메뉴 건너뛰기




Volumn 3, Issue 4, 2012, Pages e201210008-

Genome-based modeling and design of metabolic interactions in microbial communities

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84902144538     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201210008     Document Type: Short Survey
Times cited : (26)

References (57)
  • 2
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox
    • DOI 10.1038/nprot.2007.99, PII NPROT.2007.99
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson BO, Herrgard MJ. 2007. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocols. 2:727-738. (Pubitemid 47040034)
    • (2007) Nature Protocols , vol.2 , Issue.3 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.O.5    Herrgard, M.J.6
  • 3
    • 0036324056 scopus 로고    scopus 로고
    • High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates
    • DOI 10.1128/AEM.68.8.3878-3885.2002
    • Connon SA, and Giovannoni SJ. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl.Environ. Microbiol.68:3878-3885. (Pubitemid 34836698)
    • (2002) Applied and Environmental Microbiology , vol.68 , Issue.8 , pp. 3878-3885
    • Connon, S.A.1    Giovannoni, S.J.2
  • 5
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in escherichia coli
    • Covert MW, Xiao N, Chen TJ, Karr Jr. 2008. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics. 24:2044-2050.
    • (2008) Bioinformatics. , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 7
    • 0021892226 scopus 로고
    • A cybernetic view of microbial-growth - Modeling of cells as optimal strategists
    • Dhurjati P, Ramkrishna D, Flickinger MC, Tsao GT. 1985. A Cybernetic View of Microbial-Growth - Modeling of Cells As Optimal Strategists. Biotechnol. Bioeng. 27:1-9.
    • (1985) Biotechnol. Bioeng. , vol.27 , pp. 1-9
    • Dhurjati, P.1    Ramkrishna, D.2    Flickinger, M.C.3    Tsao, G.T.4
  • 8
    • 0021403731 scopus 로고
    • Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A
    • Domach MM, Leung SK, Cahn RE, Cocks GG, Shuler ML. 1984. Computer-Model for Glucose-Limited Growth of A Single Cell of Escherichia coli B/R-A. Biotechnol. Bioeng. 26:203-216. (Pubitemid 14145292)
    • (1984) Biotechnology and Bioengineering , vol.26 , Issue.3 , pp. 203-216
    • Domach, M.M.1    Leung, S.K.2    Cahn, R.E.3
  • 9
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • DOI 10.1038/84379
    • Edwards JS, Ibarra RU, Palsson BO. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19:125-130. (Pubitemid 32144439)
    • (2001) Nature Biotechnology , vol.19 , Issue.2 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 11
    • 45249103536 scopus 로고    scopus 로고
    • A co-fermentation strategy to consume sugar mixtures effectively
    • DOI 10.1186/1754-1611-2-3
    • Eiteman MA, Lee SA, Altman E. 2008. A co-fermentation strategy to consume sugar mixtures effectively.J. Biol. Eng. 2:3. doi: 10.1186/1754-1611-2-3. (Pubitemid 351837363)
    • (2008) Journal of Biological Engineering , vol.2 , pp. 3
    • Eiteman, M.A.1    Lee, S.A.2    Altman, E.3
  • 12
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: From networks to models
    • doi: 10.1038/nrmicro2832; 10.1038/nrmicro2832
    • Faust K, and Raes J. 2012. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10:538-550. doi: 10.1038/nrmicro2832; 10.1038/nrmicro2832.
    • (2012) Nat. Rev. Microbiol. , vol.10 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 13
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • DOI 10.1038/ng1432
    • Fong SS, and Palsson BO. 2004. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36:1056-1058. (Pubitemid 41184464)
    • (2004) Nature Genetics , vol.36 , Issue.10 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.O.2
  • 18
    • 84856011484 scopus 로고    scopus 로고
    • Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
    • doi: 10.1073/pnas.l 116053109
    • Greenblum S, Turnbaugh PJ, Borenstein E. 2012. Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc. Natl. Acad. Sci. U. S. A. 109:594-599. doi: 10.1073/pnas.l 116053109.
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 594-599
    • Greenblum, S.1    Turnbaugh, P.J.2    Borenstein, E.3
  • 19
    • 19144364745 scopus 로고    scopus 로고
    • Sorting out metagenomes
    • DOI 10.1038/nbt0105-38
    • Handelsman J. 2005. Sorting out metagenomes. Nat. Biotechnol. 23:38-39. (Pubitemid 41724622)
    • (2005) Nature Biotechnology , vol.23 , Issue.1 , pp. 38-39
    • Handelsman, J.1
  • 20
    • 78650215306 scopus 로고    scopus 로고
    • Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
    • doi: 10.1002/bit.22954
    • Hanly TJ, and Henson MA. 2011. Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures.Biotechnol.Bioeng.108:376-385.doi: 10.1002/bit.22954.
