Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.

Microbial communities have become a major research focus due to their importance for biogeochemical cycles, biomedicine and biotechnological applications. While some biotechnological applications, such as anaerobic digestion, make use of naturally arising microbial communities, the rational design o...

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Autores principales:	Pavlos Stephanos Bekiaris, Steffen Klamt
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b0400f2373b74a229ac0089275bc2f3b
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spelling	oai:doaj.org-article:b0400f2373b74a229ac0089275bc2f3b2021-11-25T05:40:37ZDesigning microbial communities to maximize the thermodynamic driving force for the production of chemicals.1553-734X1553-735810.1371/journal.pcbi.1009093https://doaj.org/article/b0400f2373b74a229ac0089275bc2f3b2021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009093https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Microbial communities have become a major research focus due to their importance for biogeochemical cycles, biomedicine and biotechnological applications. While some biotechnological applications, such as anaerobic digestion, make use of naturally arising microbial communities, the rational design of microbial consortia for bio-based production processes has recently gained much interest. One class of synthetic microbial consortia is based on specifically designed strains of one species. A common design principle for these consortia is based on division of labor, where the entire production pathway is divided between the different strains to reduce the metabolic burden caused by product synthesis. We first show that classical division of labor does not automatically reduce the metabolic burden when metabolic flux per biomass is analyzed. We then present ASTHERISC (Algorithmic Search of THERmodynamic advantages in Single-species Communities), a new computational approach for designing multi-strain communities of a single-species with the aim to divide a production pathway between different strains such that the thermodynamic driving force for product synthesis is maximized. ASTHERISC exploits the fact that compartmentalization of segments of a product pathway in different strains can circumvent thermodynamic bottlenecks arising when operation of one reaction requires a metabolite with high and operation of another reaction the same metabolite with low concentration. We implemented the ASTHERISC algorithm in a dedicated program package and applied it on E. coli core and genome-scale models with different settings, for example, regarding number of strains or demanded product yield. These calculations showed that, for each scenario, many target metabolites (products) exist where a multi-strain community can provide a thermodynamic advantage compared to a single strain solution. In some cases, a production with sufficiently high yield is thermodynamically only feasible with a community. In summary, the developed ASTHERISC approach provides a promising new principle for designing microbial communities for the bio-based production of chemicals.Pavlos Stephanos BekiarisSteffen KlamtPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 6, p e1009093 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Pavlos Stephanos Bekiaris Steffen Klamt Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
description	Microbial communities have become a major research focus due to their importance for biogeochemical cycles, biomedicine and biotechnological applications. While some biotechnological applications, such as anaerobic digestion, make use of naturally arising microbial communities, the rational design of microbial consortia for bio-based production processes has recently gained much interest. One class of synthetic microbial consortia is based on specifically designed strains of one species. A common design principle for these consortia is based on division of labor, where the entire production pathway is divided between the different strains to reduce the metabolic burden caused by product synthesis. We first show that classical division of labor does not automatically reduce the metabolic burden when metabolic flux per biomass is analyzed. We then present ASTHERISC (Algorithmic Search of THERmodynamic advantages in Single-species Communities), a new computational approach for designing multi-strain communities of a single-species with the aim to divide a production pathway between different strains such that the thermodynamic driving force for product synthesis is maximized. ASTHERISC exploits the fact that compartmentalization of segments of a product pathway in different strains can circumvent thermodynamic bottlenecks arising when operation of one reaction requires a metabolite with high and operation of another reaction the same metabolite with low concentration. We implemented the ASTHERISC algorithm in a dedicated program package and applied it on E. coli core and genome-scale models with different settings, for example, regarding number of strains or demanded product yield. These calculations showed that, for each scenario, many target metabolites (products) exist where a multi-strain community can provide a thermodynamic advantage compared to a single strain solution. In some cases, a production with sufficiently high yield is thermodynamically only feasible with a community. In summary, the developed ASTHERISC approach provides a promising new principle for designing microbial communities for the bio-based production of chemicals.
format	article
author	Pavlos Stephanos Bekiaris Steffen Klamt
author_facet	Pavlos Stephanos Bekiaris Steffen Klamt
author_sort	Pavlos Stephanos Bekiaris
title	Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
title_short	Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
title_full	Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
title_fullStr	Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
title_full_unstemmed	Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
title_sort	designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/b0400f2373b74a229ac0089275bc2f3b
work_keys_str_mv	AT pavlosstephanosbekiaris designingmicrobialcommunitiestomaximizethethermodynamicdrivingforcefortheproductionofchemicals AT steffenklamt designingmicrobialcommunitiestomaximizethethermodynamicdrivingforcefortheproductionofchemicals
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Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.

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