An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus
During batch fermentation, a variety of compounds are synthesized, as microorganisms undergo distinct growth phases: lag, exponential, growth-no-growth transition, stationary, and decay. A detailed understanding of the metabolic pathways involved in these phases is crucial for optimizing the product...
| Autores: | , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2025 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/382009 |
| Acceso en línea: | http://hdl.handle.net/10261/382009 |
| Access Level: | acceso abierto |
| Palabra clave: | Saccharomyces genus Dynamic flux balance analysis Fermentation Secondary metabolism Time-varying cellular objective Yeast Saccharomyces fermentation metabolism |
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| dc.title.none.fl_str_mv |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| title |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| spellingShingle |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus Moimenta, Artai R. Saccharomyces genus Dynamic flux balance analysis Fermentation Secondary metabolism Time-varying cellular objective Yeast Saccharomyces fermentation metabolism |
| title_short |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| title_full |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| title_fullStr |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| title_full_unstemmed |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| title_sort |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genus |
| dc.creator.none.fl_str_mv |
Moimenta, Artai R. Troitiño, Diego Henriques, David Contreras Ruiz, Alba Minebois, Romain Morard, Miguel Barrio, Eladio Querol, Amparo Balsa-Canto, Eva |
| author |
Moimenta, Artai R. |
| author_facet |
Moimenta, Artai R. Troitiño, Diego Henriques, David Contreras Ruiz, Alba Minebois, Romain Morard, Miguel Barrio, Eladio Querol, Amparo Balsa-Canto, Eva |
| author_role |
author |
| author2 |
Troitiño, Diego Henriques, David Contreras Ruiz, Alba Minebois, Romain Morard, Miguel Barrio, Eladio Querol, Amparo Balsa-Canto, Eva |
| author2_role |
author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Ministerio de Ciencia e Innovación (España) Agencia Estatal de Investigación (España) Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
Saccharomyces genus Dynamic flux balance analysis Fermentation Secondary metabolism Time-varying cellular objective Yeast Saccharomyces fermentation metabolism |
| topic |
Saccharomyces genus Dynamic flux balance analysis Fermentation Secondary metabolism Time-varying cellular objective Yeast Saccharomyces fermentation metabolism |
| description |
During batch fermentation, a variety of compounds are synthesized, as microorganisms undergo distinct growth phases: lag, exponential, growth-no-growth transition, stationary, and decay. A detailed understanding of the metabolic pathways involved in these phases is crucial for optimizing the production of target compounds. Dynamic flux balance analysis (dFBA) offers insight into the dynamics of metabolic pathways. However, explaining secondary metabolism remains a challenge. A multiphase and multi-objective dFBA scheme (MPMO model) has been proposed for this purpose. However, its formulation is discontinuous, changing from phase to phase; its accuracy in predicting intracellular fluxes is hampered by the lack of a mechanistic link between phases; and its simulation requires considerable computational effort. To address these limitations, we combine a novel model with a genome-scale model to predict the distribution of intracellular fluxes throughout batch fermentation. This integrated multiphase continuous model (IMC) has a unique formulation over time, and it incorporates empirical regulatory descriptions to automatically identify phase transitions and incorporates the hypotheses that yeasts might vary their cellular objective over time to adapt to the changing environment. We validated the predictive capacity of the IMC model by comparing its predictions with intracellular metabolomics data for Saccharomyces uvarum during batch fermentation. The model aligns well with the data, confirming its predictive capabilities. Notably, the IMC model accurately predicts trehalose accumulation, which was enforced in the MPMO model. We further demonstrate the generalizability of the IMC model, explaining the dynamics of primary and secondary metabolism of three Saccharomyces species. The model provides biological insights consistent with the literature and metabolomics data, establishing it as a valuable tool for exploring the dynamics of novel fermentation processes.IMPORTANCEThis work presents an integrated multiphase continuous dynamic genome-scale model (IMC model) for batch fermentation, a crucial process widely used in industry to produce biofuels, enzymes, pharmaceuticals, and food products or ingredients. The IMC model integrates a continuous kinetic model with a genome-scale model to address the critical limitations of existing dynamic flux balance analysis schemes, such as the difficulty of explaining secondary metabolism, the lack of mechanistic links between growth phases, or the high computational demands. The model also introduces the hypothesis that cells adapt the FBA objective over time. The IMC improves the accuracy of intracellular flux predictions and simplifies the implementation process with a unique dFBA formulation over time. Its ability to predict both primary and secondary metabolism dynamics in different Saccharomyces species underscores its versatility and robustness. Furthermore, its alignment with empirical metabolomics data validates its predictive power, offering valuable insights into metabolic processes during batch fermentation. These advances pave the way for optimizing fermentation processes, potentially leading to more efficient production of target compounds and novel biotechnological applications. |
| publishDate |
2025 |
| dc.date.none.fl_str_mv |
