메뉴 건너뛰기




Volumn 9, Issue 1, 2016, Pages

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

Author keywords

Anaerobic digestion; Hierarchical optimization; Microbial communities; Prediction of community composition; Stoichiometric and constraint based modeling

Indexed keywords

ANAEROBIC DIGESTION; BACTERIA; BIOGAS; BIOLOGY; BIOMASS; FORECASTING; GROWTH RATE; METABOLISM; METHANE; MICROORGANISMS; SUBSTRATES;

EID: 84961286195     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-016-0429-x     Document Type: Article
Times cited : (26)

References (33)
  • 1
    • 0029662913 scopus 로고    scopus 로고
    • A mini-review of microbial consortia: their roles in aquatic production and biogeochemical cycling
    • Paerl HW, Pinckney JL. A mini-review of microbial consortia: their roles in aquatic production and biogeochemical cycling. Microbial Ecol. 1996;31(3):225-47.
    • (1996) Microbial Ecol , vol.31 , Issue.3 , pp. 225-247
    • Paerl, H.W.1    Pinckney, J.L.2
  • 2
    • 49449087467 scopus 로고    scopus 로고
    • Microbial contributions to climate change through carbon cycle feedbacks
    • 1:CAS:528:DC%2BD1cXhtVWmtrrP
    • Bardgett RD, Freeman C, Ostle NJ. Microbial contributions to climate change through carbon cycle feedbacks. ISME J. 2008;2(8):805-14.
    • (2008) ISME J , vol.2 , Issue.8 , pp. 805-814
    • Bardgett, R.D.1    Freeman, C.2    Ostle, N.J.3
  • 3
    • 77957744758 scopus 로고    scopus 로고
    • The evolution and future of Earth's nitrogen cycle
    • 1:CAS:528:DC%2BC3cXht1Cgt77K
    • Canfield DE, Glazer AN, Falkowski PG. The evolution and future of Earth's nitrogen cycle. Science. 2010;330(6001):192-6.
    • (2010) Science , vol.330 , Issue.6001 , pp. 192-196
    • Canfield, D.E.1    Glazer, A.N.2    Falkowski, P.G.3
  • 4
    • 35348968286 scopus 로고    scopus 로고
    • The human microbiome project: exploring the microbial part of ourselves in a changing world
    • 1:CAS:528:DC%2BD2sXhtFOjt7nP
    • Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett C, Knight R, Gordon JI. The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature. 2007;449(7164):804.
    • (2007) Nature , vol.449 , Issue.7164 , pp. 804
    • Turnbaugh, P.J.1    Ley, R.E.2    Hamady, M.3    Fraser-Liggett, C.4    Knight, R.5    Gordon, J.I.6
  • 5
    • 84858439578 scopus 로고    scopus 로고
    • Applications of next-generation sequencing. the human microbiome: at the interface of health and disease
    • 1:CAS:528:DC%2BC38Xjs1Wguro%3D
    • Cho I, Blaser MJ. Applications of next-generation sequencing. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260-70.
    • (2012) Nat Rev Genet , vol.13 , Issue.4 , pp. 260-270
    • Cho, I.1    Blaser, M.J.2
  • 6
    • 84863920287 scopus 로고    scopus 로고
    • Microbial interactions: from networks to models
    • 1:CAS:528:DC%2BC38XhtVehsL3M
    • Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol. 2012;10(8):538-50.
    • (2012) Nat Rev Microbiol , vol.10 , Issue.8 , pp. 538-550
    • Faust, K.1    Raes, J.2
  • 7
    • 76649102408 scopus 로고    scopus 로고
    • Biogas production: current state and perspectives
    • Weiland P. Biogas production: current state and perspectives. Appl Microbiol Biotechnol. 2009;85(4):849-60.
    • (2009) Appl Microbiol Biotechnol , vol.85 , Issue.4 , pp. 849-860
    • Weiland, P.1
  • 8
    • 0028108519 scopus 로고
    • Metabolic flux balancing - basic concepts, scientific and practical use
    • 1:CAS:528:DyaK2MXhtFansL0%3D
    • Varma A, Palsson BO. Metabolic flux balancing - basic concepts, scientific and practical use. Bio-Technol. 1994;12(10):994-8.
    • (1994) Bio-Technol , vol.12 , Issue.10 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 9
    • 0037385718 scopus 로고    scopus 로고
    • Genome-scale microbial in silico models: the constraints-based approach
    • 1:CAS:528:DC%2BD3sXisFWlu7w%3D
    • Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 2003;21(4):162-9.
    • (2003) Trends Biotechnol , vol.21 , Issue.4 , pp. 162-169
    • Price, N.D.1    Papin, J.A.2    Schilling, C.H.3    Palsson, B.O.4
  • 10
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • 1:CAS:528:DC%2BC3cXivV2rtL4%3D
    • Orth JD, Thiele I, Palsson BO. What is flux balance analysis? Nat Biotechnol. 2010;28(3):245-8.
    • (2010) Nat Biotechnol , vol.28 , Issue.3 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.3
  • 12
    • 77953618954 scopus 로고    scopus 로고
    • Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions
    • 1:CAS:528:DC%2BC3cXksFWmurk%3D
    • Bizukojc M, Dietz D, Sun J, Zeng AP. Metabolic modelling of syntrophic-like growth of a 1,3-propanediol producer, Clostridium butyricum, and a methanogenic archeon, Methanosarcina mazei, under anaerobic conditions. Bioprocess Biosyst Eng. 2010;33(4):507-23.
    • (2010) Bioprocess Biosyst Eng , vol.33 , Issue.4 , pp. 507-523
    • Bizukojc, M.1    Dietz, D.2    Sun, J.3    Zeng, A.P.4
  • 13
    • 84861180223 scopus 로고    scopus 로고
    • OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities
    • 1:CAS:528:DC%2BC38XisFeqsr8%3D
    • Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol. 2012;8(2):e1002363.
    • (2012) PLoS Comput Biol , vol.8 , Issue.2
    • Zomorrodi, A.R.1    Maranas, C.D.2
  • 14
    • 84878575301 scopus 로고    scopus 로고
    • Community flux balance analysis for microbial consortia at balanced growth
    • 1:CAS:528:DC%2BC3sXpslOgtrs%3D
    • Khandelwal RA, Olivier BG, Roling WF, Teusink B, Bruggeman FJ. Community flux balance analysis for microbial consortia at balanced growth. PLoS One. 2013;8(5):e64567.
    • (2013) PLoS One , vol.8 , Issue.5
    • Khandelwal, R.A.1    Olivier, B.G.2    Roling, W.F.3    Teusink, B.4    Bruggeman, F.J.5
  • 15
    • 84901273253 scopus 로고    scopus 로고
    • Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
    • 1:CAS:528:DC%2BC2cXnsVajsb4%3D
    • Harcombe WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. Cell Rep. 2014;7(4):1104-15.
    • (2014) Cell Rep , vol.7 , Issue.4 , pp. 1104-1115
    • Harcombe, W.R.1    Riehl, W.J.2    Dukovski, I.3    Granger, B.R.4    Betts, A.5    Lang, A.H.6
  • 17
    • 84905483334 scopus 로고    scopus 로고
    • Emergent biosynthetic capacity in simple microbial communities
    • Chiu HC, Levy R, Borenstein E. Emergent biosynthetic capacity in simple microbial communities. PLoS Comput Biol. 2014;10(7):e1003695.
    • (2014) PLoS Comput Biol , vol.10 , Issue.7
    • Chiu, H.C.1    Levy, R.2    Borenstein, E.3
  • 18
    • 74049119822 scopus 로고    scopus 로고
    • In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study
    • Taffs R, Aston JE, Brileya K, Jay Z, Klatt CG, McGlynn S, et al. In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Syst Biol. 2009;3(1):114.
    • (2009) BMC Syst Biol , vol.3 , Issue.1 , pp. 114
    • Taffs, R.1    Aston, J.E.2    Brileya, K.3    Jay, Z.4    Klatt, C.G.5    McGlynn, S.6
  • 19
    • 78751584992 scopus 로고    scopus 로고
    • Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
    • Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, Mahadevan R, et al. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J. 2011;5(2):305-16.
    • (2011) ISME J , vol.5 , Issue.2 , pp. 305-316
    • Zhuang, K.1    Izallalen, M.2    Mouser, P.3    Richter, H.4    Risso, C.5    Mahadevan, R.6
  • 20
    • 78650215306 scopus 로고    scopus 로고
    • Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures
    • 1:CAS:528:DC%2BC3cXhsFOjsLbL
    • Hanly TJ, Henson MA. Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures. Biotechnol Bioeng. 2011;108(2):376-85.
    • (2011) Biotechnol Bioeng , vol.108 , Issue.2 , pp. 376-385
    • Hanly, T.J.1    Henson, M.A.2
  • 21
    • 84899012698 scopus 로고    scopus 로고
    • D-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities
    • 1:CAS:528:DC%2BC2cXisFait78%3D
    • Zomorrodi AR, Islam MM, Maranas CD. d-OptCom: dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol. 2014;3(4):247-57.
    • (2014) ACS Synth Biol , vol.3 , Issue.4 , pp. 247-257
    • Zomorrodi, A.R.1    Islam, M.M.2    Maranas, C.D.3
  • 22
    • 0002372703 scopus 로고
