What’s the real difference between a shake flask, a microtiter plate, and a full-scale bioreactor—and why do so many experiments go sideways, even when the SOP looks perfect?

If you’ve ever scratched your head about irreproducible results or the so-called “black box” of pre-culture history, you’re not alone. In this episode, host David Brühlmann sits down with Tibor Anderlei, a pioneer in orbital shaking technology, whose career spans from startup founder to long-haul leader at Kühner. Tibor isn’t just the guy who helped design the tools; he’s spent decades troubleshooting with everyone from viral vector scientists to cultivated meat innovators.

Key Topics Discussed

• Bioprocess development is shaped by the tension between increasing complexity and the need for simplification in CMC workflows.
• Aeration and oxygen transfer challenges are central to bioprocess performance, especially under oxygen-limited conditions.
• Oxygen transfer rate (OTR) and carbon dioxide transfer rate (CTR) provide more meaningful process insight than dissolved oxygen alone.
• Small-scale systems like microtiter plates can now support OTR and CTR measurement, enabling earlier process understanding.
• Process Analytical Technology (PAT) at small scale is shifting workflows from offline measurements to continuous online monitoring.
• Emerging biotechnologies such as cell and gene therapies, mRNA, and cultivated meat require improved control of shear sensitivity and real-time monitoring.
• Orbital shakers and small-scale cultivation systems have applications beyond biology, including industrial mixing and materials processing.
• Strong biotech organizations and startups rely on combining technical innovation with leadership judgment, agility, and customer proximity.

Episode Highlights

• The importance of measuring oxygen transfer rate (OTR) and carbon dioxide transfer rate (CTR) for reproducible bioprocesses—why DO is not sufficient [02:55]
• Real-time process analytical technology (PAT) for small-scale bioreactors, including microtiter plates and shake flasks [06:47]
• Pre-culture reproducibility: transferring at the right OTR and its impact on main cultures [07:56]
• Price sensitivity and scale-up challenges in cultivated meat—implications for media and equipment selection [10:36]
• Expansion of shaking technology to fields such as mixing, storage, and thawing, including applications in liquid crystal production [12:10]
• Leadership lessons from competing with bigger players: how smaller companies stay innovative, agile, and close to their customers [14:20]
• The significance of strong business partner relationships and trusting gut feeling in decision-making [16:32]
• Key advice for smart biotech scientists: careful definition of screening conditions and the use of online measurement tools at small scale [18:09]

In Their Words

All the new modalities you mentioned have one thing in common: they are more shear-sensitive than, for example, bacteria or CHO cells. Orbital shaken bioreactors are very suitable for shear-sensitive cells or systems, and the main reason is that they are surface-aerated, meaning we have nearly no bubbles. And bubbles rise, they burst, and they create very high local power input when they burst, which can damage the cells.

Why Your Shake Flask Culture Doesn't Scale: OTR, Shaking Diameter, and How to Fix It - Part 2

David Brühlmann [00:00:36]:
Welcome back. In Part one, Tibor Anderlei walked us through the hidden physics of shake flasks and microtiter plates, and why reproducibility challenges are so often rooted in fundamentals that get overlooked, such as the shaking diameter. Now in Part two, we continue our conversation and go deeper—exploring next-generation modalities, cultivated meat, and the surprising range of fields where shaking technology is making an impact beyond bioprocessing, plus leadership lessons from three decades in the industry. Let's continue.

I would like to dive a bit deeper into aeration, since you mentioned that this is one of the pitfalls where people work under oxygen-limited conditions. One way to measure aeration is by dissolved oxygen, like in bioreactors, for instance. Can you tell us what the best way is? Is DO sufficient, or should you do more sophisticated measurements? What is your recommendation there?

Tibor Anderlei [00:02:55]:
It's a little bit questioned: what is the difference between DO, for example, or another parameter? In my opinion, the more relevant parameters are the oxygen transfer rate (OTR) and the carbon dioxide transfer rate (CTR). I often hear people say, “I have DO—why should I also consider OTR and CTR?” I usually compare it with a bathtub: the water level corresponds to the concentration, and DO is the concentration, while the change in water level over time is a rate—that is the oxygen transfer rate.

With a rate, you can tell whether the water level is increasing, decreasing, or staying stable—you gain insight into the future. You can ask yourself: what would you like to know when leaving the house for five minutes while filling a bathtub? In my opinion, the rate is much more informative than the water level (DO).

