Scaling a microbial process is the critical step that converts successful biological proof-of-concept into a robust, scalable manufacturing system attractive to investors. It is also where many projects stall: the physics changes, variability increases and "lab success" stops predicting performance at pilot and manufacturing scale.
Isomerase provides bioprocessign services that help partners move from bench experiments to reliable, transferable processes; combining upstream and downstream development and scale-up through CDMO network.
What is microbial bioprocessing?
Microbial bioprocessing is the engineered use of microorganisms, typically bacteria, yeast, or filamentous fungi, to manufacture proteins, enzymes, metabolites, or other high-value products at industrial scale. The science doesn’t stop once the strain performs in shake flasks or small bioreactors. In practice, the “make-or-break” phase is building a process that remains stable when oxygen demand rises, gradients appear, and the bioreactor environment becomes heterogeneous.
For many organisations, the fastest way to close that gap is to outsource bioprocessing to a team that can translate bench performance into a process that is scalable, transferable, and controllable.
Why microbial scale-up behaves differently than bench experiments
Scale-up rarely fails because the biology “stops working.” It fails because the operating conditions change and the process becomes sensitive to effects that were negligible at small volume:
- Mass transfer limitations (especially oxygen transfer)
- Mixing gradients across the vessel
- Shear and foam behavior
- Metabolic state variability throughout the tank
- Downstream impurity and stability shifts
At scale, the goal is not to chase peak titre in a single run. The goal is to define a process that is repeatable, robust and manufacturable.
DoE-driven optimization to lock down operating windows
Isomerase applies statistically Design of Experiments (DoE) to identify the parameters that truly drive performance and separate them from noise. Rather than testing one change at a time, DoE accelerates learning, defines interactions, and supports the creation of operating ranges that hold up in pilot and manufacturing environments.
Why outsource bioprocessing?
Most teams can run microbial fermentations at lab scale. Far fewer have the infrastructure and accumulated lessons to industrialise efficiently. It often makes sense to outsource bioprocessing when one or more of the following are true:
- Pilot-scale capability is episodic. Building internal pilot suites and analytics is costly, especially when demand comes in bursts.
- Timelines drive value. Delays can push funding milestones, customer commitments, and manufacturing readiness further out-often multiplying cost
- Risk is the main constraint. The biggest threat is not “zero yield,” but a process that produces inconsistent results, shifts quality attributes, or fails at tech transfer.
- Learning rate is your bottleneck. Outsourced partners bring pattern recognition from similar problems (oxygen limitation, foaming, impurity shifts, downstream bottlenecks).
When your core competency is product innovation, outsource bioprocessing to gain speed, reduce scale‑up risk, and reach a transfer‑ready process faster.
What you get when you outsource bioprocessing to Isomerase
Isomerase helps you scale with control. When you outsource bioprocessing to our team, you gain a programme designed to increase learning rate, reduce scale-up risk and produce a transfer-ready process that support CDMO execution.
Access to 20+ years of process development experience
We treat upstream with downstream in mind to avoid common failure mode - optimizing fermentation while creating downstream constraints.
Risk-led planning
We actively manage uncertainty through a ranked risk register so you can make decisions earlier, reduce rework and protect timelines.
QbD foundations for predictable manufacturing
We identify CQAs/CPPs early, define design space and translate that into a controlled strategy so quality stays stable through scale-up and transfer.
CDMO selection support
Isomerase works across sectors and helps you navigate the full range of CDMO options. Using our CDMO partner network, we identify the best-fit CDMO based on scale, geography, equipment fit, quality systems, and timelines. We support end-to-end tech transfer to ensure the process runs reliably at the receiving site.
Case Studies
Improved process for enzyme production | Scale-up to 50,000 litres
Speak with Our Experts
If you are planning to scale a microbial process, or you have already hit a plateu beyond lab scale, Isomerase can support upstream and downstream development and help you identify they right CDMO partner for your application via our network.