19-ERACoBioTech- 33 SyCoLim
Lead Research Organisation:
Imperial College London
Department Name: Bioengineering
Abstract
ERA CoBioTech seek the transition from a petroleum-based economy to a bio-based, circular economy, which can be achieved by the development of novel biotechnologies such as microbiological bioproduction processes.
The aim of this project (SyCoLim) is to produce high-value chemicals (with applications as pharmaceuticals, medicines, fragrances, nutraceuticals or cosmetics) from waste raw materials (recycling glycerol, the by-product of biodiesel industries). In order to achieve this objective, synthetic microbial communities between yeast and bacteria will be created. These communities will be engineered to present advantages over monocultures, such as division of labour, higher adaptability and robustness or an expanded metabolic network. The bioprocess carried out by the best strains generated will be scaled up in industrial conditions in the facilities of our industrial partner. Therefore, the project will help the lab-to-market transition of the sustainable production of valuable compounds and will combine this with the exploration of novel synthetic biology and microbial communities' methodologies that have the potential to be applicable to other bioprocesses, thus facilitating the global transition towards the bioeconomy.
The partners of SyCoLim has been selectively chosen to be the best fit possible to the rationale of the project, in terms not only of skills and methodologies but also in previous experience in synthetic microbial communities. Thus, together, the academic partners are world-leading researchers in yeast and bacteria engineering, in using synthetic biology to create microbial communities, in cutting-edge analytics (including metabolomics and proteomics) and in modelling communities. In addition, the industrial partner is one of the few biotech companies with expertise in commercial processes using engineered microbial communities. The scientific work packages will be developed in parallel to a Responsible Research an Innovation plan intended to evaluate the environmental and societal aspect of the process and it will guide and be guided by the experimental plans and results. SyCoLim is also committed to strict ethics and data management standards, embracing the FAIR principles. The project is accompanied by a solid Communication and Dissemination plan to reach different stakeholders and maximise the impact of the project's outcomes.
The project will be carefully managed to optimise equal participation of the partners, appropriate budgets, gender balance, risk assessment, back up strategies, efficient communication and personnel and material transfer between teams.
The aim of this project (SyCoLim) is to produce high-value chemicals (with applications as pharmaceuticals, medicines, fragrances, nutraceuticals or cosmetics) from waste raw materials (recycling glycerol, the by-product of biodiesel industries). In order to achieve this objective, synthetic microbial communities between yeast and bacteria will be created. These communities will be engineered to present advantages over monocultures, such as division of labour, higher adaptability and robustness or an expanded metabolic network. The bioprocess carried out by the best strains generated will be scaled up in industrial conditions in the facilities of our industrial partner. Therefore, the project will help the lab-to-market transition of the sustainable production of valuable compounds and will combine this with the exploration of novel synthetic biology and microbial communities' methodologies that have the potential to be applicable to other bioprocesses, thus facilitating the global transition towards the bioeconomy.
The partners of SyCoLim has been selectively chosen to be the best fit possible to the rationale of the project, in terms not only of skills and methodologies but also in previous experience in synthetic microbial communities. Thus, together, the academic partners are world-leading researchers in yeast and bacteria engineering, in using synthetic biology to create microbial communities, in cutting-edge analytics (including metabolomics and proteomics) and in modelling communities. In addition, the industrial partner is one of the few biotech companies with expertise in commercial processes using engineered microbial communities. The scientific work packages will be developed in parallel to a Responsible Research an Innovation plan intended to evaluate the environmental and societal aspect of the process and it will guide and be guided by the experimental plans and results. SyCoLim is also committed to strict ethics and data management standards, embracing the FAIR principles. The project is accompanied by a solid Communication and Dissemination plan to reach different stakeholders and maximise the impact of the project's outcomes.
The project will be carefully managed to optimise equal participation of the partners, appropriate budgets, gender balance, risk assessment, back up strategies, efficient communication and personnel and material transfer between teams.
Technical Summary
The biggest challenge of the biotechnological industry is to allow the transition to a bio-based economy. This transition can be accelerated by a sustainable microbial production of fuels and chemicals. However, not many bioprocesses reach the market due to the elevated production costs. Therefore, reducing the cost of bio-based production is essential and can be achieved by addressing the bio-manufacturing of high-value products from low-cost raw materials.
In this project, we aim at exploiting synthetic biology tools to create synthetic microbial communities for the bioproduction of natural products. In order to achieve this goal, the partners (Imperial College London, CSIC, Charite-Universitatsmedizin Berlin and AciesBio) will join forces to develop novel tools and strains with industrial applications.
In this project, we aim at exploiting synthetic biology tools to create synthetic microbial communities for the bioproduction of natural products. In order to achieve this goal, the partners (Imperial College London, CSIC, Charite-Universitatsmedizin Berlin and AciesBio) will join forces to develop novel tools and strains with industrial applications.
