The 20 curated models published in:
Siu H. J. Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas (2017) Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, 33(22), 3603–3609.
Link
si_table_2_btx453.xlsx contains the detailed curation of biomass reactions in the models
si_table_2_btx453.xlsx contains the information about the conserved metabolite quantities in the models
| Model | Organism | Reference |
|---|---|---|
| iBsu1103V2 | Bacillus subtilis 168 | Tanaka et al, 2013 |
| iAH991 | Bacteroides thetaiotamicron VPI-5482 | Heinken et al, 2013. Updated in Heinken & Thiele, 2015a. |
| iBif452 | Bifidobacterium adolescentis L2-32 | El-Semman et al, 2014 |
| iCac802 | Clostridium acetobutylicum ATCC 824 | Dash et al, 2014 |
| Yeast7 | Consensus model of yeast | Aung et al, 2013 |
| Cg_ATCC13032 | Corynebacterium glutamicum ATCC13032 | Kjeldsen & Nielsen, 2009 |
| V583 | Enterococcus faecalis V583 | Veith et al, 2015 |
| iJO1366 | Escherichia coli K-12 MG1655 | Orth et al, 2011 |
| iEre400 | Eubacterium rectale ATCC33656 | Shoaie et al, 2013 |
| iFpraus_v1.0 | Faecalibacterium prausnitzii A2-165 | Heinken et al, 2014 |
| iYL1228 | Klebsiella pneumonia MGH 78578 | Liao et al, 2011. Updated in Heinken & Thiele, 2015a. |
| iLca12A_640 | Lactobacillus casei ATCC 334 | Vinay-Lara et al, 2014 |
| Ll_MG1363 | Lactococcus lactis MG1363 | Flahaut et al, 2013 |
| iMT1026 | Pichia pastoris | Tomàs-Gamisans, Ferrer and Albiol, 2016 |
| iVM679 | Porphyromonas gingivalis W83 | Mazumdar et al, 2009 |
| iMP429 | Streptococcus thermophilus LMG18311 | Pastink et al, 2009, Updated in Heinken & Thiele, 2015a. |
| SynPCC7942 | Synechococcus elongatus PCC7942 | Mueller et al., 2017 |
| iYL619 | Yarrowia lipolytica | Pan and Hua, 2012 |
| iCyt773 | Cyanothece sp. ATCC 51142 | Saha et al., 2012 |
| iMAC868 | Methanosarcina acetivorans | Nazem‐Bokaee et al., 2016 |
References
Aung HW, Henry SA & Walker LP (2013) Revising the Representation of Fatty Acid, Glycerolipid, and Glycerophospholipid Metabolism in the Consensus Model of Yeast Metabolism. Ind. Biotechnol. 9: 215–228
Dash S, Mueller TJ, Venkataramanan KP, Papoutsakis ET & Maranas CD (2014) Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model. Biotechnol. Biofuels 7: 144
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
Flahaut NAL, Wiersma A, van de Bunt B, Martens DE, Schaap PJ, Sijtsma L, Dos Santos V a M & de Vos WM (2013) Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Appl. Microbiol. Biotechnol. 97: 8729–39
Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJM & Thiele I (2014) Functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe. J. Bacteriol. 196: 3289–3302
Heinken A, Sahoo S, Fleming RMT & Thiele I (2013) Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes 4: 28–40
"Heinken,A. and Thiele,I. (2015a) Anoxic conditions promote species-specific
mutualism between gut microbes in silico. Appl. Environ. Microbiol., 81,
4049–4061.
Heinken,A. and Thiele "
Kjeldsen KR & Nielsen J (2009) In silico genome-scale reconstruction and validation of the corynebacterium glutamicum metabolic network. Biotechnol. Bioeng. 102: 583–597
"Liao YC, Huang TW, Chen FC, Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung CA.
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.
J. Bacteriol. 2011 Apr; 193(7): 1710-1717 "
Mazumdar V, Snitkin ES, Amar S & Segre D (2009) Metabolic Network Model of a Human Oral Pathogen. J. Bacteriol. 191: 74–90
Mueller, T. J., Ungerer, J. L., Pakrasi, H. B. & Maranas, C. D. Identifying the Metabolic Differences of a Fast-Growth Phenotype in Synechococcus UTEX 2973. Sci. Rep. 7, 41569 (2017).
Nazem-Bokaee, H., Gopalakrishnan, S., Ferry, J. G., Wood, T. K. & Maranas, C. D. Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. Microb. Cell Fact. 15, 10 (2016).
"Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.
Mol. Syst. Biol. 2011; 7: 535 "
Pan P & Hua Q (2012) Reconstruction and In Silico Analysis of Metabolic Network for an Oleaginous Yeast, Yarrowia lipolytica. PLoS One 7: e51535
"Pastink MI, Teusink B, Hols P, Visser S, de Vos WM, Hugenholtz J.
Genome-scale model of Streptococcus thermophilus LMG18311 for metabolic comparison of lactic acid bacteria.
Appl. Environ. Microbiol. 2009 Jun; 75(11): 3627-3633 "
Saha, R. et al. Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. PLoS One 7, e48285 (2012).
Shoaie S, Karlsson F, Mardinoglu A, Nookaew I, Bordel S & Nielsen J (2013) Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci. Rep. 3: 2532
Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL & Noirot P (2013) Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res. 41: 687–699
Tomàs-Gamisans M, Ferrer P & Albiol J (2016) Integration and validation of the genome-scale metabolic models of Pichia pastoris: A comprehensive update of protein glycosylation pathways, lipid and energy metabolism. PLoS One 11: 1–24
Veith N, Solheim M, van Grinsven KWA, Olivier BG, Levering J, Grosseholz R, Hugenholtz J, Holo H, Nes I, Teusink B & Kummer U (2015) Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism. Appl. Environ. Microbiol. 81: 1622–1633
Vinay-Lara E, Hamilton JJ, Stahl B, Broadbent JR, Reed JL & Steele JL (2014) Genome -scale reconstruction of metabolic networks of lactobacillus casei ATCC 334 and 12A. PLoS One 9: