervaud, N.1
  • 10
    • 84876403132 scopus 로고    scopus 로고
    • Going local: Technologies for exploring bacterial microenvironments
    • Wessel, A. K., Hmelo, L., Parsek, M. R., & Whiteley, M. Going local: technologies for exploring bacterial microenvironments. Nat. Rev. Microbiol. 11, 337-348 (2013
    • (2013) Nat. Rev. Microbiol , vol.11 , pp. 337-348
    • Wessel, A.K.1    Hmelo, L.2    Parsek, M.R.3    Whiteley, M.4
  • 11
    • 84908254231 scopus 로고    scopus 로고
    • Zooming in to see the bigger picture: Microfluidic and nanofabrication tools to study bacteria
    • Hol, F. J., & Dekker, C. Zooming in to see the bigger picture: microfluidic and nanofabrication tools to study bacteria. Science 346, 1251821 (2014
    • (2014) Science , vol.346 , pp. 1251821
    • Hol, F.J.1    Dekker, C.2
  • 12
    • 80053144267 scopus 로고    scopus 로고
    • Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments
    • Zhang, Q., et al. Acceleration of emergence of bacterial antibiotic resistance in connected microenvironments. Science 333, 1764-1767 (2011
    • (2011) Science , vol.333 , pp. 1764-1767
    • Zhang, Q.1
  • 13
    • 84899655348 scopus 로고    scopus 로고
    • Models in biology: Accurate descriptions of our pathetic thinking
    • Gunawardena, J Models in biology: accurate descriptions of our pathetic thinking. BMC Biol. 12, 29 (2014
    • (2014) BMC Biol , vol.12 , pp. 29
    • Gunawardena, J.1
  • 14
    • 84884351044 scopus 로고    scopus 로고
    • Do simple models lead to generality in ecology
    • Evans, M. R., et al. Do simple models lead to generality in ecology? Trends Ecol. Evol. 28, 578-583 (2013
    • (2013) Trends Ecol Evol , vol.28 , pp. 578-583
    • Evans, M.R.1
  • 15
    • 84921656802 scopus 로고    scopus 로고
    • eds Muffler K. & Ulber R. Springer
    • Horn, H., & Lackner, S. in Productive Biofilms (eds Muffler, K., & Ulber, R.) 53-76 (Springer, 2014
    • (2014) Productive Biofilms , pp. 53-76
    • Horn, H.1    Lackner, S.2
  • 16
    • 77954339797 scopus 로고    scopus 로고
    • Mathematical description of microbial biofilms
    • Klapper, I., & Dockery, J. Mathematical description of microbial biofilms. SIAM Rev. 52, 221-265 (2010
    • (2010) SIAM Rev , vol.52 , pp. 221-265
    • Klapper, I.1    Dockery, J.2
  • 17
    • 56349159055 scopus 로고    scopus 로고
    • A bunch of tiny individuals-individual-based modeling for microbes
    • Hellweger, F. L., & Bucci, V. A bunch of tiny individuals-individual-based modeling for microbes. Ecol. Model. 220, 8-22 (2009
    • (2009) Ecol. Model , vol.220 , pp. 8-22
    • Hellweger, F.L.1    Bucci, V.2
  • 18
    • 84887289464 scopus 로고    scopus 로고
    • Mighty small: Observing and modeling individual microbes becomes big science
    • Kreft, J. U., et al. Mighty small: Observing and modeling individual microbes becomes big science. Proc. Natl Acad. Sci. USA 110, 18027-18028 (2013
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 18027-18028
    • Kreft, J.U.1
  • 19
    • 30344446670 scopus 로고    scopus 로고
    • Individual-based modeling of ecological and evolutionary processes
    • DeAngelis, D. L., & Mooij, W. M. Individual-based modeling of ecological and evolutionary processes. Annu. Rev. Ecol. Evol. Syst. 36, 147-168 (2005
    • (2005) Annu. Rev. Ecol. Evol. Syst , vol.36 , pp. 147-168
    • DeAngelis, D.L.1    Mooij, W.M.2
  • 20
    • 27744570841 scopus 로고    scopus 로고
    • Pattern-oriented modeling of agent based complex systems: Lessons from ecology
