메뉴 건너뛰기




Volumn 196, Issue 18, 2014, Pages 3289-3302

Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

Author keywords

[No Author keywords available]

Indexed keywords

ACETATE KINASE; ACETIC ACID; ACETYL COENZYME A; ADENOSINE TRIPHOSPHATE; BIOTIN; CYSTEINE; FOLIC ACID; FORMIC ACID; GALACTURONIC ACID; GLUCOSE; GLUCURONIC ACID; GLYCERALDEHYDE 3 PHOSPHATE; LACTIC ACID; NICOTINAMIDE ADENINE DINUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; PALMITIC ACID; PANTOTHENIC ACID; PENTOSE; PYRIDOXINE; PYRUVIC ACID; RIBOFLAVIN; THIAMINE; URONIC ACID; VITAMIN; BACTERIAL PROTEIN; TRANSCRIPTOME;

EID: 84906052535     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01780-14     Document Type: Article
Times cited : (180)

References (62)
  • 8
    • 84866168894 scopus 로고    scopus 로고
    • Functional interactions between the gut microbiota and host metabolism
    • Tremaroli V, Backhed F. 2012. Functional interactions between the gut microbiota and host metabolism. Nature 489:242-249. http://dx.doi.org /10.1038/nature11552.
    • (2012) Nature , vol.489 , pp. 242-249
    • Tremaroli, V.1    Backhed, F.2
  • 10
    • 63849241608 scopus 로고    scopus 로고
    • Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine
    • Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:1- 8. http://dx.doi.org/10.1111/j.1574-6968.2009 .01514.x.
    • (2009) FEMS Microbiol. Lett. , vol.294
    • Louis, P.1    Flint, H.J.2
  • 11
    • 0036866628 scopus 로고    scopus 로고
    • Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen
    • Duncan SH, Hold GL, Harmsen HJ, Stewart CS, Flint HJ. 2002. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:2141-2146. http://dx.doi.org /10.1099/ijs.0.02241-0.
    • (2002) nov., comb. nov. Int. J. Syst. Evol. Microbiol. , vol.52 , pp. 2141-2146
    • Duncan, S.H.1    Hold, G.L.2    Harmsen, H.J.3    Stewart, C.S.4    Flint, H.J.5
  • 13
    • 84855717953 scopus 로고    scopus 로고
    • Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth
    • Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. 2012. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl. Environ. Microbiol. 78:420-428. http://dx.doi.org/10.1128/AEM.06858-11.
    • (2012) Appl. Environ. Microbiol. , vol.78 , pp. 420-428
    • Lopez-Siles, M.1    Khan, T.M.2    Duncan, S.H.3    Harmsen, H.J.4    Garcia-Gil, L.J.5    Flint, H.J.6
  • 14
    • 63849164050 scopus 로고    scopus 로고
    • Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii
    • Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. 2009. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br. J. Nutr. 101:541-550. http://dx.doi.org/10.1017/S0007114508019880.
    • (2009) Br. J. Nutr. , vol.101 , pp. 541-550
    • Ramirez-Farias, C.1    Slezak, K.2    Fuller, Z.3    Duncan, A.4    Holtrop, G.5    Louis, P.6
  • 15
    • 84864795465 scopus 로고    scopus 로고
    • Recent advances in reconstruction and applications of genome-scale metabolic models
    • Kim TY, Sohn SB, Kim YB, Kim WJ, Lee SY. 2012. Recent advances in reconstruction and applications of genome-scale metabolic models. Curr. Opin. Biotechnol. 23:617-623. http://dx.doi.org/10.1016/j.copbio.2011 .10.007.
    • (2012) Curr. Opin. Biotechnol. , vol.23 , pp. 617-623
    • Kim, T.Y.1    Sohn, S.B.2    Kim, Y.B.3    Kim, W.J.4    Lee, S.Y.5
  • 16
    • 84872272279 scopus 로고    scopus 로고
    • A systems biology approach to studying the role of microbes in human health
    • Thiele I, Heinken A, Fleming RM. 2013. A systems biology approach to studying the role of microbes in human health. Curr. Opin. Biotechnol. 24:4-12. http://dx.doi.org/10.1016/j.copbio.2012.10.001.
    • (2013) Curr. Opin. Biotechnol. , vol.24 , pp. 4-12
    • Thiele, I.1    Heinken, A.2    Fleming, R.M.3
  • 20
    • 23944440242 scopus 로고    scopus 로고
    • Modeling Lactococcus lactis using a genome-scale flux model
    • Oliveira AP, Nielsen J, Forster J. 2005. Modeling Lactococcus lactis using a genome-scale flux model. BMC Microbiol. 5:39. http://dx.doi.org/10 .1186/1471-2180-5-39.
    • (2005) BMC Microbiol. , vol.5 , pp. 39
    • Oliveira, A.P.1    Nielsen, J.2    Forster, J.3
