ENGINEERING SYNTHETIC MICROBIAL COMMUNITIES FOR BIOTECHNOLOGY

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.

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.

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.