Yes, a small biotech company can access pilot-scale fermentation without building its own facility. Contract fermentation partners offer ready-to-use bioreactors, process expertise, and analytical infrastructure on a project basis, eliminating the need for capital investment in equipment that may only be needed for a defined phase of development. This model is particularly well suited to scale-ups and R&D-driven companies that need to validate a concept quickly, without committing to permanent infrastructure.

The questions below unpack what pilot-scale fermentation actually requires, where the common scale-up pitfalls lie, and what to look for when choosing an external fermentation partner.

What does pilot-scale fermentation actually involve?

Pilot-scale fermentation is the intermediate stage between laboratory experiments and full industrial production. It typically involves bioreactors ranging from roughly 50 to 2,000 liters, operated under precisely controlled conditions, to validate that a process developed at lab scale behaves predictably when volume increases. The goal is not production volume, but process understanding and reproducibility.

At this scale, parameters such as oxygen transfer rate, mixing efficiency, pH control, temperature gradients, and nutrient dosing behave differently than in a bench-top flask. These differences are not trivial. A fermentation that performs well in a 2-liter reactor can fail at 200 liters if the underlying process mechanics are not properly characterized. Pilot scale is where those mechanics are stress-tested.

Beyond the reactor itself, pilot-scale work requires downstream processing equipment for harvesting, concentrating, or purifying the microbial biomass or target compound. Centrifugation, pasteurization, and filtration are commonly needed steps. Analytical capacity, including microbial community monitoring and product quantification, is equally important to understand what is actually happening inside the fermenter at each stage of the process.

Why do small biotech companies struggle to scale up fermentation?

Small biotech companies struggle to scale up fermentation primarily because the process knowledge developed at lab scale does not automatically transfer to larger volumes. Scaling fermentation is not a matter of multiplying quantities. It requires engineering insight into fluid dynamics, mass transfer, and microbial physiology under changed conditions, expertise that most early-stage companies have not yet built internally.

Several recurring problems compound this challenge:

• Incomplete process characterization: At lab scale, it is easy to overlook which parameters are truly critical. At pilot scale, uncontrolled variables become visible as inconsistent yields or unexpected microbial behavior.
• Infrastructure gaps: Most small biotech companies have analytical labs suited to discovery work, not the controlled bioreactor environments and downstream processing equipment needed for fermentation scale-up.
• Time pressure: Investors and commercial partners often expect a proof of concept within 6 to 12 months. Building fermentation infrastructure from scratch takes far longer and consumes capital that could fund the science itself.
• Lack of microbial monitoring tools: Understanding how a microbial community evolves during fermentation, particularly in mixed-culture systems, requires molecular tools such as amplicon sequencing or qPCR that are rarely available in-house at early-stage companies.

The result is a gap between a promising lab result and a scalable, reproducible process, a gap that stalls many otherwise sound biotech concepts at a critical stage of development.

What is fermentation contract manufacturing and what does it include?

Fermentation contract manufacturing is a service arrangement in which an external organization uses its own bioreactor infrastructure and technical expertise to carry out fermentation processes on behalf of a client company. It can cover the full development arc, from feasibility testing at lab scale, through pilot-scale validation and optimization, to small-scale commercial production of the final microbial product.

Depending on the partner and the scope of the engagement, contract fermentation services typically include:

• Lab-scale feasibility studies to assess whether a fermentation concept is technically viable
• Pilot-scale process development and optimization using controlled bioreactors
• Microbial community analysis using molecular tools to monitor and steer the fermentation
• Downstream processing, including centrifugation, pasteurization, and product formulation
• Scientific documentation, including process reports relevant for patent applications, subsidy dossiers, or investor presentations
• Support for technology transfer if the client eventually moves production in-house or to a larger facility

The client retains intellectual property rights over their concept and process. A reputable contract partner operates under confidentiality agreements and treats the client’s process knowledge with the same discretion as any internal R&D team would.

How does outsourcing fermentation compare to building in-house infrastructure?