    • Grimm, V., et al. Pattern-oriented modeling of agent based complex systems: lessons from ecology. Science 310, 987-991 (2005
    • (2005) Science , vol.310 , pp. 987-991
    • Grimm, V.1
  • 22
    • 79959611518 scopus 로고    scopus 로고
    • Response of Prochlorococcus ecotypes to co culture with diverse marine bacteria
    • Sher, D., Thompson, J. W., Kashtan, N., Croal, L., & Chisholm, S. W. Response of Prochlorococcus ecotypes to co culture with diverse marine bacteria. ISME J. 5, 1125-1132 (2011
    • (2011) ISME J. , vol.5 , pp. 1125-1132
    • Sher, D.1    Thompson, J.W.2    Kashtan, N.3    Croal, L.4    Chisholm, S.W.5
  • 24
    • 84906831694 scopus 로고    scopus 로고
    • Repair rather than segregation of damage is the optimal unicellular aging strategy
    • Clegg, R. J., Dyson, R. J., & Kreft, J. U. Repair rather than segregation of damage is the optimal unicellular aging strategy. BMC Biol. 12, 52 (2014
    • (2014) BMC Biol , vol.12 , pp. 52
    • Clegg, R.J.1    Dyson, R.J.2    Kreft, J.U.3
  • 25
    • 84930630979 scopus 로고    scopus 로고
    • Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria
    • Amin, S. A., et al. Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522, 98-101 (2015
    • (2015) Nature , vol.522 , pp. 98-101
    • Amin, S.A.1
  • 26
    • 80052631835 scopus 로고    scopus 로고
    • IDynoMiCS: Next-generation individual-based modelling of biofilms
    • Lardon, L. A., et al. iDynoMiCS: next-generation individual-based modelling of biofilms. Environ. Microbiol. 13, 2416-2434 (2011
    • (2011) Environ. Microbiol , vol.13 , pp. 2416-2434
    • Lardon, L.A.1
  • 27
    • 84871288413 scopus 로고    scopus 로고
    • Modelling emergence of oscillations in communicating bacteria: A structured approach from one to many cells
    • Mina, P., di Bernardo, M., Savery, N. J., & Tsaneva Atanasova, K. Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells. J. R. Soc. Interface 10, 20120612 (2013
    • (2013) J. R. Soc. Interface , vol.10 , pp. 20120612
    • Mina, P.1    Di Bernardo, M.2    Savery, N.J.3    Tsaneva Atanasova, K.4
  • 28
    • 84883510431 scopus 로고    scopus 로고
    • Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context
    • Iranzo, J., Lobkovsky, A. E., Wolf, Y. I., & Koonin, E. V. Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context. J. Bacteriol. 195, 3834-3844 (2013
    • (2013) J. Bacteriol , vol.195 , pp. 3834-3844
    • Iranzo, J.1    Lobkovsky, A.E.2    Wolf, Y.I.3    Koonin, E.V.4
  • 29
    • 0029832083 scopus 로고    scopus 로고
    • Flow cytometry and cell sorting of heterogeneous microbial populations: The importance of single-cell analyses
    • Davey, H. M., & Kell, D. B. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses. Microbiol. Rev. 60, 641-696 (1996
    • (1996) Microbiol. Rev , vol.60 , pp. 641-696
    • Davey, H.M.1    Kell, D.B.2
  • 30
    • 56649097491 scopus 로고    scopus 로고
    • A single-cell view on the ecophysiology of anaerobic phototrophic bacteria
    • Musat, N., et al. A single-cell view on the ecophysiology of anaerobic phototrophic bacteria. Proc. Natl Acad. Sci. USA 105, 17861-17866 (2008
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 17861-17866
    • Musat, N.1
  • 31
    • 84868317361 scopus 로고    scopus 로고
    • Isolated microbial single cells and resulting micropopulations grow faster in controlled environments
    • Dusny, C., Fritzsch, F. S., Frick, O., & Schmid, A. Isolated microbial single cells and resulting micropopulations grow faster in controlled environments. Appl. Environ. Microbiol. 78, 7132-7136 (2012