  • 21
    • 41149169317 scopus 로고    scopus 로고
    • Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major
    • Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. 2008. Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol. Syst. Biol. 4:177. http://dx.doi.org/10.1038/msb.2008 .15.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 177
    • Chavali, A.K.1    Whittemore, J.D.2    Eddy, J.A.3    Williams, K.T.4    Papin, J.A.5
  • 23
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BO. 2010. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc. 5:93-121. http://dx .doi.org/10.1038/nprot.2009.203.
    • (2010) Nat. Protoc. , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 26
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genomescale metabolic models
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. 2010. High-throughput generation, optimization and analysis of genomescale metabolic models. Nat. Biotechnol. 28:977-982. http://dx.doi.org/10 .1038/nbt.1672.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 977-982
    • Henry, C.S.1    DeJongh, M.2    Best, A.A.3    Frybarger, P.M.4    Linsay, B.5    Stevens, R.L.6
  • 28
    • 84871588520 scopus 로고    scopus 로고
    • Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
    • Heinken A, Sahoo S, Fleming RM, Thiele I. 2013. Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4:28-40. http://dx.doi.org/10.4161/gmic.22370.
    • (2013) Gut Microbes , vol.4 , pp. 28-40
    • Heinken, A.1    Sahoo, S.2    Fleming, R.M.3    Thiele, I.4
  • 29
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger J, Park JO, Conrad TM, Palsson BO. 2010. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213. http://dx.doi.org/10.1186 /1471-2105-11-213.
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.O.4
  • 30
    • 34548219522 scopus 로고    scopus 로고
    • Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
    • Rodionov DA. 2007. Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem. Rev. 107:3467-3497. http: //dx.doi.org/10.1021/cr068309+.
    • (2007) Chem. Rev. , vol.107 , pp. 3467-3497
    • Rodionov, D.A.1
  • 33
    • 23144463910 scopus 로고    scopus 로고
    • RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
    • Abreu-Goodger C, Merino E. 2005. RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. Nucleic Acids Res. 33:W690-692. http://dx.doi.org/10.1093/nar/gki445.
    • (2005) Nucleic Acids Res. , vol.33
    • Abreu-Goodger, C.1    Merino, E.2
  • 34
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast.BMCSyst
    • Mo ML, Palsson BO, Herrgard MJ. 2009. Connecting extracellular metabolomic measurements to intracellular flux states in yeast.BMCSyst. Biol. 3:37. http://dx.doi.org/10.1186/1752-0509-3-37.
    • (2009) Biol. , vol.3 , pp. 37
    • Mo, M.L.1    Palsson, B.O.2    Herrgard, M.J.3
  • 35
    • 0037021804 scopus 로고    scopus 로고
    • Characterizing the metabolic phenotype: a phenotype phase plane analysis
    • Edwards JS, Ramakrishna R, Palsson BO. 2002. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77:27-36. http://dx.doi.org/10.1002/bit.10047.
    • (2002) Biotechnol. Bioeng. , vol.77 , pp. 27-36
    • Edwards, J.S.1    Ramakrishna, R.2    Palsson, B.O.3
  • 37
    • 77956914321 scopus 로고    scopus 로고
    • Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects
    • Benus RFJ, van der Werf TS, Welling GW, Judd PA, Taylor MA, Harmsen HJM, Whelan K. 2010. Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects. Br. J. Nutr. 104:693-700. http://dx.doi.org/10.1017/S000711 4510001030.
    • (2010) Br. J. Nutr. , vol.104 , pp. 693-700
    • Benus, R.F.J.1    van der Werf, T.S.2    Welling, G.W.3    Judd, P.A.4    Taylor, M.A.5    Harmsen, H.J.M.6    Whelan, K.7
  • 38
    • 84856231790 scopus 로고    scopus 로고
    • Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS)
    • Paglia G, Hrafnsdottir S, Magnusdottir M, Fleming RM, Thorlacius S, Palsson BO, Thiele I. 2012. Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Anal. Bioanal. Chem. 402:1183-1198. http://dx.doi.org/10.1007/s00216 -011-5556-4.