Planned Impact
The outcomes of the proposal are expected to have a substantial impact, for example in academic research, technological and economic development, biotechnological industry, sustainability and environment, and society. In this section, we summarise some key aspects of the expected impact, although due to its importance, the impacts and potential of the project have been described throughout the different documents and sections of this proposal.
All this will bring impact and added value for the European Research and Innovation in academia and industry. The project connects research groups from 4 European countries that are not currently collaborating together but whose expertise perfectly complements each other to achieve success in this proposal, facilitating the lab-to-market transition. This consortium will impact the career development of young researchers and a biotech SME. The research proposed here is using cutting edge and innovative science and techniques beyond the state of the art and its outcomes are expected to be published in very high impact journals as well as world patents. New production processes developed in the project will have an impact on the European economy as valorisation of biodiesel industries and the generation of novel bio-based starting molecules that can be used by the chemical industries to produce a variety of compounds with a myriad of applications.
The detailed TRL plan document explains how an increase in 2 levels of TRL will be achieved during the project. This increase, which leads to a test of the technology in industrial conditions, will have an impact on technological and economic development.
The project will impact on commercial partners and end-users. More directly, the partner Acies Bio will participate in the development of the technology and will benefit of the technological innovations. This will allow them to expand their exploitation capabilities and commercialise new bioprocesses. This capability will impact positively the positioning of Acies Bio on the industrial biotechnology market and benefit European and worldwide flavour and fragrance industries, such as Guivodan, Firmenich, Frutarom, IFF, etc. In addition, this technology will set up a methodology for using synthetic communities in biotechnology that will provide essential know-how for the implementation of novel strategies and production lines (for example, other derived products from the mevalonate pathway, like carotenoids and diterpenes), and thus expand the post-project impact of this work.
The project will have an impact on the sustainability of biotechnological research, which will be favoured by a solid Data Management (DM) plan. The DM plan, described in a separate document, will champion the responsible and efficient use of results generated in the scope of the project. It will have a positive impact on the scientific community and industry by creating datasets using FAIR principles.
All this will bring impact and added value for the European Research and Innovation in academia and industry. The project connects research groups from 4 European countries that are not currently collaborating together but whose expertise perfectly complements each other to achieve success in this proposal, facilitating the lab-to-market transition. This consortium will impact the career development of young researchers and a biotech SME. The research proposed here is using cutting edge and innovative science and techniques beyond the state of the art and its outcomes are expected to be published in very high impact journals as well as world patents. New production processes developed in the project will have an impact on the European economy as valorisation of biodiesel industries and the generation of novel bio-based starting molecules that can be used by the chemical industries to produce a variety of compounds with a myriad of applications.
The detailed TRL plan document explains how an increase in 2 levels of TRL will be achieved during the project. This increase, which leads to a test of the technology in industrial conditions, will have an impact on technological and economic development.
The project will impact on commercial partners and end-users. More directly, the partner Acies Bio will participate in the development of the technology and will benefit of the technological innovations. This will allow them to expand their exploitation capabilities and commercialise new bioprocesses. This capability will impact positively the positioning of Acies Bio on the industrial biotechnology market and benefit European and worldwide flavour and fragrance industries, such as Guivodan, Firmenich, Frutarom, IFF, etc. In addition, this technology will set up a methodology for using synthetic communities in biotechnology that will provide essential know-how for the implementation of novel strategies and production lines (for example, other derived products from the mevalonate pathway, like carotenoids and diterpenes), and thus expand the post-project impact of this work.
The project will have an impact on the sustainability of biotechnological research, which will be favoured by a solid Data Management (DM) plan. The DM plan, described in a separate document, will champion the responsible and efficient use of results generated in the scope of the project. It will have a positive impact on the scientific community and industry by creating datasets using FAIR principles.
Publications
Atkinson E
(2022)
Resource-aware whole-cell model of division of labour in a microbial consortium for complex-substrate degradation.
in Microbial cell factories
Aulakh SK
(2023)
Spontaneously established syntrophic yeast communities improve bioproduction.
in Nature chemical biology
Bamezai S
(2023)
Protein engineering in the computational age: An open source framework for exploring mutational landscapes in silico.
in Engineering biology
Bhutada G
(2022)
Production of human milk fat substitute by engineered strains of Yarrowia lipolytica.
in Metabolic engineering communications
Boo A
(2021)
Quorum sensing in synthetic biology: A review
in Current Opinion in Systems Biology
Climent-Catala A
(2023)
Evaluating DFHBI-Responsive RNA Light-Up Aptamers as Fluorescent Reporters for Gene Expression
in ACS Synthetic Biology
Coppens L
(2023)
Vibrio natriegens genome-scale modeling reveals insights into halophilic adaptations and resource allocation.
in Molecular systems biology
Ezzamouri B
(2021)
Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies.