    • (2012) Appl. Environ. Microbiol , vol.78 , pp. 7132-7136
    • Dusny, C.1    Fritzsch, F.S.2    Frick, O.3    Schmid, A.4
  • 32
    • 33747174575 scopus 로고    scopus 로고
    • Microbial cell individuality and the underlying sources of heterogeneity
    • Avery, S. V. Microbial cell individuality and the underlying sources of heterogeneity. Nat. Rev. Microbiol. 4, 577-587 (2006
    • (2006) Nat. Rev. Microbiol , vol.4 , pp. 577-587
    • Avery, S.V.1
  • 33
    • 84876492379 scopus 로고    scopus 로고
    • Microbial individuality in the natural environment
    • Ackermann, M. Microbial individuality in the natural environment. ISME J. 7, 465-467 (2013
    • (2013) ISME J. , vol.7 , pp. 465-467
    • Ackermann, M.1
  • 34
    • 84882748254 scopus 로고    scopus 로고
    • Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population
    • Labhsetwar, P., Cole, J. A., Roberts, E., Price, N. D., & Luthey-Schulten, Z. A. Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population. Proc. Natl Acad. Sci. USA 110, 14006-14011 (2013
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 14006-14011
    • Labhsetwar, P.1    Cole, J.A.2    Roberts, E.3    Price, N.D.4    Luthey-Schulten, Z.A.5
  • 35
    • 0022226623 scopus 로고
    • Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem
    • Mitchell, J. G., Okubo, A., & Fuhrman, J. A. Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem. Nature 316, 58-59 (1985
    • (1985) Nature , vol.316 , pp. 58-59
    • Mitchell, J.G.1    Okubo, A.2    Fuhrman, J.A.3
  • 36
    • 0032545478 scopus 로고    scopus 로고
    • Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria
    • Blackburn, N., Fenchel, T., & Mitchell, J. Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282, 2254-2256 (1998
    • (1998) Science , vol.282 , pp. 2254-2256
    • Blackburn, N.1    Fenchel, T.2    Mitchell, J.3
  • 37
    • 84871016428 scopus 로고    scopus 로고
    • Evolution of two-component signal transduction systems
    • Capra, E. J., & Laub, M. T. Evolution of two-component signal transduction systems. Annu. Rev. Microbiol. 66, 325-347 (2012
    • (2012) Annu. Rev. Microbiol , vol.66 , pp. 325-347
    • Capra, E.J.1    Laub, M.T.2
  • 38
    • 84908191393 scopus 로고    scopus 로고
    • Stochasticity of metabolism and growth at the single-cell level
    • Kiviet, D. J., et al. Stochasticity of metabolism and growth at the single-cell level. Nature 514, 376-379 (2014
    • (2014) Nature , vol.514 , pp. 376-379
    • Kiviet, D.J.1
  • 39
    • 79251603722 scopus 로고    scopus 로고
    • Non-genetic heterogeneity from stochastic partitioning at cell division
    • Huh, D., & Paulsson, J. Non-genetic heterogeneity from stochastic partitioning at cell division. Nat. Genet. 43, 95-100 (2011
    • (2011) Nat. Genet , vol.43 , pp. 95-100
    • Huh, D.1    Paulsson, J.2
  • 40
    • 1842484290 scopus 로고    scopus 로고
    • From molecular noise to behavioural variability in a single bacterium
    • Korobkova, E., Emonet, T., Vilar, J. M., Shimizu, T. S., & Cluzel, P. From molecular noise to behavioural variability in a single bacterium. Nature 428, 574-578 (2004
    • (2004) Nature , vol.428 , pp. 574-578
    • Korobkova, E.1    Emonet, T.2    Vilar, J.M.3    Shimizu, T.S.4    Cluzel, P.5
  • 41
    • 84856388773 scopus 로고    scopus 로고
    • Microscale patchiness leads to large and important intraspecific internal nutrient heterogeneity in phytoplankton