    • Basic principles of bioconversions in anaerobic digestion and methanogenesis
    • London: Springer
    • McInerney MJ, Bryant MP. Basic principles of bioconversions in anaerobic digestion and methanogenesis. In: Biomass conversion processes for energy and fuels. London: Springer; 1981. p. 277-96.
    • (1981) Biomass Conversion Processes for Energy and Fuels , pp. 277-296
    • McInerney, M.J.1    Bryant, M.P.2
  • 23
    • 0030871461 scopus 로고    scopus 로고
    • Energetics of syntrophic cooperation in methanogenic degradation
    • 1:CAS:528:DyaK2sXktFGqtb8%3D
    • Schink B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev. 1997;61(2):262-80.
    • (1997) Microbiol Mol Biol Rev , vol.61 , Issue.2 , pp. 262-280
    • Schink, B.1
  • 25
    • 47549119041 scopus 로고    scopus 로고
    • Methanogenic archaea: ecologically relevant differences in energy conservation
    • 1:CAS:528:DC%2BD1cXosFSktLs%3D
    • Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol. 2008;6(8):579-91.
    • (2008) Nat Rev Microbiol , vol.6 , Issue.8 , pp. 579-591
    • Thauer, R.K.1    Kaster, A.K.2    Seedorf, H.3    Buckel, W.4    Hedderich, R.5
  • 26
    • 0002620715 scopus 로고
    • Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment
    • Jones WJ, Paynter M, Gupta R. Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment. Arch Microbiol. 1983;135(2):91-7.
    • (1983) Arch Microbiol , vol.135 , Issue.2 , pp. 91-97
    • Jones, W.J.1    Paynter, M.2    Gupta, R.3
  • 27
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • (Database issue) 1:CAS:528:DC%2BD1cXhtVSku7k%3D
    • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36(Database issue):D480-4.
    • (2008) Nucleic Acids Res , vol.36 , pp. D480-D484
    • Kanehisa, M.1    Araki, M.2    Goto, S.3    Hattori, M.4    Hirakawa, M.5    Itoh, M.6
  • 28
    • 0017409091 scopus 로고
    • Growth of Desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria
    • 1:CAS:528:DyaE2sXktlGlsr0%3D
    • Bryant MP, Campbell LL, Reddy CA, Crabill MR. Growth of Desulfovibrio in lactate or ethanol media low in sulfate in association with H2-utilizing methanogenic bacteria. Appl Environ Microbiol. 1977;33(5):1162-9.
    • (1977) Appl Environ Microbiol , vol.33 , Issue.5 , pp. 1162-1169
    • Bryant, M.P.1    Campbell, L.L.2    Reddy, C.A.3    Crabill, M.R.4
  • 29
    • 0017819828 scopus 로고
    • Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources
    • 1:CAS:528:DyaE1cXltVentr4%3D
    • Badziong W, Thauer RK. Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources. Arch Microbiol. 1978;117(2):209-14.
    • (1978) Arch Microbiol , vol.117 , Issue.2 , pp. 209-214
    • Badziong, W.1    Thauer, R.K.2
  • 30
    • 33846634149 scopus 로고    scopus 로고
    • Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry
    • 1:CAS:528:DC%2BD2sXht1ehtLk%3D
    • Tang Y, Pingitore F, Mukhopadhyay A, Phan R, Hazen TC, Keasling JD. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry. J Appl Bacteriol. 2007;189(3):940-9.
    • (2007) J Appl Bacteriol , vol.189 , Issue.3 , pp. 940-949
    • Tang, Y.1    Pingitore, F.2    Mukhopadhyay, A.3    Phan, R.4    Hazen, T.C.5    Keasling, J.D.6
  • 31
    • 0024545746 scopus 로고
    • Methanogenesis from ethanol by defined mixed continuous cultures
    • 1:CAS:528:DyaL1MXhtFeit7w%3D
    • Tatton MJ, Archer DB, Powell GE, Parker ML. Methanogenesis from ethanol by defined mixed continuous cultures. Appl Environ Microbiol. 1989;55(2):440-5.
    • (1989) Appl Environ Microbiol , vol.55 , Issue.2 , pp. 440-445
    • Tatton, M.J.1    Archer, D.B.2    Powell, G.E.3    Parker, M.L.4
  • 32
    • 0012015191 scopus 로고
    • Ethanol dissimilation in Desulfovibrio
    • 1:CAS:528:DyaL1MXitV2jtQ%3D%3D
    • Kremer DR, Nienhuiskuiper HE, Hansen TA. Ethanol dissimilation in Desulfovibrio. Arch Microbiol. 1988;150(6):552-7.
    • (1988) Arch Microbiol , vol.150 , Issue.6 , pp. 552-557
    • Kremer, D.R.1    Nienhuiskuiper, H.E.2    Hansen, T.A.3
  • 33


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.