And furthermore, the advantage of measuring respiration activity, such as oxygen transfer rate (OTR) and carbon dioxide transfer rate (CTR), is that you can measure them outside the sterile boundary of your bioreactor, so you do not have any contamination risk compared to sensors measuring inside the bioreactor itself. And last but not least, the respiration quotient between CTR and OTR—so carbon dioxide transfer rate divided by oxygen transfer rate—also provides information about which carbon source is being consumed. For example, an RQ around 1 indicates glucose, while an RQ around 0.6 indicates, for example, ethanol. With this, you can start to balance a bioprocess, which is very interesting for metabolic flux analysis, for example.

And last but not least, if you want to compare different bioreactor systems, such as a shake flask versus a wave system, you cannot do that with a DO value—you cannot compare them directly. But you can compare bioreactors by using the oxygen transfer rate. So I think OTR and CTR are much more valuable parameters than, for example, DO.

David Brühlmann [00:05:17]:
And what is the minimal scale required to measure oxygen transfer rate or carbon dioxide transfer rate?

Tibor Anderlei [00:05:25]:
Nowadays, we are capable of measuring OTR even in microtiter plates. We have a system called MicroTOM, where we measure the OTR in each well of a 96-well deep-well plate. So that represents the minimum scale already. The maximum scale is large—bioreactors, which in the microbial world have been standard for decades, where OTR and CTR are routinely measured and used for control. In the cell culture world, however, this is not yet as standard as in microbial systems.

David Brühlmann [00:06:03]:
I agree—I haven’t seen this as much when I was working with microtiter plate or spin tube experiments. It’s more common in bioreactors, especially in the cell culture field. But it’s good to know that it is possible to measure these parameters at much smaller scales. I’d like to touch on PAT as well, because many people are using microtiter plates to measure different parameters—hopefully even in real time or at least semi–real time. What is the situation there? What kind of PAT are you developing or seeing companies use at that very small scale?

Tibor Anderlei [00:06:47]:
Maybe in microtiter plates I would also include shake flasks in that context. In my opinion, it is very relevant to have PAT already at small scale, because online monitoring of precultures for larger bioreactors is still not carried out very often. During my time at AC Biotec, for example, we carried out many Pichia pastoris cultivations in stirred bioreactors. We were often confronted with poor reproducibility in these runs. Initially, we focused on optimizing the main culture in the stirred bioreactor, but we later learned that the variability originated from the preculture. We also realized that transferring based on OD measurements was not reliable. With Pichia, high OD values are reached, making OD determination less robust. Instead, we shifted to transferring cultures based on OTR—for example, at an OTR of 0.03 mol·L⁻¹·h⁻¹—which led to the desired reproducibility.

In my opinion, the history and condition of the preculture are extremely important. Even today, despite advances in modeling and digital twins, I still feel that preculture conditions are not given enough attention.

David Brühlmann [00:08:28]:
Yes, I fully agree, the preculture is extremely important. I would like to talk about other modalities, because these systems have traditionally been used in the microbial space and in, I’d say, CHO or mammalian cell culture. Now we are seeing viral vectors, CAR-T, mRNA. We also see cultivated meat. How is the landscape changing or the technology evolving? What are you seeing among your different customers?

Tibor Anderlei [00:08:59]:
For me it’s a little bit easier, I would say, because at the shake flask level I do not see so many differences. All the new modalities you mentioned have one thing in common: they are more shear-sensitive than, for example, bacteria or CHO cells. Orbital shaken bioreactors are very suitable for shear-sensitive cells or systems. The main reason is that they are surface-aerated, meaning we have nearly no bubbles. Bubbles rise, burst, and create very high local power input when they burst, which can damage the cells. So I do not see major differences at the shake flask scale. Furthermore, real-time monitoring is always beneficial. When establishing a new biological system in the lab, you can analyze and optimize screening or cultivation conditions much faster. Online data also helps reduce the number of offline samples. You take samples at points of interest—for example, when an online signal like OTR shows a dip—so fewer samples mean less analysis time and lower costs.

You also mentioned the cultivated meat field. Here too, I do not see major differences at small scale. However, the food industry is very price-sensitive, especially regarding media and production equipment. Therefore, significant effort is focused on developing cost-effective media. Due to time pressure, media testing should be parallelized, and in my opinion, shifted to microtiter plate scale very early. Investing in online technology at this stage can significantly accelerate development.

