Isomerase's Microbial Fermentation Services: From Strain Design to Scalable Process

Microbial Fermentation Services: From Strain Design to Scalable Process

Fermentation is one of the oldest biotechnologies, yet it’s now driving some of the most cutting-edge innovations in health, nutrition, and sustainability. From therapeutic enzymes and precision fermentation ingredients to biodegradable materials and alternative proteins, microbial fermentation has re-emerged as a core engine of the modern bioeconomy.

However, while the science behind engineered microbes is advancing rapidly, the path from discovery to scalable production remains a challenge. The gap between lab-scale success and commercial reality is often defined by a single bottleneck: fermentation development.

To address this, Isomerase supports partners through an integrated, end-to-end fermentation development workflow, starting from proprietary host selection and early optimization, through to pilot-scale fermentation and the delivery of robust, scalable processes ready for tech transfer for commercial manufacturing.

Our integrated fermentation services include: 

• Pre-engineered proprietary strains (IsoChassis®)
• Custom strain development
• High-throughput microtiter screening
• Fermentation evaluation in stirred-tank reactors
• Quality by Design (QbD) frameworks for commercial robustness
• Development of downstream processes for product capture.
• Support with tech transfer to partner CDMO

Ultimately, this integrated approach ensures that your fermentation process flows eddiciently into downstream development, saving time and reducing scale-up risk.

Full-spectrum Fermentation Services

1. Strain Selection or Development

Our fermentation services begin with selecting the most suitable microbial host based on the specific requirements of the target molecule. We offer a range of pre-engineered production strains, as well as custom strain engineering solutions. For non-GMO applications, we also provide strain improvement via chemical or UV mutagenesis.

Our core proprietary platforms, including Escherichia coli, Pichia pastoris (syn. Komagataella phaffii), Bacillus subtilis, and Saccharomyces cerevisiae, are optimized for high expression yields and robust growth under high-cell-density conditions. These systems integrate a suite of proprietary genetic elements, expression vectors, and fermentation methods to maximize performance.

Importantly, host system selection is guided by our partner's product expression requirements, including intracellular or extracellular production, GRAS regulatory status, and post-translational modification needs. In addition to our core platforms, we have extensive experience working with industrially relevant organisms such as Aspergillus, Trichoderma, and Pseudomonas species, enabling flexible solutions across diverse project needs.

2. High-throughput Microtiter Analytical Screening System

HiMASS, Isomerase’s proprietary High-throughput Microtiter Analytical Screening System, is a modular component of our fermentation services. It is built to speed up fermentation development by enabling microscale cultures to reach high cell densities using a controlled fed-batch process.

The system allows for parallel screening of hundreds of conditions. It delivers gram-per-litre product titres in liquid cultures that mimic stirred-tank reactors.

HiMASS uses a slow-release feed system to control microbial growth. This helps identify the best-performing strain and condition combinations quickly.

By generating pilot-scale insights at microscale, HiMASS reduces development time and risk. It supports a smoother path from early screening to commercial fermentation.

3. Transitioning from Screening to Scalable Process

Scaling your process is a critical part of fermentation services. Once we identify top-performing strains, we move to controlled bench-scale bioreactors (1–30 L) to confirm growth and productivity under stirred-tank conditions.

Initially, we start with small reactors (2 L) to fine-tune nutrient feed, pH, oxygen, and other key variables. Subsequently, we scale up stepwise, up to 30 L, to reduce risk before full production.

Using Quality by Design (QbD), we define and monitor critical process parameters (CPPs) like agitation, oxygen levels, and feed strategies. This ensures your process is scalable, robust, and ready for transfer.

4. Downstream Process Development

Our microbial fermentation services go beyond yield optimization, ensuring your innovation is supported through to downstream processing and purification. At Isomerase, we align upstream development with downstream requirements to deliver efficient, scalable bioprocesses. This includes:

• Clarification and filtration compatibility
• In-process analytics (SDS-PAGE, HPLC)
• Purification trategies
• Batch-to-batch reproducibility
• Tech transfer packages (SOPs, batch records, process reports)

Ultimately, this integrated approach ensures that your fermentation process flows efficiently into downstream development, saving time and reducing scale-up risk.  

Building Scalable Fermentation Processes with Expert Support

Fermentation development is only successful when it's scalable, reproducible, and ready for handover. We focus on building robust microbial processes that align with your product goals; whether you’re aiming for early proof-of-concept, mid-stage optimisation, or preparing for commercial transfer.

To achieve this, we refine key variables like feed strategy, induction timing, and oxygen control, we apply targeted experimental design where needed, helping accelerate optimisation without overcomplicating development. Once a reliable process is established, we prepare full tech transfer packages including batch records, SOPs, and CPP documentation for internal scale-up or CDMO manufacturing.

Because of our proven track record, clients, ranging from biotech and pharma to agritech, food tech, and synthetic biology, choose us for our end-to-end capability and science-driven execution. As a fully integrated synthetic biology service provider, we cover every step of microbial product and process development from host selection to downstream and scale-up readiness.