Why Retrofitting Fermentation Infrastructure Is Harder Than It Looks
May 30,2026
CAPEX can be a killer, especially in industrial biotech.
Biotech companies eventually reach a point where they need to demonstrate their process at commercial scale. But putting steel in the ground costs a lot.
Investors are rightfully cautious. Pharma can support enormous valuations at relatively modest manufacturing scale. Industrial biotech often requires large-volume production before the economics are fully proven.
That changes the financing equation considerably.
Years ago, when the craft beer industry started to fizzle in San Diego, I was an advocate for repurposing brewery facilities. But industrial biotech was softening at the same time. Promising companies like Sapphire, Synthetic Genomics, and Verdezyme faced economic challenges. Since then, San Diego has largely become a “Pharma Town.”
Industrial biotech has repeatedly explored retrofitting existing infrastructure rather than rebuilding fermentation capacity from scratch. Cobalt Technologies, a biofuel company, explored using an idled corn ethanol plant to run their anaerobic bacterial process. But the cost of the retrofit was surprisingly high.
Part of the challenge was that seemingly minor process requirements sometimes demanded entirely new unit operations. Additional feed handling and thermal treatment steps added infrastructure and cost that were not fully anticipated at the beginning of the retrofit effort.
On paper, repurposing fermentation infrastructure sounds logical.
The tanks already exist.
The utilities are already installed.
And parts of the surrounding process infrastructure – feedstock processing, cleaning systems, heat exchange, and separation equipment may already be operational.
And sometimes, retrofit strategies work.
But retrofitting a biological process is often more complicated than it first appears.
Different organisms and products place different demands on:
- oxygen transfer
- agitation
- sterility
- cleaning validation
- downstream processing
Even when the core infrastructure is technically compatible, adapting a facility to a new process can become far more expensive than early models assume.
A brewery optimized for yeast fermentation may require significant modification for bacterial production. A facility designed around ethanol economics may not align with the operational realities of specialty biochemicals. And downstream processing often becomes a bigger mismatch than upstream fermentation itself.
The challenge is not simply whether a process can run.
It’s whether it can run economically, reliably, and at commercial scale.
Facilities also develop operational histories over time. Cleaning assumptions become embedded in workflows. Resident organisms persist in difficult-to-clean areas. Biofilms establish themselves.
Repurposing infrastructure sounds easier than it is.
Because biology remembers what ran there before.
Still, companies continue searching for ways to reduce infrastructure risk. Pacifico Biolabs recently secured a €7M Series A to scale their mycelial process using brewery facilities. Helaina also successfully raised a Series B to scale lactoferrin production.
But in a tighter financing environment, the economics of scale remain one of industrial biotech’s hardest problems.