    • Bucci, V., Nunez-Milland, D., Twining, B. S., & Hellweger, F. L. Microscale patchiness leads to large and important intraspecific internal nutrient heterogeneity in phytoplankton. Aquat. Ecol. 46, 101-118 (2012
    • (2012) Aquat. Ecol , vol.46 , pp. 101-118
    • Bucci, V.1    Nunez-Milland, D.2    Twining, B.S.3    Hellweger, F.L.4
  • 42
    • 0038375994 scopus 로고    scopus 로고
    • Biofilm formation by Pseudomonas aeruginosa wild-Type, flagella and type IV pili mutants
    • Klausen, M., et al. Biofilm formation by Pseudomonas aeruginosa wild-Type, flagella and type IV pili mutants. Mol. Microbiol. 48, 1511-1524 (2003
    • (2003) Mol. Microbiol , vol.48 , pp. 1511-1524
    • Klausen, M.1
  • 43
    • 0141818949 scopus 로고    scopus 로고
    • Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms
    • Klausen, M., Aaes-Jørgensen, A., Molin, S., & Tolker-Nielsen, T. Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms. Mol. Microbiol. 50, 61-68 (2003
    • (2003) Mol. Microbiol , vol.50 , pp. 61-68
    • Klausen, M.1    Aaes-Jørgensen, A.2    Molin, S.3    Tolker-Nielsen, T.4
  • 44
    • 34249707773 scopus 로고    scopus 로고
    • Microbial motility involvement in biofilm structure formation-A 3D modelling study
    • Picioreanu, C., et al. Microbial motility involvement in biofilm structure formation-A 3D modelling study. Water Sci. Technol. 55, 337-343 (2007
    • (2007) Water Sci. Technol , vol.55 , pp. 337-343
    • Picioreanu, C.1
  • 45
    • 48849104158 scopus 로고    scopus 로고
    • Roles of type IV pili, flagellum-mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms
    • Barken, K. B., et al. Roles of type IV pili, flagellum-mediated motility and extracellular DNA in the formation of mature multicellular structures in Pseudomonas aeruginosa biofilms. Environ. Microbiol. 10, 2331-2343 (2008
    • (2008) Environ. Microbiol , vol.10 , pp. 2331-2343
    • Barken, K.B.1
  • 46
    • 25444489027 scopus 로고    scopus 로고
    • Phenotypic diversity, population growth, and information in fluctuating environments
    • Kussell, E., & Leibler, S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075-2078 (2005
    • (2005) Science , vol.309 , pp. 2075-2078
    • Kussell, E.1    Leibler, S.2
  • 47
    • 14744282987 scopus 로고    scopus 로고
    • Diversity in times of adversity: Probabilistic strategies in microbial survival games
    • Wolf, D. M., Vazirani, V. V., & Arkin, A. P. Diversity in times of adversity: probabilistic strategies in microbial survival games. J. Theor. Biol. 234, 227-253 (2005
    • (2005) J. Theor. Biol , vol.234 , pp. 227-253
    • Wolf, D.M.1    Vazirani, V.V.2    Arkin, A.P.3
  • 48
    • 47349110588 scopus 로고    scopus 로고
    • Agent-based modeling of the complex life cycle of a cyanobacterium (Anabaena) in a shallow reservoir
    • Hellweger, F. L., Kravchuk, E. S., Novotny, V., & Gladyshev, M. I. Agent-based modeling of the complex life cycle of a cyanobacterium (Anabaena) in a shallow reservoir. Limnol. Oceanogr. 53, 1227-1241 (2008
    • (2008) Limnol. Oceanogr , vol.53 , pp. 1227-1241
    • Hellweger, F.L.1    Kravchuk, E.S.2    Novotny, V.3    Gladyshev, M.I.4
  • 49
    • 0035950145 scopus 로고    scopus 로고
    • Gene expression in Pseudomonas aeruginosa biofilms
    • Whiteley, M., et al. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413, 860-864 (2001
    • (2001) Nature , vol.413 , pp. 860-864
    • Whiteley, M.1
  • 50
    • 0036157549 scopus 로고    scopus 로고
    • Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm
    • Sauer, K., Camper, A. K., Ehrlich, G. D., Costerton, J. W., & Davies, D. G. Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J. Bacteriol. 184, 1140-1154 (2002
    • (2002) J. Bacteriol , vol.184 , pp. 1140-1154
    • Sauer, K.1    Camper, A.K.2    Ehrlich, G.D.3    Costerton, J.W.4    Davies, D.G.5
  • 51
    • 20644457332 scopus 로고    scopus 로고
    • Transcriptome analysis of Pseudomonas aeruginosa biofilm development: Anaerobic respiration and iron limitation
    • Hentzer, M., Eberl, L., & Givskov, M. Transcriptome analysis of Pseudomonas aeruginosa biofilm development: anaerobic respiration and iron limitation. Biofilms 2, 37-61 (2005
    • (2005) Biofilms , vol.2 , pp. 37-61
    • Hentzer, M.1    Eberl, L.2    Givskov, M.3
  • 52
    • 84856557095 scopus 로고    scopus 로고
    • The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing
    • Dötsch, A., et al. The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing. PLoS ONE 7, e31092 (2012
    • (2012) PLoS ONE , vol.7 , pp. e31092
    • Dötsch, A.1
  • 53
    • 84883691189 scopus 로고    scopus 로고
    • eds Jaykus, L. A., Wang, H. H., & Schlesinger, L. S. (ASM Press
    • Kreft, J. U. in Food-Borne Microbes: Shaping the Host Ecosystem (eds Jaykus, L. A., Wang, H. H., & Schlesinger, L. S.) 347-377 (ASM Press, 2009
    • (2009) Food-Borne Microbes: Shaping the Host Ecosystem , pp. 347-377
    • Kreft, J.U.1
  • 54
    • 4344639715 scopus 로고    scopus 로고
    • Assessment of three-dimensional biofilm models through direct comparison with confocal microscopy imaging
    • Xavier, J. B., Picioreanu, C., & van Loosdrecht, M. C. Assessment of three-dimensional biofilm models through direct comparison with confocal microscopy imaging. Water Sci. Technol. 49, 177-185 (2004
    • (2004) Water Sci. Technol , vol.49 , pp. 177-185
    • Xavier, J.B.1    Picioreanu, C.2    Van Loosdrecht, M.C.3
  • 56
    • 84899505083 scopus 로고    scopus 로고
    • Molecular mechanisms underlying bacterial persisters
    • Maisonneuve, E., & Gerdes, K. Molecular mechanisms underlying bacterial persisters. Cell 157, 539-548 (2014
    • (2014) Cell , vol.157 , pp. 539-548
    • Maisonneuve, E.1    Gerdes, K.2
  • 57
    • 84868129172 scopus 로고    scopus 로고
    • Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c di GMP production
    • O'Connor, J. R., Kuwada, N. J., Huangyutitham, V., Wiggins, P. A., & Harwood, C. S. Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c di GMP production. Mol. Microbiol. 86, 720-729 (2012
    • (2012) Mol. Microbiol , vol.86 , pp. 720-729
    • O'Connor, J.R.1    Kuwada, N.J.2    Huangyutitham, V.3    Wiggins, P.A.4    Harwood, C.S.5
  • 59
    • 0033817313 scopus 로고    scopus 로고
    • Apparent surface associated lag time in growth of primary biofilm cells
    • Rice, A. R., Hamilton, M. A., & Camper, A. K. Apparent surface associated lag time in growth of primary biofilm cells. Microb. Ecol. 40, 8-15 (2000
    • (2000) Microb. Ecol , vol.40 , pp. 8-15
    • Rice, A.R.1    Hamilton, M.A.2    Camper, A.K.3
  • 60
    • 4444233112 scopus 로고    scopus 로고
    • Biofilms promote altruism
    • Kreft, J. U. Biofilms promote altruism. Microbiology 150, 2751-2760 (2004
    • (2004) Microbiology , vol.150 , pp. 2751-2760
    • Kreft, J.U.1
  • 61
    • 84887794439 scopus 로고    scopus 로고
    • Spatial self organization favors heterotypic cooperation over cheating
    • Momeni, B., Waite, A. J., & Shou, W. Spatial self organization favors heterotypic cooperation over cheating. eLife 2, e00960 (2013
    • (2013) ELife , vol.2 , pp. e00960
    • Momeni, B.1    Waite, A.J.2    Shou, W.3
