Publicação
Genome-Scale Metabolic Network Reconstruction of the dairy bacterium Streptococcus thermophilus
| Resumo: | The dairy food industry is constantly changing as novel biotechnological techniques improve the manufacturing process of dairy products. Widely used over the years in the yogurt and cheese manufacturing, Streptococcus thermophilus is now considered as an extremely valuable lactic acid bacterium for the annual market of the dairy industry. A specific, but of easy-access knowledge regarding the thermophilic bacteria metabolism would be a plus for the continuous growth of such industry. In this work, we present the Genome-Scale Metabolic (GSM) model for the LMD- 9 strain of S. thermophilus together with the detailed description of the species metabolic capabilities at the cellular level. The reconstruction of the genome-scale metabolic model, was performed using Metabolic Models Reconstruction Using Genome-Scale Information (merlin) together with COBRApy tool and OptFlux platform. S. thermophilus LMD-9 genome was functionally annotated and the encoded metabolic information was afterwards used to assemble a draft network. After extensive manual curation, the metabolic network was converted to a comprehensive metabolic model. The assembled GSM model was then validated against experimental data. The metabolism of this important stater for the dairy industry has been accessed in detail through the reconstruction. The organism possesses a simple machinery for central carbon metabolism and shows a narrow spectrum of carbohydrate utilization. The genome-scale metabolic model additionally suggests the existence of several pyruvate dissipating pathways which end in the synthesis of various compounds of interest. In silico simulations demonstrated the production of lactate and residual amounts of formate, acetolactate and acetaldehyde. Regarding the amino acid metabolism, the organism possesses complete pathways for the biosynthesis of all amino acids, except for lysine, methionine and cysteine. Furthermore, the GSM model can be used to simulate other relevant features of the S. thermophilus metabolism, such as the aroma compounds and Exopolysaccharides (EPS) synthesis, oxygen tolerance, absence of complete citrate cycle and pentose phosphate pathway, urea metabolism or amino acid catabolism. |
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| Autores principais: | Cruz, Fernando João Pereira da |
| Assunto: | Systems biology Genome-scale metabolic models Metabolic networks Constraint-based modeling Merlin Streptococcus thermophilus Lactic acid bacteria metabolism |
| Ano: | 2017 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | The dairy food industry is constantly changing as novel biotechnological techniques improve the manufacturing process of dairy products. Widely used over the years in the yogurt and cheese manufacturing, Streptococcus thermophilus is now considered as an extremely valuable lactic acid bacterium for the annual market of the dairy industry. A specific, but of easy-access knowledge regarding the thermophilic bacteria metabolism would be a plus for the continuous growth of such industry. In this work, we present the Genome-Scale Metabolic (GSM) model for the LMD- 9 strain of S. thermophilus together with the detailed description of the species metabolic capabilities at the cellular level. The reconstruction of the genome-scale metabolic model, was performed using Metabolic Models Reconstruction Using Genome-Scale Information (merlin) together with COBRApy tool and OptFlux platform. S. thermophilus LMD-9 genome was functionally annotated and the encoded metabolic information was afterwards used to assemble a draft network. After extensive manual curation, the metabolic network was converted to a comprehensive metabolic model. The assembled GSM model was then validated against experimental data. The metabolism of this important stater for the dairy industry has been accessed in detail through the reconstruction. The organism possesses a simple machinery for central carbon metabolism and shows a narrow spectrum of carbohydrate utilization. The genome-scale metabolic model additionally suggests the existence of several pyruvate dissipating pathways which end in the synthesis of various compounds of interest. In silico simulations demonstrated the production of lactate and residual amounts of formate, acetolactate and acetaldehyde. Regarding the amino acid metabolism, the organism possesses complete pathways for the biosynthesis of all amino acids, except for lysine, methionine and cysteine. Furthermore, the GSM model can be used to simulate other relevant features of the S. thermophilus metabolism, such as the aroma compounds and Exopolysaccharides (EPS) synthesis, oxygen tolerance, absence of complete citrate cycle and pentose phosphate pathway, urea metabolism or amino acid catabolism. |
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