    • (2012) Anal. Bioanal. Chem. , vol.402 , pp. 1183-1198
    • Paglia, G.1    Hrafnsdottir, S.2    Magnusdottir, M.3    Fleming, R.M.4    Thorlacius, S.5    Palsson, B.O.6    Thiele, I.7
  • 39
    • 84863989287 scopus 로고    scopus 로고
    • The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases
    • Khan MT, Duncan SH, Stams AJ, van Dijl JM, Flint HJ, Harmsen HJ. 2012. The gut anaerobe Faecalibacterium prausnitzii uses an extracellular electron shuttle to grow at oxic-anoxic interphases. ISME J. 6:1578-1585. http://dx.doi.org/10.1038/ismej.2012.5.
    • (2012) ISME J. , vol.6 , pp. 1578-1585
    • Khan, M.T.1    Duncan, S.H.2    Stams, A.J.3    van Dijl, J.M.4    Flint, H.J.5    Harmsen, H.J.6
  • 40
    • 77955437093 scopus 로고    scopus 로고
    • A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate
    • Ames TD, Rodionov DA, Weinberg Z, Breaker RR. 2010. A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate. Chem. Biol. 17:681-685. http://dx.doi.org/10.1016/j.chembiol.2010.05.020.
    • (2010) Chem. Biol. , vol.17 , pp. 681-685
    • Ames, T.D.1    Rodionov, D.A.2    Weinberg, Z.3    Breaker, R.R.4
  • 43
    • 84906067601 scopus 로고    scopus 로고
    • Novel physiological and metabolic insights into the beneficial gut microbe Faecalibacterium prausnitzii-from carbohydrates to current
    • University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    • Khan MT. 2013. Novel physiological and metabolic insights into the beneficial gut microbe Faecalibacterium prausnitzii-from carbohydrates to current. University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
    • (2013)
    • Khan, M.T.1
  • 45
    • 13244273427 scopus 로고    scopus 로고
    • Characterization of the RokA and HexA broad-substrate-specificity hexokinases from Bacteroides fragilis and their role in hexose and N-acetylglucosamine utilization
    • Brigham CJ, Malamy MH. 2005. Characterization of the RokA and HexA broad-substrate-specificity hexokinases from Bacteroides fragilis and their role in hexose and N-acetylglucosamine utilization. J. Bacteriol. 187: 890-901. http://dx.doi.org/10.1128/JB.187.3.890-901.2005.
    • (2005) J. Bacteriol. , vol.187 , pp. 890-901
    • Brigham, C.J.1    Malamy, M.H.2
  • 46
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth JD, Thiele I, Palsson BO. 2010. What is flux balance analysis? Nat. Biotechnol. 28:245-248. http://dx.doi.org/10.1038/nbt.1614.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.O.3
  • 48
    • 84880783396 scopus 로고    scopus 로고
    • Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM
    • Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. 2013. Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM. PLoS Comput. Biol. 9:e1003126. http://dx.doi.org/10.1371/journal .pcbi.1003126.
    • (2013) PLoS Comput. Biol. , vol.9
    • Dreyfuss, J.M.1    Zucker, J.D.2    Hood, H.M.3    Ocasio, L.R.4    Sachs, M.S.5    Galagan, J.E.6
  • 49
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. 2004. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92-96. http://dx.doi.org/10.1038/nature02456.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 51
    • 84866975246 scopus 로고    scopus 로고
    • Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
    • Thiele I, Fleming RM, Que R, Bordbar A, Diep D, Palsson BO. 2012. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS One 7:e45635. http://dx.doi.org/10.1371/journal.pone.0045635.
    • (2012) PLoS One , vol.7
    • Thiele, I.1    Fleming, R.M.2    Que, R.3    Bordbar, A.4    Diep, D.5    Palsson, B.O.6
  • 52
    • 77952774546 scopus 로고    scopus 로고
    • Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
    • Thiele I, Fleming RM, Bordbar A, Schellenberger J, Palsson BO. 2010. Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophys. J. 98:2072- 2081. http://dx.doi.org/10.1016/j.bpj.2010.01.060.
    • (2010) Biophys. J. , vol.98
    • Thiele, I.1    Fleming, R.M.2    Bordbar, A.3    Schellenberger, J.4    Palsson, B.O.5
  • 53
    • 84880860962 scopus 로고    scopus 로고
    • Robust flux balance analysis of multiscale biochemical reaction networks
