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Volumn 3, Issue , 2013, Pages

Understanding the interactions between bacteria in the human gut through metabolic modeling

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL PHENOMENA AND FUNCTIONS; BIOLOGICAL MODEL; COMPUTER SIMULATION; GASTROINTESTINAL TRACT; HUMAN; METAGENOME; MICROBIOLOGY; MICROFLORA; PHYSIOLOGY;

EID: 84883389182     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep02532     Document Type: Article
Times cited : (210)

References (52)
  • 2
    • 79952712983 scopus 로고    scopus 로고
    • Gut microbiome-host interactions in health and disease
    • Kinross, J. M., Darzi, A. W. & Nicholson, J. K. Gut microbiome-host interactions in health and disease. Genome medicine 3, 14 (2011).
    • (2011) Genome Medicine , vol.3 , pp. 14
    • Kinross, J.M.1    Darzi, A.W.2    Nicholson, J.K.3
  • 3
    • 58749112734 scopus 로고    scopus 로고
    • A core gut microbiome in obese and lean twins
    • Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
    • (2009) Nature , vol.457 , pp. 480-484
    • Turnbaugh, P.J.1
  • 4
    • 84867074831 scopus 로고    scopus 로고
    • A metagenome-wide association study of gut microbiota in type 2 diabetes
    • Qin, J. J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
    • (2012) Nature , vol.490 , pp. 55-60
    • Qin, J.J.1
  • 5
    • 84878709716 scopus 로고    scopus 로고
    • Gut metagenome in European women with normal impaired and diabetic glucose control
    • Karlsson, F. H. et al.Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498, 99-103 (2013).
    • (2013) Nature , vol.498 , pp. 99-103
    • Karlsson, F.H.1
  • 6
    • 84871814687 scopus 로고    scopus 로고
    • Symptomatic atherosclerosis is associated with an altered gut metagenome
    • Karlsson, F. H. et al. Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3, 1245 (2012).
    • (2012) Nat Commun , vol.3 , pp. 1245
    • Karlsson, F.H.1
  • 7
    • 84864722033 scopus 로고    scopus 로고
    • Gut microbiota composition correlates with diet and health in the elderly
    • Claesson,M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184 (2012).
    • (2012) Nature , vol.488 , pp. 178-184
    • Claesson, M.J.1
  • 8
    • 77950251400 scopus 로고    scopus 로고
    • A human gut microbial gene catalogue established by metagenomic sequencing
    • Qin, J. J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-U70 (2010).
    • (2010) Nature , vol.464
    • Qin, J.J.1
  • 9
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Huttenhower, C. et al. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
    • (2012) Nature , vol.486 , pp. 207-214
    • Huttenhower, C.1
  • 10
    • 85027927719 scopus 로고    scopus 로고
    • Enterotypes of the human gut microbiome
    • Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
    • (2011) Nature , vol.473 , pp. 174-180
    • Arumugam, M.1
  • 11
    • 33845874101 scopus 로고    scopus 로고
    • An obesity-associated gut microbiome with increased capacity for energy harvest
    • DOI 10.1038/nature05414, PII NATURE05414
    • Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006). (Pubitemid 46018515)
    • (2006) Nature , vol.444 , Issue.7122 , pp. 1027-1031
    • Turnbaugh, P.J.1    Ley, R.E.2    Mahowald, M.A.3    Magrini, V.4    Mardis, E.R.5    Gordon, J.I.6
  • 12
    • 33846434794 scopus 로고    scopus 로고
    • The effects of short-chain fatty acids on colon epithelial proliferation and survival depend on the cellular phenotype (vol 132, pg 487, 2006)
    • Comalada, M. et al. The effects of short-chain fatty acids on colon epithelial proliferation and survival depend on the cellular phenotype (vol 132, pg 487, 2006). J Cancer Res Clin 133, 211-211 (2007).
