The main mission of the BioEngineering Center of Excellence is to design, build, improve and test living microorganisms, such as new yeasts, bacteria and filamentous fungi, using conventional non-genetically modified technologies as well as modern genetic engineering. “We are at the forefront of this process of improving existing industrial strains and building them de novo,” stresses Massimo Merighi, Director of the BioEngineering Center of Excellence.
The CoE BioEngineering is in itself a recent creation, with the launch of the biofoundry in 2022, but it is the natural heir to the Group’s historic expertise in strain engineering. It has enabled us to make a quantum leap in know-how, scope and methods in microorganism engineering.
From classical genetics to genome editing
The performance of organisms in processes and applications can be improved by modifying genotypes(1) or fine-tuning phenotypes. Bioengineering focuses on the manipulating the genotypes, with a strong eye towards the performance under industrial and application conditions (our phenotypes of interest).
Bioengineering also provides a vast toolbox for the system biology analysis of genotype performance under specific conditions, therefore enabling fermentation and DownStream processes (DSP) optimization.
Various approaches are being studied to improve microorganisms:
- Classical genetic approaches with techniques such as chemical and physical mutagenesis, spore segregation and spore crossings, protoplast fusion…, increasingly aided by marker-assisted techniques based on QTL(2) and GWAS(3).
- Genetic engineering approaches: next-generation sequencing, CRISPR-CAS genome editing and advanced bioinformatics have opened up a new era in systemic(4) and synthetic(5) biology. The bioengineering team uses these modern genetic engineering techniques applied to various microorganisms such as Saccharomyces spp, Pichia pastoris, Yarrowia lipolytica, Aspergillus niger, Escherichia coli, Bacillus subtilis.
Incredible reach and speed thanks to the BioEngineering center of excellence
Thanks to its two Biofoundries located in France and the USA (known as the Biological Foundry for Advance Bioengineering or BioFAB), CoE BioEngineering is able to increase the speed of construction and testing, reduce unit costs and development time, and amplify the “volume” of new genotypes constructed and/or tested, multiplying overall the chances of finding the optimal strain and the probability of project success.
Indeed, the main feature of modern bioengineering is the acceleration of the design-build-test-learn cycle. The ability to design and build numerous prototype strains, then rapidly test them in small volumes on automated platforms, leads to a reduction in the unit cost of design-build-test, meaning that for the same amount of money, more attempts can be made to identify the correct strains.
“New genotype designs are created with the help of computers. This is also true, to some extent, for non-genetically modified approaches, when certain marker-assisted approaches are attempted. When genetically modified organisms are created, this means that databases containing hundreds of thousands of candidate genes are sifted through computers to find interesting genes, then synthesized in the laboratory, introduced into the host strain, expressed and tested for the desired behavior,” explains Massimo Merighi
Complete metabolic pathways involving dozens of steps can be assembled in the same way. Genome editing can also directly modify the strain genome. Overall, it’s like creating hundreds or thousands of prototypes, which are then tested in small quantities using automated methods.
“These vast sets of prototypes have to be created because in the current state of biology, the de novo design of complete organisms is not yet possible. This may change in the future, as computational biology expands our understanding of life. Overall, the Biofoundry approach to bioengineering doesn’t necessarily reduce the total cost of development, but it allows greater scope and speed, augmenting the probability of success given a set development timeline,” emphasizes Massimo Merighi.
The corollary of this approach is that data becomes the queen, as shown by some key figures from Bioengineering . So if we consider the metadata associated with the various LIMS(6), we’re talking about dozens of terabytes per year.
“My teams therefore take great care in developing computational methods, databases, data dictionaries, transfer protocols to collect, track, classify, understand this huge mole of data. Learning from this data is a core part of our mission. Bioengineering’s computational infrastructure is probably the most complex and integrated of Lesaffre,” adds Massimo Merighi.
A well-oiled organization France and the United States
The BioEngineering CoE should be seen as a “global” Bioengineering team, comprising Bioengineering-France and Bioengineering-USA (i.e. Recombia Biosciences).
The CoE was structured in several stages with:
- The creation of the Biofoundry (2020-2022),
- Joint venture with Recombia Biosciences (2020-2022),
- Restructuring of the Genetics and Enzyme teams in 2022
- The acquisition of Double Rainbow in 2023.
The organization of our teams has also been designed to match technology, team expertise and geographical location with specific added value:
- projects involving non-genetically modified approaches are led by the microbial engineering team based in France. The team benefits from the recognized European research ecosystem in the field of yeast genetics (France, Belgium and Denmark).
