Shene2020 - flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium

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Model Identifier
MODEL2006010001
Short description
Modelo_mod3_032020.m is a Matlab code used for the simulation of the growth curve of Antarctic thraustochytrid Oblongichytrium sp. RT2316-13. The model is based on the genome scale model adapted for the strain that is found in the Excel file ExcelAurant_28102019.xlsx. Flux balance analysis is used to predict the specific growth rate of the biomass, specific synthesis of neutral lipids and specific consumption rate of the nutrients. The code crea_modelo.m transform the excel file into the array model_T.mat used in by Modelo_mod3_032020.m This model was used to generate data presented in the manuscript Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316-13, 2020, Carolina Shene, Paris Paredes, Liset Flores, Allison Leyton, Juan A. Asenjo, Yusuf Chisti, Biotechnology and Bioengineering, DOI: 10.1002/bit.27463.
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Other
Related Publication
  • Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316‐13
  • Paris Paredes, Liset Flores, Allison Leyton, Juan A. Asenjo, Yusuf Chisti
  • Biotechnology and Bioengineering , 6/ 2020 , DOI: 10.1002/bit.27463
  • Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB)
  • Production of biomass and lipids in batch cultures of the Antarctic thraustochytrid Oblongichytrium sp. RT2316‐13, is reported. The microorganism proved capable of producing nearly 67% docosahexaenoic acid (DHA) and 15% eicosapentaenoic acid (EPA) in its total lipid fraction. Biomass with a maximum total lipid content of 33.5% (wt/wt) could be produced at 15°C in batch culture using a medium containing glucose (20 g/L), yeast extract (10.5 g/L), and other minor components. A lower culture temperature (5°C) reduced biomass and lipid productivities compared to culture at 15°C, but enhanced the DHA and EPA content of the lipids by 6.4‐ and 3.3‐fold, respectively. Both a simple minimally structured mathematical model and a more complex genome‐scale metabolic model (GEM) allowed the fermentation profiles in batch cultures to be satisfactorily simulated, but the GEM provided much greater insight in the biochemical and physiological phenomena underlying the observed behavior. Unlike the simpler model, the GEM could be interrogated for the possible effects of various external factors such as oxygen supply, on the expected outcomes. In silico predictions of oxygen effects were consistent with literature observations for DHA producing thraustochytrids.
Contributors
Carolina Shene, Krishna Kumar Tiwari

Metadata information


Curation status
Non-curated

Modelling approach(es)

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Model files

Modelo_mod3_032020.m Matlab codes for growth curves of Oblongychitrium sp (RT2316-13) using GEM 5.63 KB Preview | Download

Additional files

imprimeResultadosMinMax.m Matlab function; print results of FVA 588.00 bytes Preview | Download
model_T.mat Matlab array; output from crea_modelo.m 175.46 KB Preview | Download
crea_modelo.m Matlab file; creates the .mat file from reactions and metabolites in ExcelAurant_28102019.xlsx 378.00 bytes Preview | Download
ExcelAurant_28102019.xlsx Excel file with reactions and metabolites in the GEM 267.24 KB Preview | Download
uptake_r.m Matlab function; compute uptake rates 1.86 KB Preview | Download
curva8.txt Text file; contains experimental data 260.00 bytes Preview | Download
imprimeResultadosDual.m Matlab function; print results of dual problem 397.00 bytes Preview | Download

  • Model originally submitted by : Carolina Shene
  • Submitted: 16-Jul-2020 18:05:12
  • Last Modified: 16-Jul-2020 18:05:12
Revisions
  • Version: 6 public model Download this version
    • Submitted on: 16-Jul-2020 18:05:12
    • Submitted by: Krishna Kumar Tiwari
    • With comment: Edited model metadata online.