  • 62
    • 84901273253 scopus 로고    scopus 로고
    • Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
    • Harcombe, W. R., et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 7, 1104-1115 (2014
    • (2014) Cell Rep , vol.7 , pp. 1104-1115
    • Harcombe, W.R.1
  • 63
    • 84892741486 scopus 로고    scopus 로고
    • Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities
    • Estrela, S., & Brown, S. P. Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities. PLoS Comput. Biol. 9, e1003398 (2013
    • (2013) PLoS Comput. Biol , vol.9 , pp. e1003398
    • Estrela, S.1    Brown, S.P.2
  • 64
    • 33747799940 scopus 로고    scopus 로고
    • Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms
    • Batstone, D. J., Picioreanu, C., & van Loosdrecht, M. C. Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms. Water Res. 40, 3099-3108 (2006
    • (2006) Water Res , vol.40 , pp. 3099-3108
    • Batstone, D.J.1    Picioreanu, C.2    Van Loosdrecht, M.C.3
  • 65
    • 84879045964 scopus 로고    scopus 로고
    • Strong inter-population cooperation leads to partner intermixing in microbial communities
    • Momeni, B., Brileya, K. A., Fields, M. W., & Shou, W. Strong inter-population cooperation leads to partner intermixing in microbial communities. eLife 2, e00230 (2013
    • (2013) ELife , vol.2 , pp. e00230
    • Momeni, B.1    Brileya, K.A.2    Fields, M.W.3    Shou, W.4
  • 66
    • 84945438695 scopus 로고    scopus 로고
    • Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces
    • Wang, G., & Or, D. Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces. Sci. Rep. 4, 6757 (2014
    • (2014) Sci. Rep , vol.4 , pp. 6757
    • Wang, G.1    Or, D.2
  • 67
    • 34249730872 scopus 로고    scopus 로고
    • Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-Aerated biofilm
    • Matsumoto, S., et al. Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-Aerated biofilm. Water Sci. Technol. 55, 283-290 (2007
    • (2007) Water Sci. Technol , vol.55 , pp. 283-290
    • Matsumoto, S.1
  • 68
    • 73349125782 scopus 로고    scopus 로고
    • Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses
    • Matsumoto, S., et al. Microbial community structure in autotrophic nitrifying granules characterized by experimental and simulation analyses. Environ. Microbiol. 12, 192-206 (2010
    • (2010) Environ. Microbiol , vol.12 , pp. 192-206
    • Matsumoto, S.1
  • 69
    • 80755159413 scopus 로고    scopus 로고
    • Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters
    • Clark, J. R., Daines, S. J., Lenton, T. M., Watson, A. J., & Williams, H. T. P. Individual-based modelling of adaptation in marine microbial populations using genetically defined physiological parameters. Ecol. Model. 222, 3823-3837 (2011
    • (2011) Ecol. Model , vol.222 , pp. 3823-3837
    • Clark, J.R.1    Daines, S.J.2    Lenton, T.M.3    Watson, A.J.4    Williams, H.T.P.5
  • 70
    • 84877750884 scopus 로고    scopus 로고
    • Environmental selection and resource allocation determine spatial patterns in picophytoplankton cell size
    • Clark, J. R., Lenton, T. M., Williams, H. T. P., & Daines, S. J. Environmental selection and resource allocation determine spatial patterns in picophytoplankton cell size. Limnol. Oceanogr. 58, 1008-1022 (2013
    • (2013) Limnol. Oceanogr , vol.58 , pp. 1008-1022
    • Clark, J.R.1    Lenton, T.M.2    Williams, H.T.P.3    Daines, S.J.4
  • 71
    • 84915749321 scopus 로고    scopus 로고
    • Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: Models and observations on virus-host coevolution