- projects involving metabolic and genetic engineering are led by Recombia teams in the United States, due to the long history of industrialization of the technology since the 1970s and interactions with leading universities in these 2 fields.
- the technological development and construction of high-throughput organisms in the field of genetic engineering are led by the French Biofoundry. The team also benefits from synthetic biology capabilities based in San Francisco.
- all high-throughput screening and systems biology analyses are also carried out at the French Biofoundry.
“Today, with the addition of the platform dedicated to adaptive evolution in the laboratory (ex-Altar), synergies will reach new heights at Lesaffre”, emphasizes Massimo Merighi
Naturally, the Bioengineering CoE relies on LIST’s R&D ecosystem throughout its projects, and in particular on the MOS , Fermentation Process Design, Analytical Science & Discovery and Downstream Process CoEs.
The major challenges facing CoE Bioengineering
“The moonshot(7) for the future is to reduce the development time to 12 months, from design to pilot test, for a standard metabolic engineering strain development or non-GM development,” explains Massimo Merighi.
These goals are achievable. To achieve them, we need to leverage the force multiplier power of the French Biofoundry and solve the challenges of data and process optimization. It is essential to proceed to further data structure standardization, metadata ontologies, automation and data modeling. Much progress has already been made by the CoE BioEngineering team, in coordination with BioData and Digital Data Tech teams, in the field of data analysis and engineering.
“We also need a greater routine and faster effort to learn from our datasets, in order to optimize our design and testing process. The cycle between omics data collection, analysis and first automated interpretation needs to be reduced to two weeks. Certain processes such as “Build” need to be parallelized so that 2-week design-build-verify cycles can be established: this turn-over time would allow 26 construction cycles per year, a force multiplier for metabolic and microbial engineering teams.
The overall aim is to “fail quickly and safely”. Failure is part of the daily work of engineering teams, and embracing risk and failure is part of the game, if we want to investigate unexplored areas of industrial biotechnology,” emphasizes Massimo Merighi. He concludes by adding: “People are also the key to a successful bioengineering team: making my teams more connected, educated in the latest advances, at ease with computation, and data, will contribute to our future success”.
The pride of our French biofoundry
Read the testimonial from Massimo Merighi, Director of the BioEngineering Center of Excellence, who helped set up the Biofoundry on the Lesaffre Campus.
“Building Europe’s largest industrial Biofoundry is certainly one of the highlights of my career. I tried to learn from my past experience at Gingko Bioworks and challenge myself to build a cost-effective scalable Biofoundry, with standardized robots, off-the-shelf software and data structures ties to biological and biotechnological objectives.
Last year, we worked on 35 projects, created over 95,000 biological samples, almost 10,000 genetically modified strains (NGT1, 2, 3), sent 230 strains to bioreactor fermentation, of which 46 were promoted to the laboratory pilot stage and 22 to the industrial pilot stage. All this just two years after commissioning the Biofoundry! Today, our aim is to reduce the development time of a project from 5 years to one year: it won’t happen overnight, but I’m confident. I expect 2025 to be an even more exciting and productive year. The best is yet to come. ”
- (1) All of the genetic characteristics of a living organism, whether or not they are expressed in its phenotype (all of the physical and biological characteristics of an individual, e.g., the resistance of yeast to high concentrations of sugar).
- (2) The QTL mapping method allows the link between genetic variation (such as that of molecular markers) and phenotypic variation to be statistically tested.
- (3) GWAS (Genome Wide Association Study) consists of identifying nucleotide variations or SNPs (single nucleotide polymorphisms) associated with a trait of interest.
- (4) Systems biology seeks to understand how different parts of an organism (genes, proteins, cells, organs, etc.) interact and combine to produce complex biological behaviors. Systems biology uses mathematical models, algorithms, and simulations to analyze these interactions.
- (5) Synthetic biology seeks to create new living organisms or modify existing ones by introducing new functions or behaviors. This may include creating new metabolic pathways, constructing artificial cells, or even integrating genes from different species into a single organism.
- (6) LIMS (Laboratory Information Management System) is a laboratory information management system.
- (7) The Moonshot research and development program encourages high-risk, high-impact research and development to achieve ambitious goals and solve problems that future society will face.
- (8) Ontology is a data model containing concepts and relationships that can be used to model a set of knowledge in a given domain.