    • (2011) Biotechnol. Bioeng. , vol.108 , pp. 376-385
    • Hanly, T.J.1    Henson, M.A.2
  • 21
    • 84862272463 scopus 로고    scopus 로고
    • Dynamic flux balance modeling of s. Cerevisiae e. Coli co-cultures for efficient consumption of glucosexylose mixtures
    • doi: 10.1007/s00253-011-3628-1
    • Hanly TJ, Urello M, Henson MA. 2012. Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures. Appl. Microbiol. Biotechnol. 93:2529-2541. doi: 10.1007/s00253-011- 3628-1.
    • (2012) Appl. Microbiol. Biotechnol. , pp. 932529-932541
    • Hanly, T.J.1    Urello, M.2    Henson, M.A.3
  • 22
    • 84902151172 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature biotechnology. . 23.hess m, sczyrba a, egan r, kim tw, chokhawala h, schroth g, luo s, clark ds, chen f, zhang t, mackie ri, pennacchio la, tringe sg, visel a, woyke t, wang z, rubin em. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    • doi: 10.1126/science.l200387
    • Henry CS, Dejongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. 2010. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature Biotechnology. . 23.Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 331:463-467. doi: 10.1126/science.l200387.
    • (2010) Science. , vol.331 , pp. 463-467
    • Henry, C.S.1    Dejongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 23
    • 33749996165 scopus 로고    scopus 로고
    • Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models
    • DOI 10.1021/bp060059v
    • Hjersted JL, and Henson MA.2006.Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models. Biotechnol. Prog. 22:1239-1248. (Pubitemid 44568797)
    • (2006) Biotechnology Progress , vol.22 , Issue.5 , pp. 1239-1248
    • Hjersted, J.L.1    Henson, M.A.2
  • 24
    • 34447308322 scopus 로고    scopus 로고
    • Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture
    • DOI 10.1002/bit.21332
    • Hjersted JL, Henson MA, Mahadevan R. 2007. Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol. Bioeng. 97:1190-1204. (Pubitemid 47195316)
    • (2007) Biotechnology and Bioengineering , vol.97 , Issue.5 , pp. 1190-1204
    • Hjersted, J.L.1    Henson, M.A.2    Mahadevan, R.3
  • 25
    • 84867609258 scopus 로고    scopus 로고
    • Comparative metagenomics of three dehalococcoides-containing enrichment cultures: The role of the non-dechlorinating community
    • doi: 10.1186/1471-2164-13-327
    • Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA. 2012. Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. BMCGenomics. 13:327. doi: 10.1186/1471-2164-13-327.
    • (2012) BMC Genomics , vol.13 , pp. 327
    • Hug, L.A.1    Beiko, R.G.2    Rowe, A.R.3    Richardson, R.E.4    Edwards, E.A.5
  • 26
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • DOI 10.1038/nature01149
    • Ibarra RU, Edwards JS, Palsson BO. 2002. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature. 420:186-189. (Pubitemid 35340123)
    • (2002) Nature , vol.420 , Issue.6912 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 27
    • 79951492842 scopus 로고    scopus 로고
    • Complex function by design using spatially pre-structured synthetic microbial communities: Degradation of pentachlorophenol in the presence of hg(ii)
    • doi: 10.1039/c0ib00019a
    • Kim HJ, Du W, Ismagilov RF. 2011. Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(II). Integr. Biol. (Camb). 3:126-133. doi: 10.1039/c0ib00019a.
    • (2011) Integr. Biol. (Camb). , vol.3 , pp. 126-133
    • Kim, H.J.1    Du, W.2    Ismagilov, R.F.3
  • 29
    • 78649677586 scopus 로고    scopus 로고
    • Environments that induce synthetic microbial ecosystems
    • doi: 10.1371 /journal.pcbi.1001002
    • Klitgord N, and Segre D. 2010. Environments that induce synthetic microbial ecosystems.PLoS Comput.Biol.6:el001002. doi: 10.1371 /journal.pcbi. 1001002.
    • (2010) PLoS Comput. Biol. , vol.6
    • Klitgord, N.1    Segre, D.2
  • 31
    • 84861440312 scopus 로고    scopus 로고
    • Systems metabolic engineering of microorganisms for natural and non-natural chemicals
    • doi: 10.1038/nchembio.970; 10.1038/nchembio.970
    • Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY. 2012. Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat. Chem. Biol. 8:536-546. doi: 10.1038/nchembio.970; 10.1038/nchembio.970.
