Importance of Sterile Design in Aseptic Fermentation – How to keep from getting burned : Biofuels Digest


By Mark Warner, PE, Founder, Warner Advisors LLC

Special to The Digest

If you’ve spent any time in commercial fermentation facilities, then you already know it’s a hot bed of contaminants and has steam coming out all over the place. This is because heat (in the form of steam) is just one of the keys to keeping fermentation sterile. As companies look to scale industrial biotechnology based on aseptic fermentation, many look for ways to cut capital costs and the robustness of sterile design is often a target. Be aware though, removing items such as steam sterilization can cause you to get burned in a different manner (financially). It often comes down to spend now or pay for it later, let’s explore.

Easiest way to determine the potential impact of aggressive decisions on sterile design is to take the current version of the technoeconomic model and change the “failed batch” rate from a typical 1 – 5% failed batch rate for a mature operation to 30% and see how the economics of the process change. All the labor and raw materials will be expended, but 30% or more of the production will not be usable. Even worse, the facility will likely have to pay increased treatment or disposal costs to get rid of the bad batch, while slowing down overall plant production. This is the downside of a poor sterile design and the cold hard reality of being overly aggressive.

For aseptic fermentation, where there is an expectation of only one desired target organism at the end of a batch, sterile design is best summarized by creating a boundary that keeps all non-target (foreign) organisms out. This is done by ensuring the fermenter is clean and sterile, with everything coming in or going out being sterilized by one of the two primary methods, heat and filtration. Heat above 130°C is used to kill all organisms. This can be done by sparging steam into the fermenter, or in the case of streams like sugar, heating them up for a short period of time to target temperature. For items that are heat sensitive, they are sent through a 0.2 micron filter (commonly known as “sterile filter” in the fermentation industry), that ensures no organism can make it into the system. The following graphic summarizes how a sterile boundary is maintained.

This sounds very straight forward, so what is the problem? Money, properly designed systems are expensive. Aseptic aerobic fermentation systems are capital intensive and much more on a per unit of fermenter volume basis than other systems such as corn ethanol, which can be about 1/10th of the equivalent capital cost. For a fermenter to be steam sterilizable, it needs to be pressure rated to at least 25 psi and vacuum rated. Interior surfaces need to be polished to keep organisms from grabbing on and the sterile filters can be expensive. This makes using lower standard designs attractive from a capital perspective, but can end very badly if the fermentation system cannot operate in a sterile manner. Some additional perspectives follow.

Do all processes need highly sterile design? – No, systems like ethanol and syngas operate at much lower design standards with their fermentation systems having only a fraction of the capital cost of aseptic fermentation. No pressure vessels or metal surfaces you can see your reflection on are required. There are critical differences though: ethanol is anaerobic and has ethanol that limits many organism’s ability to grow. Another factor is presence of other organisms: while this is not typically acceptable for foods or most aseptic fermentations, many industrial fermentations can have a high presence of non-target organisms and still meet quality targets.

Differences that matter – There are many factors that make different microbial fermentations more or less prone to contamination, but at a high level, it comes down to how strong the target organism is compared to competitors and how favorable/unfavorable the general fermentation conditions are to microbial growth. Processes operating an aerobic fermentation on sugar at normal metabolic temperatures (25-40oC) and near neutral pH (above ~5-6) are more prone to contamination than other processes. Many anaerobic processes that generate acidic broths are much less prone to contamination as the environment is less inviting to most organisms. Having inherently unfavorable fermentation conditions as a primary sterile design basis is not very common and I would recommend thinking twice about alternate sterile designs unless it has been proven in a pilot or demonstration scale system.

A fork in the road – The hardest part of sterile design is that is must be decided up front. A fermenter that is purchased without the ability to be steam sterilized cannot practically be retrofitted. If the system does not run sterile, there are limited options to correct it. The one-time savings from decreased design standards are real, but so are the repeat and long-term dire consequences of being overly aggressive.

Capital cost savings from a decreased sterile design are real and I do not mean to downplay the value they could provide to an early stage company, but simply offer a framework that should be considered before heading down what can be a risky path.

Mark Warner is a registered professional engineer with 30 years of experience in process commercialization, focusing for the last 10 years on taking first-of-a-kind-technologies from bench-top to commercial operation. He has worked for four companies who have held the #1 spot in biofuels digest’s top company list, in a range of advanced biotechnologies including biodiesel, cellulosic ethanol, phototrophic algae, heterotrophic algae and innovative food products. He is the founder of Warner Advisors, providing consulting services and acting in interim engineering leadership roles for advanced bioeconomy clients. He can be reached at [email protected] or visit

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