A high quality genome-scale metabolic model of probiotic L. reuteri KUB-AC5
- Brief Repository Description
This repository contains a genome-scale metabolic model iTN656 for Limosilactobacillus reuteri KUB-AC5.
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Abstract: Limosilactobacillus reuteri KUB-AC5 displays the hallmark features of probiotic properties for food and feed industries. Optimization of cultivation condition for the industrial production is important to reach cell concentration and cost reduction. Considering the strain-specific growth physiology, metabolic capability and essential nutrients of L. reuteri KUB-AC5, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5 was developed. Hereby, the GSMM of iTN656 was successfully constructed which contained 656 genes, 831 metabolites, and 953 metabolic reactions. The iTN656 model could show a metabolic capability under various carbon sources and guide potentially 14 essential single nutrients (e.g., vitamin B complex and amino acids) and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth through single and double omission analysis. Promisingly, the iTN656 model was further integrated with transcriptome data suggesting that putative metabolic routes as preferable paths e.g., sucrose uptake, nucleotide biosynthesis, urea cycle and glutamine transporter for L. reuteri KUB-AC5 growth. The developed GSMM offers a powerful tool for multi-level omics analysis, enabling probiotic strain optimization for biomass overproduction in industrial scale.
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Model KeyWords: Probiotic, Limosilactobacillus reuteri, Genome-scale metabolic modeling, Essential nutrients, Systems biology GSMM Category: Species; Utilisation: Predictive simulation; Field: Genome-scale modeling; Metabolic engineering; Type of Model: Reconstruction and refinement; Taxonomy: Limosilactobacillus reuteri ; Metabolic System: General Metabolism; Condition: Synthetic media;
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Reference: Thanawat Namrak, Nachon Raethong, Theeraphol Jatuponwiphat, Sunee Nitisinprasert, Wanwipa Vongsangnak and Massalin Nakphaichit. Probing genome-scale model reveals metabolic capability and essential nutrients for growth of probiotic Limosilactobacillus reuteri KUB-AC5. Biology 2022, 11, x. https://doi.org/10.3390/xxxxx
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Pubmed ID: TBA
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PMC ID: TBA
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Last update: 2022-02-07
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The model contains:
| Taxonomy | Model Name | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Limosilactobacillus reuteri | iTN656 | 953 | 831 | 656 |
This repository is administered by Nachon Raethong, Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand
- A functional Matlab installation (MATLAB 7.3 or higher).
- RAVEN Toolbox 2.0 for MATLAB (required for contributing to development).
- libSBML MATLAB API (version 5.16.0 is recommended).
- Gurobi Optimizer for MATLAB.
- For contributing to development: a git wrapper added to the search path.
- Clone the master branch from sysbiomics GitHub.
- Nachon Raethong (https://www.researchgate.net/profile/Nachon_Raethong) (@nachonase), Institute of Nutrition, Mahidol University, Nakhon Pathom, Thailand