    • (2007) J Cancer Res Clin , vol.133 , pp. 211-211
    • Comalada, M.1
  • 13
    • 0018888157 scopus 로고
    • Absorption of short-chain fatty acids by the colon
    • Ruppin, H., Bar-Meir, S., Soergel, K. H., Wood, C. M. & Schmitt, M. G., Jr. Absorption of short-chain fatty acids by the colon. Gastroenterology 78, 1500-1507 (1980). (Pubitemid 10116160)
    • (1980) Gastroenterology , vol.78 , Issue.6 , pp. 1500-1507
    • Ruppin, H.1    Bar-Meir, S.2    Soergel, K.H.3
  • 14
    • 0018128601 scopus 로고
    • Short chain fatty acid absorption by the human large intestine
    • McNeil, N. I., Cummings, J. H.& James, W. P. Short chain fatty acid absorption by the human large intestine. Gut 19, 819-822 (1978). (Pubitemid 9020988)
    • (1978) Gut , vol.19 , Issue.9 , pp. 819-822
    • McNeil, N.I.1    Cummings, J.H.2    James, W.P.T.3
  • 15
    • 0021349077 scopus 로고
    • The contribution of the large intestine to energy supplies in man
    • McNeil, N. I. The contribution of the large intestine to energy supplies in man. The American journal of clinical nutrition 39, 338-342 (1984). (Pubitemid 14186434)
    • (1984) American Journal of Clinical Nutrition , vol.39 , Issue.2 , pp. 338-342
    • McNeil, N.I.1
  • 16
    • 79955634137 scopus 로고    scopus 로고
    • The microbial-mammalian metabolic axis: Beyond simple metabolism
    • Dumas, M. E. The microbial-mammalian metabolic axis: beyond simple metabolism. Cell metabolism 13, 489-490 (2011).
    • (2011) Cell Metabolism , vol.13 , pp. 489-490
    • Dumas, M.E.1
  • 17
    • 0038676409 scopus 로고    scopus 로고
    • Inhibition of histone deacetylase activity by butyrate
    • Davie, J. R. Inhibition of histone deacetylase activity by butyrate. J Nutr 133, 2485S-2493S (2003). (Pubitemid 36828858)
    • (2003) Journal of Nutrition , vol.133 , Issue.7 SUPPL.
    • Davie, J.R.1
  • 20
    • 84870389262 scopus 로고    scopus 로고
    • The warburg effect dictates the mechanism of butyratemediated histone acetylation and cell proliferation
    • Donohoe, D. R. et al. The warburg effect dictates the mechanism of butyratemediated histone acetylation and cell proliferation. Molecular cell 48, 612-626 (2012).
    • (2012) Molecular Cell , vol.48 , pp. 612-626
    • Donohoe, D.R.1
  • 21
    • 56549122798 scopus 로고    scopus 로고
    • Human colonic microbiota associated with diet, obesity and weight loss
    • Duncan, S. H. et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes (Lond) 32, 1720-1724 (2008).
    • (2008) Int J Obes (Lond) , vol.32 , pp. 1720-1724
    • Duncan, S.H.1
  • 22
    • 80053618114 scopus 로고    scopus 로고
    • Linking long-term dietary patterns with gut microbial enterotypes
    • Wu,G.D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).
    • (2011) Science , vol.334 , pp. 105-108
    • Wu, G.D.1
  • 23
    • 79959855078 scopus 로고    scopus 로고
    • Predicting a human gut microbiota? S response to diet in gnotobiotic mice
    • Faith, J. J., McNulty, N. P., Rey, F. E. & Gordon, J. I. Predicting a human gut microbiota?s response to diet in gnotobiotic mice. Science 333, 101-104 (2011).
    • (2011) Science , vol.333 , pp. 101-104
    • Faith, J.J.1    McNulty, N.P.2    Rey, F.E.3    Gordon, J.I.4
  • 25
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotypephenotype relationship using a phylogeny of in silico methods
    • Lewis, N. E.,Nagarajan,H. & Palsson, B. O. Constraining the metabolic genotypephenotype relationship using a phylogeny of in silico methods. Nature reviews. Microbiology 10, 291-305 (2012).
    • (2012) Nature Reviews. Microbiology , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 27
    • 57649184474 scopus 로고    scopus 로고
    • Genome-scale analyses of health-promoting bacteria: Probiogenomics
    • Ventura, M. et al. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nature reviews. Microbiology 7, 61-71 (2009).
    • (2009) Nature Reviews. Microbiology , vol.7 , pp. 61-71
    • Ventura, M.1
  • 28
    • 33947276100 scopus 로고    scopus 로고
    • Metabolic modeling of a mutualistic microbial community
    • Stolyar, S. et al. Metabolic modeling of a mutualistic microbial community. Molecular systems biology 3, (2007).
    • (2007) Molecular Systems Biology , vol.3
    • Stolyar, S.1
  • 29
    • 84861180223 scopus 로고    scopus 로고
    • OptCom: A multi-level optimization framework for the metabolic modeling and analysis of microbial communities
    • Zomorrodi, A. R. & Maranas, C. D. OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities. PLoS computational biology 8, (2012).
    • (2012) PLoS Computational Biology , vol.8
    • Zomorrodi, A.R.1    Maranas, C.D.2
  • 32
    • 70349631208 scopus 로고    scopus 로고
    • Monitoring bacterial community of human gut microbiota reveals an increase in lactobacillus in obese patients and methanogens in anorexic patients
    • Armougom, F., Henry, M., Vialettes, B., Raccah, D. & Raoult, D. Monitoring Bacterial Community of Human Gut Microbiota Reveals an Increase in Lactobacillus in Obese Patients and Methanogens in Anorexic Patients. PlosOne 4 (2009).
    • (2009) PlosOne , vol.4
    • Armougom, F.1    Henry, M.2    Vialettes, B.3    Raccah, D.4    Raoult, D.5
  • 34
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • DOI 10.1073/pnas.0406811102
    • Patil, K. R. & Nielsen, J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proceedings of the National Academy of Sciences of the United States of America 102, 2685-2689 (2005). (Pubitemid 40299853)
    • (2005) Proceedings of the National Academy of Sciences of the United States of America , vol.102 , Issue.8 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 35
    • 78049304837 scopus 로고    scopus 로고
    • Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    • Bordel, S., Agren, R. & Nielsen, J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS computational biology 6, e1000859 (2010).
    • (2010) PLoS Computational Biology , vol.6
    • Bordel, S.1    Agren, R.2    Nielsen, J.3
  • 36
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K- 12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist, A. M. et al. A genome-scale metabolic reconstruction for Escherichia coli K- 12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular systems biology 3 (2007).
    • (2007) Molecular Systems Biology , vol.3
    • Feist, A.M.1
  • 37
    • 33644829256 scopus 로고    scopus 로고
    • In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network
    • Heinemann, M., Kummel, A., Ruinatscha, R. & Panke, S. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnology and bioengineering 92, 850-864 (2005).
    • (2005) Biotechnology and Bioengineering , vol.92 , pp. 850-864
    • Heinemann, M.1    Kummel, A.2    Ruinatscha, R.3    Panke, S.4
  • 38
    • 79851515763 scopus 로고    scopus 로고
    • Metabolic reconstruction of the archaeon methanogen methanosarcina acetivorans
    • Kumar, V. S., Ferry, J. G. & Maranas, C. D. Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC systems biology 5, (2011).
    • (2011) BMC Systems Biology , vol.5
    • Kumar, V.S.1    Ferry, J.G.2    Maranas, C.D.3
  • 40
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Henry, C. S. et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature biotechnology 28, 977-U922 (2010).
    • (2010) Nature Biotechnology , vol.28
    • Henry, C.S.1
  • 41
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • Agren, R. et al. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS computational biology 9, e1002980 (2013).