2025 2025 2025 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article http://purl.org/coar/resource_type/c_6501 Publisher's version info:eu-repo/semantics/publishedVersion |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/382009 |
| url |
http://hdl.handle.net/10261/382009 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
#PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/CEX2021-001189-S info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C32 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C31 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C33 mSystems The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1128/msystems.01615-24 https://doi.org/10.1128/msystems.01615-24 Sí |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
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American Society for Microbiology |
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American Society for Microbiology |
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reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
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Consejo Superior de Investigaciones Científicas (CSIC) |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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1869420551018119168 |
| spelling |
An integrated multiphase dynamic genome-scale model explains batch fermentations led by species of the Saccharomyces genusMoimenta, Artai R.Troitiño, DiegoHenriques, DavidContreras Ruiz, AlbaMinebois, RomainMorard, MiguelBarrio, EladioQuerol, AmparoBalsa-Canto, EvaSaccharomyces genusDynamic flux balance analysisFermentationSecondary metabolismTime-varying cellular objectiveYeastSaccharomycesfermentationmetabolismDuring batch fermentation, a variety of compounds are synthesized, as microorganisms undergo distinct growth phases: lag, exponential, growth-no-growth transition, stationary, and decay. A detailed understanding of the metabolic pathways involved in these phases is crucial for optimizing the production of target compounds. Dynamic flux balance analysis (dFBA) offers insight into the dynamics of metabolic pathways. However, explaining secondary metabolism remains a challenge. A multiphase and multi-objective dFBA scheme (MPMO model) has been proposed for this purpose. However, its formulation is discontinuous, changing from phase to phase; its accuracy in predicting intracellular fluxes is hampered by the lack of a mechanistic link between phases; and its simulation requires considerable computational effort. To address these limitations, we combine a novel model with a genome-scale model to predict the distribution of intracellular fluxes throughout batch fermentation. This integrated multiphase continuous model (IMC) has a unique formulation over time, and it incorporates empirical regulatory descriptions to automatically identify phase transitions and incorporates the hypotheses that yeasts might vary their cellular objective over time to adapt to the changing environment. We validated the predictive capacity of the IMC model by comparing its predictions with intracellular metabolomics data for Saccharomyces uvarum during batch fermentation. The model aligns well with the data, confirming its predictive capabilities. Notably, the IMC model accurately predicts trehalose accumulation, which was enforced in the MPMO model. We further demonstrate the generalizability of the IMC model, explaining the dynamics of primary and secondary metabolism of three Saccharomyces species. The model provides biological insights consistent with the literature and metabolomics data, establishing it as a valuable tool for exploring the dynamics of novel fermentation processes.IMPORTANCEThis work presents an integrated multiphase continuous dynamic genome-scale model (IMC model) for batch fermentation, a crucial process widely used in industry to produce biofuels, enzymes, pharmaceuticals, and food products or ingredients. The IMC model integrates a continuous kinetic model with a genome-scale model to address the critical limitations of existing dynamic flux balance analysis schemes, such as the difficulty of explaining secondary metabolism, the lack of mechanistic links between growth phases, or the high computational demands. The model also introduces the hypothesis that cells adapt the FBA objective over time. The IMC improves the accuracy of intracellular flux predictions and simplifies the implementation process with a unique dFBA formulation over time. Its ability to predict both primary and secondary metabolism dynamics in different Saccharomyces species underscores its versatility and robustness. Furthermore, its alignment with empirical metabolomics data validates its predictive power, offering valuable insights into metabolic processes during batch fermentation. These advances pave the way for optimizing fermentation processes, potentially leading to more efficient production of target compounds and novel biotechnological applications.This work has received funding from MCIU/AEI/FEDER grant references: PID2021-126380OB-C31, PID2021-126380OB-C32, PID2021-126380OB-C33, and Xunta de Galicia (IN607B 2023/04). IATA-CSIC received funding from the Spanish Government, ref. MCIN/AEI/10.13039/501100011033, as a "Severo Ochoa" Center of Excellence (CEX2021-001189-S), with A.Q. as PI.With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2021-001189-S)Peer reviewedAmerican Society for MicrobiologyMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/382009reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/CEX2021-001189-Sinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C32info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C31info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-126380OB-C33mSystemsThe underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1128/msystems.01615-24https://doi.org/10.1128/msystems.01615-24Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3820092026-05-22T06:33:51Z |
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15,811543 |