Because of cost sensitivity, expensive consumables such as specialized flasks or plates are not practical. That is why, when we developed systems like the CunaTOM or MicroTOM, we consistently use standard plates and standard shake flasks to keep operating costs low for the customer. I believe that is key in this field also.

David Brühlmann [00:11:45]:
Besides cultivation for cell culture processes, do you also see people using your systems for other applications we have not touched upon yet? Can they be used in different areas?

Tibor Anderlei [00:12:01]:
Oh yeah, we have a lot of different customers in that field. One area is mixing. When you use orbital shakers for mixing, you always work with a closed system. For example, a bag can remain closed, whereas if you use a stirrer, you need to open the system and insert it. So with a shaker, you can mix in a closed system, which is a major advantage. For instance, we have a customer—a large company in the Asian region—using our system for liquid crystal mixing, used in mobile phones, TVs, and similar applications. That is a completely different market.

We also increasingly see customers using our systems for storage. For example, fermentation broths containing cells often need to be stored while still being gently mixed. In some cases, this is done manually in cold rooms by shaking bags, but that is not a controlled or defined process. Here, our systems provide a defined and reproducible way to handle such applications. This also applies to thawing processes—for example, thawing fermentation broths—which must be done in a controlled manner. Our systems are also widely used in these contexts.

David Brühlmann [00:13:28]:
That’s exciting, because it’s not what people initially think of when they hear about shaken bioreactors and microtiter plates. It shows how broad the applications really are.

Tibor Anderlei [00:13:40]:
Yes, definitely.

David Brühlmann [00:13:42]:
I would like to circle back to your entrepreneurial experience. We discussed this at the beginning of our conversation—you founded AC Biotec and have now been with Kühner for two decades. I’d be interested in your perspective. At Kühner, you are competing with larger players in the field, such as Sartorius, Cytiva, and Thermo Fisher. What have you learned as an entrepreneur and leader to not only survive but thrive in such a dynamic market?

Tibor Anderlei [00:14:20]:
That is a combination of questions. First of all, yes, we are competing with companies like Sartorius, Cytiva, and Thermo Fisher. As Kühner, we must be innovative and agile, and we must stay very close to our customers. I think that is something we do quite well. On the one hand, these are competitors, but on the other hand, they are also customers, as they have acquired companies that were already working with us. So there is always a dual relationship.

I also believe that pharmaceutical and biotech companies benefit from maintaining flexibility and independence in their supplier landscape. This creates opportunities for smaller and mid-sized companies like ours to compete with global players. In that sense, recent events such as the COVID-19 pandemic have reinforced the importance of supply chain diversity and resilience.

David Brühlmann [00:15:35]:
At least dual sourcing is a pretty good idea. This leads me to the next question, because I would love to hear about your leadership experience and understand what your most important leadership lesson is that you have learned about building successful technical organizations in biotech.

Tibor Anderlei [00:15:57]:
Okay. Of course, I had experience with a startup, and then maybe I’m boring because I went to another company, Kühner Shaker, and I have been there for 20 years. From my experience, when you launch a company, you should always have a product idea in mind. Being only a service provider in the beginning is good to generate faster cash flow, which is needed, but you should also use that time to develop a product.

A second thing I would say is that you should learn to trust your gut feeling. Of course, you have to analyze as much as possible before making a decision, but you cannot analyze everything—that’s not possible. And in many cases, a complete analysis takes a long time and does not significantly change the final decision.

Third, I would say that I initially underestimated the importance of personal chemistry between business partners. A good relationship between partners is a very important factor for successful collaboration and trust, which is also very important to me. In general, I’m very glad to be working in the field of biotechnology, because you nearly always work with very nice people.

David Brühlmann [00:17:38]:
Yes, I agree—biotech is a great place to work. I’ve met many great people throughout my career.

Tibor Anderlei [00:17:46]:
Definitely.

David Brühlmann [00:17:47]:
As we are wrapping up, Tibor, I’d like to make this actionable for the Smart Biotech Scientist listeners. What is one piece of advice you would give them if they are starting out using microtiter plates or shake flasks, or trying to make these systems work well?

Tibor Anderlei [00:18:09]:
You know I like shaking diameter—that is one important aspect. But more generally, I would say: recognize the importance of shaken bioreactors and define your screening conditions very carefully. I would also strongly recommend using online measurement tools even at small scale. At larger scales, online monitoring is common, but at small scale it is still underutilized.