    • (2013) PLoS Computational Biology , vol.9
    • Agren, R.1
  • 42
    • 84871588520 scopus 로고    scopus 로고
    • Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    • Heinken, A., Sahoo, S., Fleming, R. M. & Thiele, I. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut microbes 4, 28-40 (2013).
    • (2013) Gut Microbes , vol.4 , pp. 28-40
    • Heinken, A.1    Sahoo, S.2    Fleming, R.M.3    Thiele, I.4
  • 43
    • 0020312528 scopus 로고
    • Utilization of chondroitin sulfate by Bacteroides thetaiotaomicron growing in carbohydrate-limited continuous culture
    • Salyers, A. A., Obrien, M. & Kotarski, S. F. Utilization of Chondroitin Sulfate by Bacteroides-Thetaiotaomicron Growing in Carbohydrate-Limited Continuous Culture. J Bacteriol 150, 1008-1015 (1982). (Pubitemid 12010866)
    • (1982) Journal of Bacteriology , vol.150 , Issue.3 , pp. 1008-1015
    • Salyers, A.A.1    O'Brien, M.2    Kotarski, S.F.3
  • 45
    • 0025082884 scopus 로고
    • Cellulose fermentation by continuous cultures of Ruminococcus albus and Methanobrevibacter smithii
    • Pavlostathis, S. G., Miller, T. L. & Wolin, M. J. Cellulose Fermentation by Continuous Cultures of Ruminococcus-Albus and Methanobrevibacter-Smithii. Applied microbiology and biotechnology 33, 109-116 (1990). (Pubitemid 20262893)
    • (1990) Applied Microbiology and Biotechnology , vol.33 , Issue.1 , pp. 109-116
    • Pavlostathis, S.G.1    Miller, T.L.2    Wolin, M.J.3
  • 46
    • 77954336201 scopus 로고    scopus 로고
    • Mathematical modelling of carbohydrate degradation by human colonic microbiota
    • Munoz-Tamayo, R., Laroche, B., Walter, E., Dore, J. & Leclerc, M. Mathematical modelling of carbohydrate degradation by human colonic microbiota. J Theor Biol 266, 189-201 (2010).
    • (2010) J Theor Biol , vol.266 , pp. 189-201
    • Munoz-Tamayo, R.1    Laroche, B.2    Walter, E.3    Dore, J.4    Leclerc, M.5
  • 48
    • 84859587827 scopus 로고    scopus 로고
    • Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms
    • Lin, H. V. et al. Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. Plos One 7, e35240 (2012).
    • (2012) Plos One , vol.7
    • Lin, H.V.1
  • 49
    • 33847352401 scopus 로고    scopus 로고
    • A combined 1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-α null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndrome
    • DOI 10.1152/physiolgenomics.00060.2006
    • Atherton, H. J. et al.Acombined 1H-NMR spectroscopy- and mass spectrometrybased metabolomic study of the PPAR-alpha null mutantmouse defines profound systemic changes in metabolism linked to the metabolic syndrome. Physiological genomics 27, 178-186 (2006). (Pubitemid 46702031)
    • (2006) Physiological Genomics , vol.27 , Issue.2 , pp. 178-186
    • Atherton, H.J.1    Bailey, N.J.2    Zhang, W.3    Taylor, J.4    Major, H.5    Shockcor, J.6    Clarke, K.7    Griffin, J.L.8
  • 50
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
    • (2012) Nature , vol.486 , pp. 207-214
  • 52
    • 84877309040 scopus 로고    scopus 로고
    • Enriching the gene set analysis of genomewide data by incorporating directionality of gene expression and combining statistical hypotheses and methods
    • Varemo, L., Nielsen, J. & Nookaew, I. Enriching the gene set analysis of genomewide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic acids research (2013).
    • (2013) Nucleic Acids Research
    • Varemo, L.1    Nielsen, J.2    Nookaew, I.3


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