    • Sun Y, Fleming RM, Thiele I, Saunders MA. 2013. Robust flux balance analysis of multiscale biochemical reaction networks. BMC Bioinformatics 14:240. http://dx.doi.org/10.1186/1471-2105-14-240.
    • (2013) BMC Bioinformatics , vol.14 , pp. 240
    • Sun, Y.1    Fleming, R.M.2    Thiele, I.3    Saunders, M.A.4
  • 54
    • 84866283114 scopus 로고    scopus 로고
    • How can Faecalibacterium prausnitzii employ riboflavin for extracellular electron transfer?
    • Khan MT, Browne WR, van Dijl JM, Harmsen HJ. 2012. How can Faecalibacterium prausnitzii employ riboflavin for extracellular electron transfer? Antioxid. Redox Signal. 17:1433-1440. http://dx.doi.org/10 .1089/ars.2012.4701.
    • (2012) Antioxid. Redox Signal. , vol.17 , pp. 1433-1440
    • Khan, M.T.1    Browne, W.R.2    van Dijl, J.M.3    Harmsen, H.J.4
  • 55
    • 67449122992 scopus 로고    scopus 로고
    • Insights into the evolution of sialic acid catabolism among bacteria
    • Almagro-Moreno S, Boyd EF. 2009. Insights into the evolution of sialic acid catabolism among bacteria. BMC Evol. Biol. 9:118. http://dx.doi.org /10.1186/1471-2148-9-118.
    • (2009) BMC Evol. Biol. , vol.9 , pp. 118
    • Almagro-Moreno, S.1    Boyd, E.F.2
  • 56
    • 84897947195 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
    • El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. 2014. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst. Biol. 8:41. http://dx.doi.org/10.1186/1752 -0509-8-41.
    • (2014) BMC Syst. Biol. , vol.8 , pp. 41
    • El-Semman, I.E.1    Karlsson, F.H.2    Shoaie, S.3    Nookaew, I.4    Soliman, T.H.5    Nielsen, J.6
  • 57
    • 79956157487 scopus 로고    scopus 로고
    • Prospects for systems biology and modeling of the gut microbiome
    • Karlsson FH, Nookaew I, Petranovic D, Nielsen J. 2011. Prospects for systems biology and modeling of the gut microbiome. Trends Biotechnol. 29:251-258. http://dx.doi.org/10.1016/j.tibtech.2011.01.009.
    • (2011) Trends Biotechnol. , vol.29 , pp. 251-258
    • Karlsson, F.H.1    Nookaew, I.2    Petranovic, D.3    Nielsen, J.4
  • 58
    • 34249284197 scopus 로고    scopus 로고
    • Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota
    • Smith K, McCoy KD, Macpherson AJ. 2007. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin. Immunol. 19:59-69. http://dx.doi.org/10.1016/j .smim.2006.10.002.
    • (2007) Semin. Immunol. , vol.19 , pp. 59-69
    • Smith, K.1    McCoy, K.D.2    Macpherson, A.J.3
  • 60
    • 84877913270 scopus 로고    scopus 로고
    • Bacteroides thetaiotaomicron and Faecali- bacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent
    • Wrzosek L, Miquel S, Noordine ML, Bouet S, Chevalier-Curt MJ, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M. 2013. Bacteroides thetaiotaomicron and Faecali- bacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 11:61. http://dx.doi.org/10.1186/1741-7007-11 -61.
    • (2013) BMC Biol. , vol.11 , pp. 61
    • Wrzosek, L.1    Miquel, S.2    Noordine, M.L.3    Bouet, S.4    Chevalier-Curt, M.J.5    Robert, V.6    Philippe, C.7    Bridonneau, C.8    Cherbuy, C.9    Robbe-Masselot, C.10    Langella, P.11    Thomas, M.12
  • 61
    • 84877356167 scopus 로고    scopus 로고
    • Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates
    • Ze X, Le Mougen F, Duncan SH, Louis P, Flint HJ. 2013. Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates. Gut Microbes 4:236-240. http://dx.doi.org/10 .4161/gmic.23998.
    • (2013) Gut Microbes , vol.4 , pp. 236-240
    • Ze, X.1    Le Mougen, F.2    Duncan, S.H.3    Louis, P.4    Flint, H.J.5
  • 62
    • 68249110221 scopus 로고    scopus 로고
    • The role of pH in determining the species composition of the human colonic microbiota
    • Duncan SH, Louis P, Thomson JM, Flint HJ. 2009. The role of pH in determining the species composition of the human colonic microbiota. Environ. Microbiol. 11:2112-2122. http://dx.doi.org/10.1111/j.1462 -2920.2009.01931.x.
    • (2009) Environ. Microbiol. , vol.11 , pp. 2112-2122
    • Duncan, S.H.1    Louis, P.2    Thomson, J.M.3    Flint, H.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.