ENGINEERING SYNTHETIC MICROBIAL COMMUNITIES FOR BIOTECHNOLOGY

Lead Research Organisation: Imperial College London
Department Name: Bioengineering

Abstract

In nature, microorganisms live in communities -microbiota- where each member interacts with the others and with the environment. These microbial consortia are responsible for human, animal and crop health, ecological stability, and industrial bioprocesses. For example, in the recent years, human gut microbiota has been associated with many important diseases from cardiovascular diseases to diabetes. As another example, the most stable and robust industrial bioprocesses are carried out by microbial communities, such as the production of most fermented food and drink. Despite the very well known importance of microbiota, and our recent progress towards the identification of the members of the communities we still know very little about how these communities are established and maintained, which limit our possibilities to engineer them in order to tackle microbiota diseases or create new robust bioprocesses.

To this end, there is significant interest in developing simplified microbial communities which can serve as a platform to address basic biological questions on microbial interactions and to create more efficient bioprocesses than those based on a single engineered microorganism.

The work proposed here aims to design and build synthetic microbial communities using synthetic biology. Synthetic biology uses engineering principles in biological systems in a predictable, controllable and standardized manner in order to get new biological insights and create cells with improved abilities. This project, firstly, will generate stable synthetic microbial communities, and secondly, will use some of these communities to perform specific tasks, such as the production of biofuels and pharmaceuticals. This work will, therefore, be able to produce specialist strains valuable for use in biotechnology.

To achieve these goals, I plan to use knowledge and tools gained from my previous experiences in microbial metabolite exchange, which is the basis for establishing communities. Engineering metabolism has proven useful to generate synthetic communities, as shown by my preliminary results and previous works, indicating the feasibility of the proposed work. Therefore, we will create a series of engineered microbial strains that are able to interact with each other in different manners and generate stable communities.

In addition, the generated synthetic microbial communities will be used to create more complex population behaviours and learn by building how natural communities interact and evolve. This way, we will be able to control the abundance of the members in the population, we will generate new population-level functionalities, and we will re-create ecological relationships found in nature. This will generate important new insights for understanding how cells form and maintain microbiota.

Finally, we will prove that synthetic microbial communities can be designed and build to improve the production of biotechnologically relevant compounds. Firstly, a community where two microorganisms cooperate to maximize the production of an industrial pharmaceutical will be engineered. Secondly, a community designed to select the best mutants to produce biodiesel will be generated and used. Both strategies are strongly supported by competitive industrial partners in the field, which indicates the enormous potential of this new technology.

This project is, therefore, developing a new synthetic biology technology that can be used in a variety of fields, from helping us to better understand natural microbiota and tackle the associated diseases to create more robust and versatile bioprocesses, which may allow us to move towards the bioeconomy.

Technical Summary

This project is designed to take synthetic biology to a next level -the population level- and to develop a toolbox of synthetic microbial communities that will be used to 1) learn how microbes interact to form stable consortia and 2) to build artificial communities with enhanced industrial capabilities. Due to the huge importance of microbiome on human disease and biotechnological applications reliable tools to study microbial composition have been developed. However, we still lack the basic knowledge of the generation and maintenance of microbial communities, which indicates a necessity to develop simple models of study. Moreover, current microbial biotechnology, mostly based on single strains, is facing limitations that could be overcome with the use of more robust and versatile communities. One example would be the distribution of metabolic burden among the members of the community by task distribution or pathway compartmentalization.

This project aims first to engineer microbial strains with enhanced capacities to interact with each other and form communities. These strains will be created by overexpressing or deleting genes involved in the appropriate metabolic pathways. Golden Gate cloning system will be used in an automated platform to quickly assemble synthetic DNA parts and accelerate strain generation. As a result, a toolbox of strains with the ability to form communities will be developed.

Then, the toolbox will be used to generate emergent and complex community behaviours, which will be used to simulate naturally-occurring microbial communities and to get insights into the kinetics and the evolution of microbial populations.

In addition, synthetic microbial communities with industrial applications will be created. In particular, a first community will be designed to optimize the production of an industrial polyphenol via pathway compartmentalization and a second community will allow us to select improved biodiesel producer strains.

Planned Impact

This project is designed to provide the foundations for the next phase of synthetic biology, where custom synthetic microbial communities will be built-to-design. Over the past 5 years, the UK has followed a strategy of high-profile investments in synthetic biology which has been intentionally designed to fund ambitious foundational work such as that proposed here. The aim of this strategy is to aid downstream industrialisation of scientific work. The UK strategy will allow us to exploit our world-leading research base in biological sciences to create new industries, rejuvenate the biotechnology sector, support many SMEs, and to attract inward investment and create new jobs. Apart from the industrial and economic relevance, the dissemination of the project to the general public is expected to have a wide social impact such as education and career development, increasing public understanding of science, and artistic inspiration.

This project will have a clear impact on the two biotech companies supporting this proposal, Evolva and Fgen. Both will benefit from the generated knowledge and the specific industrial applications, as they state in their letters of support. Moreover, the fact that this work generates a general toolbox to easily study and use microbial communities will have enormous repercussions for other industries, specifically biotech and pharma, which may foster global economic performance and competitiveness. It is also especially relevant that this work is done in S. cerevisiae and E. coli, the most economically important microbes on earth. In this respect, the knowledge and skills generated by this project will likely lead to significant economic impact in many areas e.g., in biofuels, fine-chemical production and in agro biotech too. In addition, potential impacts in industries interested in microbiome studies could lead to an enhancement of the quality of life and health, by advancement in the treatment of microbiome-associated diseases. The new technology generated in this research will pave the way to novel research based on communities instead of on single strains which could end up in the creation of new start-ups and the associated new jobs.