in Frontiers in microbiology
Graham AE
(2023)
The microbial food revolution.
in Nature communications
Description | We have created synthetic microbial communities able to communicate to each other and to distribute tasks to maximise the production of compounds of interest We have created a bioinformatic tool that is open to be used by the RNA community |
Exploitation Route | The company AciesBio will be testing our strains in industrial conditions The knowledge generated in engineering yarrowia for the production of limonene can be used for the production of other terpenes. |
Sectors | Agriculture Food and Drink Chemicals Manufacturing including Industrial Biotechology |
URL | https://sycolim.eu/ |
Description | The company AciesBio is testing some of the strains produced in this project in their industrial facilities. They are also assessing using Life Cycle Assessement the feasibility and environmental impact of these new processes. |
First Year Of Impact | 2022 |
Sector | Agriculture, Food and Drink,Chemicals |
Impact Types | Societal Economic |
Description | Podcast: The Living Revolution |
Geographic Reach | National |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | improved understanding on how industrial biotechnology can help the green economy |
URL | https://linktr.ee/thelivingrevolution |
Description | Promotional video |
Geographic Reach | Europe |
Policy Influence Type | Contribution to new or Improved professional practice |
Impact | convincing people of the benefit of synthetic biology in a sustainable society |
Description | Bio-based Industries Joint |
Amount | € 6,250,541 (EUR) |
Funding ID | 101022370 |
Organisation | European Commission H2020 |
Sector | Public |
Country | Belgium |
Start | 04/2021 |
End | 04/2024 |
Description | ERC starting grant |
Amount | € 1,500,000 (EUR) |
Funding ID | 949080 |
Organisation | European Research Council (ERC) |
Sector | Public |
Country | Belgium |
Start | 03/2021 |
End | 04/2026 |
Description | Imperial College London UKRI Impact Acceleration Account- Scaling-up the production of a novel blue dye using a yeast-based platform |
Amount | £46,660 (GBP) |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2023 |
End | 09/2024 |
Description | Imperial College London UKRI Impact Acceleration Account- Scaling-up the production of a novel blue dye using a yeast-based platform |
Amount | £15,553 (GBP) |
Funding ID | BBSRC -BB/X511055/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 09/2023 |
End | 09/2024 |
Description | skind microbial devices |
Amount | € 2,718,000 (EUR) |
Funding ID | 101098826 |
Organisation | Pompeu Fabra University |
Sector | Academic/University |
Country | Spain |
Start | 02/2023 |
End | 01/2027 |
Description | Collaboration with Markus Ralser |
Organisation | Charité - University of Medicine Berlin |
Country | Germany |
Sector | Academic/University |
PI Contribution | We have worked on a HTP experiment to screen yeast variants with complementary features that can be used for bioproduction and division of labour |
Collaborator Contribution | The Ralser lab provided support with the design of the automated experiments using lab robots as well as data analysis and mass spec characterisation or metabolites of interest. |
Impact | Article under review in Nature Chemical Biology |
Start Year | 2021 |
Description | Collaboration with Victor de Lorenzo's lab |
Organisation | Spanish National Research Council (CSIC) |
Department | National Center for Biotechnology (CNB) |
Country | Spain |
Sector | Public |
PI Contribution | We are exchanging strains and plasmids |
Collaborator Contribution | We are exchanging strains and plasmids They are producing Antibodies for us |
Impact | -Construction of strains -Construction of plasmids -Meetings |
Start Year | 2020 |
Description | ERA CoBioTech meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Policymakers/politicians |
Results and Impact | all the funded project from ERA Cobiotech presented their project in a meeting that lasted a week. |
Year(s) Of Engagement Activity | 2020 |
Description | Kick off meeting |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | 10 people attended the kick off meeting and the first results of the project were presented and the future directions discussed. |
Year(s) Of Engagement Activity | 2020 |
Description | Presentation in GreenWin conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | A conference with companies and academics where I present the progress of my projects |
Year(s) Of Engagement Activity | 2020 |
URL | https://www.greenwin.be/en/news/consult/204/meet-dr-rodrigo-ledesma-amaro-from-imperial-college-lond... |
Description | Talk and scientific committe in Metabolic Engineering 15 (Singapore): Next-generation tools for metabolic engineering |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Scientific committee: help orgainsation Chair of sesssion: selection of talks and posters Talk: scientific talk on the progress of several of my projects |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.aiche.org/imes/conferences/metabolic-engineering-conference/2023 |
Description | Talk at Oxford Synthetic Biology Network |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | A talk about my research projects for the Synthetic Biology network at Oxford |
Year(s) Of Engagement Activity | 2020 |
URL | http://synbio-oxford.org/events.html |
Description | Talk in Talant Acadmy |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Opportunity to present my research to other young academics in order to make partnerships to apply for EU funding |
Year(s) Of Engagement Activity | 2021 |