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 536-546
    • Lee, J.W.1    Na, D.2    Park, J.M.3    Lee, J.4    Choi, S.5    Lee, S.Y.6
  • 32
    • 0036708443 scopus 로고    scopus 로고
    • Dynamic Flux Balance Analysis of diauxic growth in Escherichia coli
    • Mahadevan R, Edwards JS, Doyle FJ. 2002. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83:1331-1340. (Pubitemid 34977706)
    • (2002) Biophysical Journal , vol.83 , Issue.3 , pp. 1331-1340
    • Mahadevan, R.1    Edwards, J.S.2    Doyle III, F.J.3
  • 33
    • 78650298909 scopus 로고    scopus 로고
    • In situ to in silico and back: Elucidating the physiology and ecology of geobacter spp. Using genome-scale modelling
    • Mahadevan R, Palsson BO, Lovley D. 2011. In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling. Nat.Rev.Microbiol. 9:39-50.
    • (2011) Nat. Rev. Microbiol. , vol.9 , pp. 39-50
    • Mahadevan, R.1    Palsson, B.O.2    Lovley, D.3
  • 34
    • 0025405421 scopus 로고
    • Simple constrained-optimization view of acetate overflow in E. Coli
    • DOI 10.1002/bit.260350711
    • Majewski R, and Domach M.1990.Simple Constrained-optimization View of Acetate Overflow in Escherichia-coli. Biotechnol. Bioeng. 35:732-738. (Pubitemid 20150014)
    • (1990) Biotechnology and Bioengineering , vol.35 , Issue.7 , pp. 732-738
    • Majewski, R.A.1    Domach, M.M.2
  • 37
    • 11844280852 scopus 로고    scopus 로고
    • Game-theoretical approaches to studying the evolution of biochemical systems
    • DOI 10.1016/j.tibs.2004.11.006, PII S0968000404002968
    • Pfeiffer T, and Schuster S. 2005. Game-theoretical approaches to studying the evolution of biochemical systems. Trends Biochem. Sci. 30:20-25. doi: 10.1016/j.tibs.2004.11.006. (Pubitemid 40093737)
    • (2005) Trends in Biochemical Sciences , vol.30 , Issue.1 , pp. 20-25
    • Pfeiffer, T.1    Schuster, S.2
  • 38
    • 0035917865 scopus 로고    scopus 로고
    • Cooperation and competition in the evolution of ATP-producing pathways
    • Pfeiffer T, Schuster S, Bonhoeffer S. 2001. Cooperation and competition in the evolution of ATP-producing pathways. Science. 292:504-507. doi: 10.1126/science.l058079. (Pubitemid 32335953)
    • (2001) Science , vol.292 , Issue.5516 , pp. 504-507
    • Pfeiffer, T.1    Schuster, S.2    Bonhoeffer, S.3
  • 39
    • 77956649528 scopus 로고    scopus 로고
    • Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
    • doi: 10.1016/j.copbio.2010.07.002
    • Ruppin E, Papin JA, de Figueiredo LF, Schuster S. 2010. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr. Opin. Biotechnol. 21:502-510. doi: 10.1016/j.copbio.2010.07.002.
    • (2010) Curr. Opin. Biotechnol. , vol.21 , pp. 502-510
    • Ruppin, E.1    Papin, J.A.2    De Figueiredo, L.F.3    Schuster, S.4
  • 40
    • 77954724818 scopus 로고    scopus 로고
    • Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
    • doi: 10.1002/biot.201000159
    • Salimi F, Zhuang K, Mahadevan R. 2010. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing Biotechnol. J. 5:726-738. doi: 10.1002/biot.201000159.
    • (2010) Biotechnol. J. , vol.5 , pp. 726-738
    • Salimi, F.1    Zhuang, K.2    Mahadevan, R.3
  • 41
    • 84860487758 scopus 로고    scopus 로고
    • Multidimensional optimality of microbial metabolism
    • doi: 10.1126/science.l216882
    • Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U. 2012.Multidimensional optimality of microbial metabolism. Science. 336:601-604. doi: 10.1126/science.l216882.
    • (2012) Science. , vol.336 , pp. 601-604
    • Schuetz, R.1    Zamboni, N.2    Zampieri, M.3    Heinemann, M.4    Sauer, U.5
  • 42
    • 79956287318 scopus 로고    scopus 로고
    • Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean
    • doi: 10.1038/ismej.2010.189
    • Shi Y, Tyson GW, Eppley JM, DeLong EF.2011. Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean.ISME J.5:999-1013.doi: 10.1038/ismej.2010.189.