In addition to the economic aspects, this project is expected to have an impact in society at different levels. Interestingly, the project has already attracted the attention of Tania Blanco a contemporary artist at the Royal Academy of Arts, who has written a letter of support for this work indicating her interest and the potential impact in others in her field. Moreover, the media tend to have a high coverage of synthetic biology research and we expect that the outcomes of this project will be highly diffused as it happened with some of my previous articles and patents. This will definitely help to expand the public understanding of science, specially in the key role that microorganisms have in our health and fermented products (foods and chemicals) and in how synthetic biology can engineer them to improve our quality of life.

More directly, this project will have a strong impact on the career development of those involved in it. First, the PDRA will learn from different aspects of biology and bioengineering, will be in close contact with industries (where research stay could be done), will work in one of the top institutions in synthetic biology and will attend the most important international conferences. It will also have the opportunity to supervise master students in projects related to this work. At the same time, the master students will also benefit from this project. Our interdisciplinary collaboration with Guy-Bart Stan for the model development will be enriching for both sides because we can learn from each other expertise. In addition, being granted with this BBSRC new investigator scheme would be essential for the development of my career as an independent researcher and will allow me to carry out high-impact research.

Publications

10 25 50
 
Description We have created a library of strains that can form communities
We have engineered co-culture strains to vary their population ratios
Exploitation Route The library of strains can be used by other researchers for their own studies on microbiome, synthetic communities or microbiome engineering.
Sectors Manufacturing

including Industrial Biotechology

URL https://www.imperial.ac.uk/news/251334/new-molecular-toolkit-boosts-useful-molecule/
 
Description Besides academic impact with numerous publications, and novel collaborations (including collaborations with industry), we have received interest from a company working on space, to partner and send some of our yeast strains (made in this and other projects) to the international space station. This could help to produce products of interest, such as food or materials directly into space. We hope to be able to deliver impact in this space and the UKSA has shown interest in it. In addition, the company AciesBio is testing some of our co-cultures in their industrial setups to assess their potential for commercialisation.
First Year Of Impact 2022
Sector Aerospace, Defence and Marine,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 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 EuroTechPostdoc2 fellowship (This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 899987)
Amount € 152,720 (EUR)
Organisation Technical University of Denmark 
Sector Academic/University
Country Denmark
Start 01/2022 
End 12/2023
 
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 Mathatical modelling in microbial communities 
Organisation University of Warwick
Country United Kingdom 
Sector Academic/University 
PI Contribution I will provide the experiment data of yeast communities
Collaborator Contribution My collaborator use my wet lab experiment data for mathematic model training.
Impact Still in progress
Start Year 2021
 
Description Metabolic engineering of yeast for high value aromatics 
Organisation Nankai University
Country China 
Sector Academic/University 
PI Contribution I help supervise the visiting student Ms Ruiqi Chen from Nankai University on the project
Collaborator Contribution Ms Ruiqi Chen help implement the experiment and data analysis
Impact Still in progress
Start Year 2021
 
Description Microbial coculture plus yeast surface display 
Organisation South China University of Technology
Country China 
Sector Academic/University 
PI Contribution I help supervise a visiting Ph.D. student Mr. Haohong Chen from the South China University of Technology who works on the project.
Collaborator Contribution Mr Haohong Chen help finish the designed experiments and data analysis.
Impact still in progress
Start Year 2021
 
Description Explore Science for Sustainability Webinar. Low cost open source automation tools applied to the design of microbial cell factores 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Presentation and dissemination of results in a webminar.
Year(s) Of Engagement Activity 2021
URL https://www.ibioic.com/events-database/explore-science-for-sustainability-webinar-3
 
Description Key note presentation in the 2nd International Congress on NanoBioEngineering: Trends and New Applications. " Low cost automation tools for diagnostics and metabolic engineering applications" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation in the conference. New collaborations.
Year(s) Of Engagement Activity 2020
URL https://www.cinbi2020.com/sciprogram
 
Description Oral presentation at The 27th Joint Annual Conference of the Chinese Society of Chemical Science and Technology (27th CSCST SCI), 11th -12th Sep 2020, Queen's University Belfast, UK, online 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact More than 200 people in the area of chemical engineering and biochemical engineering attended this conference and shared ideas, which gave me some clues in the applications of my coculture application.
Year(s) Of Engagement Activity 2020
URL https://pure.qub.ac.uk/en/activities/27th-joint-annual-conference-of-the-chinese-society-of-chemical...
 
Description Oral presentation at the conference of Synthetic Biology UK 2021 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented my progress with around 200 researchers in the field of synthetic biology who attended this conference of Synthetic Biology UK 2021. My presentation arouses other researchers' interests and allows potential collaboration chances.
Year(s) Of Engagement Activity 2021
URL https://www.eventsforce.net/biochemsoc/frontend/reg/tAgendaWebsite.csp?pageID=53504&ef_sel_menu=849&...
 
Description Oral presentation at the seminar of Imperial College Center for Synthetic Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact 50 postgraduate students and professors attended this seminar and asked questions, which gave me some new clues/ideas for my next step of this project.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation at 5th Applied Synthetic Biology in Europe meeting (ASBE V), 2-4 Nov 2020, online 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact > 100 people in the area of synbio and metabolic engineering attended this conference and shared ideas, which greatly broaden my eyes and understanding of my own research topic.
Year(s) Of Engagement Activity 2020
URL https://www.efbiotechnology.org/syntheticbiology
 
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