David Brühlmann [00:18:39]:
Fantastic. Before we wrap up, Tibor—what is one question I haven’t asked that you would like to share with the biotech community?

Tibor Anderlei [00:18:48]:
I think you already covered many important topics. Maybe I can leave one key takeaway: when shaken bioreactors such as shake flasks, tubes, or microtiter plates are applied correctly, they provide an easy-to-handle, inexpensive, automatable tool with low running costs and scalable results.

I believe knowledge at small scale is critical, and this topic should also be taught more at universities. We also offer a webinar series on this topic, where my colleague David Flitsch explains over several sessions how to properly handle microtiter plates, tubes, and shake flasks.

David Brühlmann [00:19:57]:
There you have it—Smart Biotech Scientist, a great takeaway. Thank you, Tibor, for highlighting how shaken bioreactor systems can be such a powerful tool. Where can people connect with you and access your resources?

Tibor Anderlei [00:20:16]:
You can reach me via LinkedIn, and you can also meet me and my team at conferences and trade fairs. Our booth features rings in the logo, representing orbital motion—since we focus on orbital shaking. LinkedIn is probably the easiest way to connect.

David Brühlmann [00:20:44]:
Fantastic. I’ll include the links in the show notes, so please take the opportunity to reach out to Tibor and his team. Tibor, thank you again for sharing your expertise, passion, and practical insights.

Tibor Anderlei [00:21:04]:
Thank you very much, David. I’m looking forward to the next podcast.

David Brühlmann [00:21:14]:
Tibor Anderlei’s combination of scientific rigor, entrepreneurial experience, and customer-facing work makes him a rare voice in this space. Whether you’re troubleshooting scale-up or preparing a CDMO transfer, today’s conversation provides a valuable framework.

Thanks for listening to the Smart Biotech Scientist Podcast. If this episode was useful, please leave a review on Apple Podcasts or your favorite platform and share it with a colleague. Stay tuned for more biotech insights in our next episode. Until then, let’s continue to smarten up biotech.

Disclaimer: This transcript was generated with the assistance of artificial intelligence. While efforts have been made to ensure accuracy, it may contain errors, omissions, or misinterpretations. The text has been lightly edited and optimized for readability and flow. Please do not rely on it as a verbatim record.

Next Step

Book a free consultation to help you get started on any questions you may have about bioprocess development: https://bruehlmann-consulting.com/call

About Tibor Anderlei

Tibor Anderlei is a passionate advocate for improving how bioprocess development begins—at the small scale. With a career spanning academic research, startup innovation, and industry leadership, he focuses on the often-overlooked role of shake flasks and orbital shaken bioreactors in critical early decisions. 

He works to raise awareness of their importance in education and industry, helping teams build more reliable and scalable bioprocesses from the start.

Connect with Tibor Anderlei on LinkedIn.

Further Listening

If you’re interested in this topic, check out these episodes on building a robust scale-up strategy. To get it right, you need to view the process from multiple angles—regulatory, digital, and operational.

Episode 03 - 04: How to Master Biotech Scale-up Without Guesswork with Leonardo Sibilio

Episode 25 - 26: 9 Critical Steps for a Seamless Transition to Large-Scale Production

Episode 231-232: From IND to BLA: The Biologics CMC Decisions That Determine Regulatory Success with Henri Kornmann

Episode 233-234: Why Most Bioprocess Automation Projects Fail with Anthony Catacchio

Episode 237-238: High-Throughput Microbial Screening with Sebastian Blum

Smart Biotech Scientist Toolkit

Below, you’ll find a curated collection of resources shared by our guest.

• Shaking Technology Forum, supported by Kühner Shaker.
• Shaking Technology LinkedIn Group: for users, researcher & biotechnology students
• Kühner Seminars and Trainings
• OTR calculator: Determine the maximum oxygen supply

He is also a biotech technology innovation coach, technology transfer leader, and host of the Smart Biotech Scientist podcast—the go-to podcast for biotech scientists who want to master biopharma CMC development and biomanufacturing.  

Hear It From The Horse’s Mouth

Want to listen to the full interview? Go to Smart Biotech Scientist Podcast. 

Want to hear more? Do visit the podcast page and check out other episodes. 
Do you wish to simplify your biologics drug development project? Contact Us