    • (2011) ISME J. , vol.5 , pp. 999-1013
    • Shi, Y.1    Tyson, G.W.2    Eppley, J.M.3    DeLong, E.F.4
  • 44
    • 84861663597 scopus 로고    scopus 로고
    • Evolutionary trade-offs, pareto optimality, and the geometry of phenotype space
    • doi: 10.1126/science.l217405
    • Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, Mayo A, Dekel E, Kavanagh K, Alon U.2012.Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space.Science. 336:1157-1160. doi: 10.1126/science. l217405.
    • (2012) Science. , vol.336 , pp. 1157-1160
    • Shoval, O.1    Sheftel, H.2    Shinar, G.3    Hart, Y.4    Ramote, O.5    Mayo, A.6    Dekel, E.7    Kavanagh, K.8    Alon, U.9
  • 45
    • 77953080992 scopus 로고    scopus 로고
    • Prediction of metabolic function from limited data: Lumped hybrid cybernetic modeling (l-hcm)
    • doi: 10.1002/bit.22692
    • Song HS, and Ramkrishna D. 2010. Prediction of metabolic function from limited data: Lumped hybrid cybernetic modeling (L-HCM). Biotechnol. Bioeng. 106:271-284. doi: 10.1002/bit.22692.
    • (2010) Biotechnol. Bioeng. , vol.106 , pp. 271-284
    • Song, H.S.1    Ramkrishna, D.2
  • 48
    • 80054115962 scopus 로고    scopus 로고
    • A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
    • doi: 10.1186/1752-0509-5-167
    • Tzamali E, Poirazi P, Tollis IG, Reczko M. 2011. A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities.BMC Syst. Biol. 5:167. doi: 10.1186/1752-0509-5-167.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 167
    • Tzamali, E.1    Poirazi, P.2    Tollis, I.G.3    Reczko, M.4
  • 49
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific and practical use
    • Varma A, and Palsson B.1994. Metabolic Flux Balancing: Basic concepts, Scientific and Practical Use. Bio/Technology. 12:994-998.
    • (1994) Bio/Technology. , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.2
  • 50
    • 60749119754 scopus 로고    scopus 로고
    • Systems biology: Functional analysis of natural microbial consortia using community proteomics
    • doi: 10.1038/nrmicro2080
    • VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF. 2009. Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat. Rev. Microbiol. 7:196-205. doi: 10.1038/nrmicro2080.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 196-205
    • VerBerkmoes, N.C.1    Denef, V.J.2    Hettich, R.L.3    Banfield, J.F.4
  • 52
    • 77956415336 scopus 로고    scopus 로고
    • Emergent cooperation in microbial metabolism
    • doi: 10.1038/msb.2010.66
    • Wintermute EH, and Silver PA. 2010. Emergent cooperation in microbial metabolism. Mol. Syst. Biol. 6:407. doi: 10.1038/msb.2010.66.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 407
    • Wintermute, E.H.1    Silver, P.A.2
  • 55
    • 84902172907 scopus 로고    scopus 로고
    • Genome-scale dynamic modeling of the competition between rhodoferax and geobacter in anoxic subsurface environments
    • Zhuang K, Izallalen M, Mouser PM.R., Lovely D. 2010. Genome-Scale Dynamic Modeling of the Competition Between Rhodoferax and Geobacter in Anoxic Subsurface Environments. ISME Journal. 107:352.
    • (2010) ISME Journal , vol.107 , pp. 352
    • Zhuang, K.1    Izallalen, M.2    Mouser, P.M.R.3    Lovely, D.4
  • 56
    • 84865358026 scopus 로고    scopus 로고
    • The design of long-term effective uranium bioremediation strategy using a community metabolic model
    • doi: 10.1002/bit.24528; 10.1002/bit.24528
    • Zhuang K, Ma E, Lovley DR, Mahadevan R. 2012. The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnol. Bioeng. . doi: 10.1002/bit.24528; 10.1002/bit.24528.
    • (2012) Biotechnol. Bioeng.
    • Zhuang, K.1    Ma, E.2    Lovley, D.R.3    Mahadevan, R.4
  • 57
    • 84861180223 scopus 로고    scopus 로고
    • Optcom: A multi-level optimization framework for the metabolic modeling and analysis of microbial communities
    • doi: 10.1371/journal.pcbi.l002363
    • Zomorrodi AR, and Maranas CD. 2012. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput. Biol. 8:el002363. doi: 10.1371/journal.pcbi.l002363.
    • (2012) PLoS Comput. Biol. , vol.8
    • Zomorrodi, A.R.1    Maranas, C.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.