Outsourcing fermentation is faster, lower-risk, and significantly cheaper in the short term than building equivalent infrastructure in-house. Setting up a pilot fermentation facility with bioreactors, downstream processing equipment, and qualified analytical capacity requires substantial capital investment, regulatory compliance work, and time to hire and train specialized staff. For a company at concept or early validation stage, that investment is rarely justified.

The practical comparison looks like this:

• Speed to first results: A contract partner with existing infrastructure can begin experimental work within weeks. Building in-house takes months to years.
• Cost structure: Outsourcing converts a large fixed capital expenditure into a variable project cost, which is easier to justify to investors and easier to stop if the concept does not validate.
• Access to expertise: A specialized fermentation partner brings process knowledge accumulated across many projects and microbial systems. An in-house team, even if well-resourced, starts from a narrower base.
• Flexibility: Contract partners can scale reactor volume up or down as the project demands. In-house infrastructure is fixed.

The case for building in-house becomes stronger once a process is fully validated, volumes are predictable, and the company has the resources to operate and maintain fermentation equipment reliably. For the validation phase, outsourcing is almost always the more rational choice.

Avecom’s fermentation R&D and contract manufacturing service is structured precisely for this phase, offering aerobic and anaerobic bioreactors up to 2,000 liters alongside the analytical and downstream processing capacity needed to move from concept to validated process without infrastructure investment.

What should a biotech company look for in a fermentation partner?

A biotech company looking for a fermentation partner should prioritize demonstrated process expertise, appropriate infrastructure, and a clear approach to confidentiality. The partner’s technical capability should match the specific fermentation system involved, whether that is aerobic or anaerobic, batch or continuous, pure culture or mixed microbial community. A partner that works only with standard model organisms may not be equipped to handle more complex or novel fermentation concepts.

Key criteria to evaluate include:

• Bioreactor range and control: Does the partner operate reactors at the scale you need, with reliable control over temperature, pH, dissolved oxygen, and nutrient feeding?
• Analytical depth: Can they characterize what is happening inside the fermenter, including microbial community dynamics, not just bulk process metrics?
• Downstream processing: Do they have the equipment to harvest and process the product, or will you need to arrange that separately?
• Scientific credibility: A partner with a research background and publication track record can strengthen your IP and subsidy documentation, which matters increasingly in 2026 as funding bodies scrutinize technical credibility.
• Confidentiality practices: Ask directly how the partner handles client process data, IP, and results. Non-disclosure agreements should be standard, not optional.
• Flexibility and communication: The best contract partners function as an extension of your R&D team, engaging with the science rather than simply executing instructions.

Avecom, founded as a spin-out of Ghent University, combines over 30 years of applied fermentation experience with a scientific network that can add genuine weight to client R&D dossiers, a combination that is difficult to find in purely commercial contract manufacturers.

How quickly can a company move from concept to pilot-scale proof of concept?

With an experienced contract fermentation partner and a reasonably well-characterized concept, a company can typically move from initial lab-scale feasibility work to a pilot-scale proof of concept within three to nine months. The exact timeline depends on the complexity of the microbial system, how much process understanding already exists, and how quickly the client can provide the biological material and process parameters needed to begin.

A realistic progression looks like this:

1. Technical intake and feasibility design (weeks 1 to 4): The partner reviews the concept, identifies critical parameters, and designs an initial lab-scale experiment to test core assumptions.
2. Lab-scale feasibility testing (weeks 4 to 10): Controlled experiments at small scale establish whether the fermentation concept is viable and identify which parameters drive performance.
3. Pilot-scale transfer and optimization (months 3 to 7): The process moves to a larger bioreactor. This phase focuses on reproducing lab results at scale and troubleshooting the differences that emerge.
4. Proof of concept validation (months 6 to 9): Consistent, reproducible results at pilot scale, supported by analytical data and process documentation, constitute the proof of concept that investors or commercial partners require.

This timeline is significantly shorter than the 18 to 36 months typically needed to design, build, and commission equivalent in-house infrastructure. For companies under investor pressure to demonstrate scalability, working with an established fermentation partner is one of the most reliable ways to compress the development timeline without cutting corners on scientific rigor.

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