    • Koonin, E. V., & Wolf, Y. I. Evolution of the CRISPR-Cas adaptive immunity systems in prokaryotes: models and observations on virus-host coevolution. Mol. Biosyst. 11, 20-27 (2014
    • (2014) Mol. Biosyst , vol.11 , pp. 20-27
    • Koonin, E.V.1    Wolf, Y.I.2
  • 72
    • 42149109049 scopus 로고    scopus 로고
    • Relationship between cellular response and behavioral variability in bacterial chemotaxis
    • Emonet, T., & Cluzel, P. Relationship between cellular response and behavioral variability in bacterial chemotaxis. Proc. Natl Acad. Sci. USA 105, 3304-3309 (2008
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 3304-3309
    • Emonet, T.1    Cluzel, P.2
  • 74
    • 84878047546 scopus 로고    scopus 로고
    • Dynamic modeling of cellular populations within iBioSim
    • Stevens, J. T., & Myers, C. J. Dynamic modeling of cellular populations within iBioSim. ACS Synth. Biol. 2, 223-229 (2013
    • (2013) ACS Synth. Biol , vol.2 , pp. 223-229
    • Stevens, J.T.1    Myers, C.J.2
  • 75
    • 84905730761 scopus 로고    scopus 로고
    • Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    • Nielsen, H. B., et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822-828 (2014
    • (2014) Nat. Biotechnol , vol.32 , pp. 822-828
    • Nielsen, H.B.1
  • 77
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis, N. E., Nagarajan, H., & Palsson, B. O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 10, 291-305 (2012
    • (2012) Nat. Rev. Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 78
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • Klitgord, N., & Segrè, D. Environments that induce synthetic microbial ecosystems. PLoS Comput. Biol. 6, e1001002 (2010
    • (2010) PLoS Comput. Biol , vol.6 , pp. e1001002
    • Klitgord, N.1    Segrè, D.2
  • 80
    • 80052630416 scopus 로고    scopus 로고
    • Growth dependence of conjugation explains limited plasmid invasion in biofilms: An individual-based modelling study
    • Merkey, B. V., Lardon, L. A., Seoane, J. M., Kreft, J. U., & Smets, B. F. Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environ. Microbiol. 13, 2435-2452 (2011
    • (2011) Environ. Microbiol , vol.13 , pp. 2435-2452
    • Merkey, B.V.1    Lardon, L.A.2    Seoane, J.M.3    Kreft, J.U.4    Smets, B.F.5
  • 81
    • 79954618936 scopus 로고    scopus 로고
    • Biofilm image reconstruction for assessing structural parameters
    • Renslow, R., Lewandowski, Z., & Beyenal, H. Biofilm image reconstruction for assessing structural parameters. Biotechnol. Bioeng. 108, 1383-1394 (2011
    • (2011) Biotechnol. Bioeng , vol.108 , pp. 1383-1394
    • Renslow, R.1    Lewandowski, Z.2    Beyenal, H.3
  • 82
    • 33745310267 scopus 로고    scopus 로고
    • Resource competition and social conflict in experimental populations of yeast
    • MacLean, R. C., & Gudelj, I. Resource competition and social conflict in experimental populations of yeast. Nature 441, 498-501 (2006
    • (2006) Nature , vol.441 , pp. 498-501
    • MacLean, R.C.1    Gudelj, I.2
  • 83
    • 33745981794 scopus 로고    scopus 로고
    • Local migration promotes competitive restraint in a host-pathogen tragedy of the commons
    • Kerr, B., Neuhauser, C., Bohannan, B. J., & Dean, A. M. Local migration promotes competitive restraint in a host-pathogen tragedy of the commons. Nature 442, 75-78 (2006
    • (2006) Nature , vol.442 , pp. 75-78
    • Kerr, B.1    Neuhauser, C.2    Bohannan, B.J.3    Dean, A.M.4
  • 84
    • 33646495327 scopus 로고    scopus 로고
