As UK startups face a critical scale-up bottleneck, the Earlham Biofoundry is providing the automation, infrastructure and specialist expertise to translate laboratory breakthroughs into commercial-scale biomanufacturing.
Harnessing microbes as sustainable biofactories offers a cleaner way to produce high-value compounds for the pharmaceutical, cosmetics, food and agricultural sectors. Yet for early-stage startups and SMEs, the R&D pipeline is fraught with technical and financial challenges including low-throughput screening limits, complex protocol optimisation and high infrastructure costs.
Dr Eleonora Tassinari, a Senior Research Technician in the Earlham Biofoundry, works directly with scientists across academia and the biomanufacturing industry to help them automate their workflows, establish proof-of-concept and generate experimental evidence to enable future commercial scale-up.
“Scale-up is a major bottleneck in biomanufacturing,” Eleonora explains. “Because the UK lacks sufficient capacity to support it, innovative startups risk being forced to look overseas just to test their processes at scale. On top of that, automation requires extremely expensive equipment which most SMEs and startups simply can’t afford, alongside specialist expertise to run complex protocols.”
Established as a BBSRC-funded National Bioscience Research Infrastructure (NBRI), the Earlham Biofoundry provides the UK biology and biotechnology communities with access to advanced equipment, automation and specialist expertise to radically increase the speed and throughput of engineering biology research. By facilitating early-stage testing, it helps homegrown companies de-risk their processes and keep their innovations here in the UK.
Eleonora supports the Biofoundry’s activities through project design, testing, optimisation and troubleshooting of both manual and automated protocols. She also strengthens national capacity building by designing and delivering training to the wider scientific community.
Dr Eleonora Tassinari, left, with Dr Carolina Grandellis, right, Head of the Earlham Biofoundry
With a background in molecular biology and microbiology, Eleonora joined the Earlham Institute in 2022, drawn by its collaborative environment, the opportunity to develop expertise in high-throughput automation approaches for engineering biology and the chance to support the Earlham Biofoundry’s diverse range of research.
“I wanted to do more applied work with real-world impact,” she recollects, “and I was fascinated by the potential of engineering biology to create sustainable solutions.”
“I love the variety of projects I work on,” she adds. “I collaborate with researchers across different sectors and organisation types and I get to apply my knowledge to a range of microorganisms. I contribute to projects across diverse scientific areas – from developing tools to track and study mammalian cells to genetically modifying microbial strains to produce useful compounds. It's a constant learning journey.”
Her industry partnerships include working with an international food technology company to help generate and evaluate yeast strains engineered to produce animal-free lipids that give alternative proteins a meat-like flavour.
She also collaborates with academic groups like the Truman lab at the John Innes Centre, where she helped develop a semi-automated transformation protocol for a non-standard chassis to boost production of an anticancer peptide.
I contribute to projects across diverse scientific areas – from developing tools to track and study mammalian cells to genetically modifying microbial strains to produce useful compounds. It's a constant learning journey.
Part of Eleonora’s work relies on the BioLector, a high-throughput automated microfermentation platform. Capable of growing up to 48 microbial cultures in parallel on a microscale, it allows her to evaluate the performance of different combinations of strains and media types in a single experiment. By increasing throughput, it accelerates screening time from months to weeks, while miniaturising the culture volume saves money by dramatically reducing the quantity of growth medium, antibiotics, reagents and lab space needed.
Another critical feature of the BioLector is its ability to continuously monitor and record multiple key parameters in real time, such as biomass, oxygen, pH and the production of recombinant protein.
“Not only does this automation free up valuable scientist time by eliminating the need for slow, manual sampling,” says Eleonora, “it captures far more data in a single run than a person ever could. This gives our industry partners a much deeper understanding of the bioprocesses they’re developing and allows them to optimise growth conditions before moving to expensive, larger-scale production.”
As one of the best-equipped BioLector platforms in the UK, the system significantly expands the range of applications the team can undertake. Its advanced gassing capabilities tightly regulate oxygen and carbon dioxide levels, closely mimicking industrial bioreactor conditions to reveal how both aerobic and anaerobic microbes behave when grown at scale. This overcomes one of the central challenges in biomanufacturing, where small-scale results often fail to translate to larger cultures due to differences in oxygen transfer, mixing and environmental control.
The system is also fitted with a specialised light array module, making it the only public research facility in the UK capable of testing phototrophic microbes like cyanobacteria and microalgae.
One of Eleonora’s recent collaborations using the BioLector was with Dr Aaron Macauyag, a Postdoctoral Research Associate in the Open Bioeconomy Lab at the University of Cambridge. As part of the BBSRC-funded Open BioMaps project, Aaron and colleagues have developed open-source plasmids and industrially relevant chassis, such as E. coli and K. phaffii expression strains, for the distributed, low-cost biomanufacturing of enzymes, antibodies and other biological products. The aim is to provide industry with an accessible alternative to proprietary expression systems, reducing barriers to entry for biotechnology startups and manufacturers.
Eleonora trained Aaron alongside his colleague Hannah, and facilitated his use of the BioLector, helping him benchmark and compare the performance of his newly generated strains and tools.
"We were keen to work with the Earlham Biofoundry because of its expertise in high-throughput strain characterisation and process development,” Aaron highlights. “The BioLector platform is particularly valuable because it combines the throughput needed to evaluate many experimental conditions simultaneously with cultivation conditions that better resemble those used in industrial bioprocesses.”
Designing and translating complex protocols for robotic platforms requires a rare hybrid skill set, combining wet lab molecular biology and microbiology with a deep understanding of automation. Eleonora’s expertise bridges this gap, enabling her to anticipate technical hurdles and overcome them through iterative problem-solving.
“A large part of my day is spent troubleshooting,” says Eleonora. “I’m naturally curious, so when something doesn’t go as expected, I enjoy going back to the literature to work out what went wrong. It can be frustrating and often takes several attempts, but I find the process of figuring things out and learning more about biological systems very rewarding.”
While high-throughput machines provide the scale, it takes human ingenuity to make them work. Whether she’s refining protocols or navigating unexpected hurdles, specialists like Eleonora provide the technical expertise needed to turn benchtop concepts into commercial reality.
Authored by Dr Mimi Tanimoto, writing for Earlham Institute
