Synthetic biology for microbial lipids production from lignocellulosic biomass using multi-functional synthetic consortia

Project Information

SynBioLipid

Grant agreement ID: 101022536

DOI

10.3030/101022536

Project closed

EC signature date 14 April 2021

Start date 1 March 2022

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 337 400,64

EU contribution

€ 337 400,64

Coordinated by

IMPERIAL COLLEGE OF SCIENCE TECHNOLOGY AND MEDICINE
United Kingdom

Periodic Reporting for period 1 - SynBioLipid (Synthetic biology for microbial lipids production from lignocellulosic biomass using multi-functional synthetic consortia)

Reporting period: 2022-03-01 to 2025-02-28

Summary of the context and overall objectives of the project

The growing demand to transition towards a sustainable and low-carbon economy has driven the widespread development of microbial cell factories aimed at producing a broad range of high-value products. However, many of these bioprocesses never go beyond academic research and fail to be translated into industrial applications. This is mainly because many bio-based products are still not cost-effective compared to petroleum-derived chemicals. To overcome this issue, the efficient use of inexpensive and abundant feedstocks such as lignocellulose in the biotechnology industries is essential to position bioproduction as a more competitive alternative compared to conventional chemical processes. Several major challenges hinder profitable bioproduction using renewable feedstocks, including i) the sensitivity of microorganisms to inhibitors present in these feedstocks, ii) high costs associated with the downstream processing, and iii) the inability of microorganisms to effectively degrade inexpensive complex substrates.
This project aimed to develop microbial cell factories driven by engineered yeast, Yarrowia lipolytica, to utilise renewable and abundant carbon sources, such as lignocellulose, for the bioproduction of high-value compounds with broad applications in food and pharmaceutical industries. By combining synthetic biology, adaptive laboratory evolution, and synthetic microbial communities, the project aimed to address some of the big challenges in bioprocessing such as incomplete substrate bioconversion, generation and accumulation of fermentation byproducts, and low product yields. A key focus of the project is to highlight the great potential of synthetic microbial communities for commercial applications. While microbial communities provide significant advantages over single cultures—such as improved utilisation of complex feedstocks, reduced metabolic burden on individual species, and increased resistance to toxic compounds—they have yet to be implemented in commercial settings.
The project had a positive impact on the society by addressing several global challenges:
i) Sustainable bioproduction: efficient utilisation of renewable and low-cost feedstocks such as lignocellulose for bioproduction advanced sustainability and circular economy.
ii) Cost-effective bioprocesses: improved bioconversion yields and overcoming byproduct accumulation reduce the bioprocess costs, strengthen the bioeconomy, improve the economic viability of bio-based industries
iii) Affordability and accessibility of bio-based products: Enhancing fermentation yields could lower prices for microbial products, making them more affordable and accessible to various industrial sectors and the public.
This project achieved significant advancements in engineering the oleaginous yeast Yarrowia lipolytica to enhance the bioproduction of high-value compounds using lignocellulose. These advancements open opportunities for utilising microbial cell factories based on this yeast to create efficient and sustainable bioprocesses, producing high-value compounds with broad industrial applications. The outcomes of this project significantly advance the development of bio-based production technologies and pave the way for future breakthroughs in industrial biotechnology.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Work Performed:
-Combined metabolic engineering and adaptive laboratory evolution to create Y.lipolytica strains capable of utilising lignocellulose components.
- Designed and optimised synthetic communities of Y.lipolytica to enhance substrate utilisation, reduce byproduct accumulation, and produce β-carotene.
Main Results:
- Engineered strains of Y. lipolytica successfully produced β-carotene from arabinose and citric acid, both of which are components of lignocellulosic substrate.
- The engineered Y. lipolytica strain could grow on arabinose, achieving a β-carotene production of 4.67 g/L in bioreactors using arabinose as the sole carbon source.
- Synthetic communities demonstrated a 104% improvement in β-carotene production using lignocellulose compared to monocultures.
A maximum β-carotene yield of 0.11 g/g glucose was achieved, which was the highest reported to date (this is particularly significant given the theoretical yield of 0.199 g/g glucose).
Exploitation:
- Filed a patent application for the synthetic communities with the capacity to upcycle fermentation byproducts
-Submitted two follow-up grants (EPSRC Standard Grant and ERC Proof-of-Concept) to exploit the results towards industrial applicatoin
Dissemination:
-Published a review paper: Rafieenia, R., Atkinson, E., & Ledesma-Amaro, R. (2022). Division of labour for substrate utilization in natural and synthetic microbial communities. Current Opinion in Biotechnology, 75, 102706. https://doi.org/10.1016/j.copbio.2022.102706
- Published a research paper: Rafieenia, R., Klemm, C., Hapeta, P., Fu, J., García, M. G., & Ledesma-Amaro, R. (2024). Designing synthetic microbial communities with the capacity to upcycle fermentation byproducts to increase production yields. Trends in Biotechnology. https://doi.org/10.1016/j.tibtech.2024.10.015
-Presented results at different conferences and meetings: Fungal Science Network, CSynB seminar series, Microbiome Network Annual Conference, Bezos Centre for Sustainable Protein: Kick-off Meeting, and received acceptance to present at Metabolic Engineering Conference 2025.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project has significantly contributed to precision fermentation, bioprocessing, and synthetic microbial communities. The innovative approach to engineering synthetic microbial communities allows for more efficient substrate utilisation and the upcycling of fermentation byproducts. This strategy has greatly advanced substrate bioconversion rates and improved bioproduction yields, achieving an increase of over two-fold compared to monocultures, and successfully achieving total bioconversion of byproducts.
The project aimed to tackle two significant challenges in bioproduction: the accumulation of byproducts and inefficient substrate utilisation. Both of these issues reduce yields and increase downstream costs. By driving innovation in these areas, the initiative enhanced bioproduction and address societal challenges. Specifically, it aimed to lower downstream costs by converting byproducts into high-value products, and improve both the environmental and economic benefits of bioproduction. Ultimately, this cost reduction could make microbial products more affordable and accessible to various industrial sectors and the public. Furthermore, by efficiently utilising renewable and low-cost feedstocks like lignocellulose, the project promoted sustainability and a circular economy, positioning bioproduction as a more competitive alternative to conventional chemical processes.

Synthetic communities for efficient utilisation of lignocellulose

Engineer y.lipolytica for arabinose-based bioproduction