    • Why is metabolic labour divided in nitrification
    • Costa, E., Pérez, J., & Kreft, J. U. Why is metabolic labour divided in nitrification? Trends Microbiol. 14, 213-219 (2006
    • (2006) Trends Microbiol , vol.14 , pp. 213-219
    • Costa, E.1    Pérez, J.2    Kreft, J.U.3
  • 85
    • 84951304663 scopus 로고    scopus 로고
    • Complete nitrification by a single microorganism
    • van Kessel, M. A. H. J., et al. Complete nitrification by a single microorganism. Nature 528, 555-559 (2015
    • (2015) Nature , vol.528 , pp. 555-559
    • Van Kessel, M.A.H.J.1
  • 86
    • 84951335346 scopus 로고    scopus 로고
    • Complete nitrification by Nitrospira bacteria
    • Daims, H., et al. Complete nitrification by Nitrospira bacteria. Nature 528, 504-509 (2015
    • (2015) Nature , vol.528 , pp. 504-509
    • Daims, H.1
  • 87
    • 77957301158 scopus 로고    scopus 로고
    • The ODD protocol: A review and first update
    • Grimm, V., et al. The ODD protocol: a review and first update. Ecol. Model. 221, 2760-2768 (2010
    • (2010) Ecol. Model , vol.221 , pp. 2760-2768
    • Grimm, V.1
  • 88
    • 84890845572 scopus 로고    scopus 로고
    • How the chemotactic characteristics of bacteria can determine their population patterns
    • Gharasoo, M., Centler, F., Fetzer, I., & Thullner, M. How the chemotactic characteristics of bacteria can determine their population patterns. Soil Biol. Biochem. 69, 346-358 (2014
    • (2014) Soil Biol. Biochem , vol.69 , pp. 346-358
    • Gharasoo, M.1    Centler, F.2    Fetzer, I.3    Thullner, M.4
  • 89
    • 0031031474 scopus 로고    scopus 로고
    • A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models
    • Wimpenny, J. W. T., & Colasanti, R. A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models. FEMS Microbiol. Ecol. 22, 1-16 (1997
    • (1997) FEMS Microbiol. Ecol , vol.22 , pp. 1-16
    • Wimpenny, J.W.T.1    Colasanti, R.2
  • 90
    • 84974635271 scopus 로고    scopus 로고
    • Revised estimates for the number of human and bacteria cells in the body
    • Sender, R., Fuchs, S., & Milo, R. Revised estimates for the number of human and bacteria cells in the body. bioRxiv http://dx.doi.org/10.1101/036103 (2016
    • (2016) BioRxiv
    • Sender, R.1    Fuchs, S.2    Milo, R.3
  • 91
    • 58249092244 scopus 로고    scopus 로고
    • Analyzing characteristic length scales in biofilm structures
    • Milferstedt, K., Pos, M. N., & Morgenroth, E. Analyzing characteristic length scales in biofilm structures. Biotechnol. Bioeng. 102, 368-379 (2009
    • (2009) Biotechnol. Bioeng , vol.102 , pp. 368-379
    • Milferstedt, K.1    Pos, M.N.2    Morgenroth, E.3
  • 92
    • 0032436318 scopus 로고    scopus 로고
    • BacSim a simulator for individual-based modelling of bacterial colony growth
    • Kreft, J. U., Booth, G., & Wimpenny, J. W. T. BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144, 3275-3287 (1998
    • (1998) Microbiology , vol.144 , pp. 3275-3287
    • Kreft, J.U.1    Booth, G.2    Wimpenny, J.W.T.3
  • 93
    • 0141844665 scopus 로고    scopus 로고
    • Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X-ray microanalysis
    • Heldal, M., Scanlan, D. J., Norland, S., Thingstad, F., & Mann, N. H. Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X-ray microanalysis. Limnol. Oceanogr. 48, 1732-1743 (2003
    • (2003) Limnol. Oceanogr , vol.48 , pp. 1732-1743
    • Heldal, M.1    Scanlan, D.J.2    Norland, S.3    Thingstad, F.4    Mann, N.H.5


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