Almost every corner of modern medicine and sustainable food production today is facing a massive challenge: how do we outpace drug-resistant “superbugs” and create food for a growing population using fewer resources? The answer, it turns out, may come down to how well we understand and control the biomanufacturing processes underpinning these biomaterials and biomolecules.

In this episode of Smart Biotech Scientist Podcast, David Brühlmann speaks with Carmen Jungo Rhême, Full Professor at the University of Applied Sciences in Fribourg, Switzerland and Director of the Biofactory Competence Center.

With years in the pharmaceutical industry at Lonza, Merck Serono, UCB Farchim, and CSL Behring, she now tackles global challenges like antimicrobial resistance, sustainable food, and digitalization. From her beginnings in chemical engineering at EPFL to leading at the nexus of academia and industry, Carmen is helping shape the future of smarter, more robust biotech.

Key Topics Discussed

• Why antimicrobial resistance is seen as a top global challenge and the new therapeutic approaches being explored, such as phage therapy and endolysins.
• An inside look at collaborative projects between the Biofactory Competence Center and Lausanne’s University Hospital, focusing on phage therapy process development.
• Parallels and differences between recombinant protein production and phage manufacturing processes.
• The case for smarter, data-driven bioprocessing—including quality by design and risk assessment.
• The critical role of professional networks in advancing biotechnology research and careers.
• Sustainable food production strategies, such as cultivating microalgae on byproduct streams from the dairy industry and the future role of precision fermentation.
• Differences in innovation culture between industry, startups, and academia, and how academic freedom can drive creative research.

Episode Highlights

• Setting the stage: Antimicrobial resistance as a global health challenge [00:00:00]
• Guest introduction: Carmen’s experience and three big challenges her center tackles [00:01:09]
• Myths about bioprocess robustness and the need for comprehensive process characterization [00:03:28]
• Carmen’s career journey through biotech industry leaders to academia [00:05:01]
• Building and maintaining a valuable professional network [00:06:59]
• The interconnection between antimicrobial resistance, sustainable food, and digitalization [00:08:07]
• Making bioprocessing smarter: Quality by design in phage therapy development [00:09:58]
• Explaining phage therapy and its revival in modern medicine [00:12:09]
• Comparisons between recombinant protein and phage process platforms [00:14:35]
• Sustainable food production: valorizing whey permeate with microalgae, and precision fermentation [00:15:42]
• The unique opportunities for innovation in academic settings [00:17:20]

In Their Words

The emergence and spread of drug-resistant pathogens challenge our ability to treat common infections with existing antimicrobials such as antibiotics. The World Health Organization has identified antimicrobial resistance as one of the top global challenges for humanity in the coming decade. Currently, several approaches are being explored by the scientific community, including the development of new vaccines, monoclonal antibodies, phage therapy, and recombinant proteins like endolysins to combat difficult-to-treat bacteria. At the Biofactory Competence Center, we are collaborating with the University Hospital in Lausanne in the field of phage therapy.

Episode Transcript: From Biology Is Messy to Designable: The Smart Bioprocessing Transformation

David Brühlmann [00:00:56]:
Welcome back to the Smart Biotech Scientist. I’m your host, David Brühlmann, and today I’m thrilled to have Carmen Jungo Rhême with us. Carmen is a Full Professor at the University of Applied Sciences in Fribourg, Switzerland, and Director of the Biofactory Competence Center.

With years of experience mastering bioprocess challenges at Lonza, Merck Serono, UCB Farchim, and CSL Behring, she now tackles global challenges including antimicrobial resistance, sustainable food production, and digitalization. From fighting superbugs to revolutionizing scalable process development, Carmen’s insights will change the way you think about the future of biotech.

Welcome, Carmen, to the Smart Biotech Scientist.

Carmen Jungo Rhême [00:03:08]:
Hello David, it’s great to see you and to be here talking with you.

David Brühlmann [00:03:12]:
It’s a pleasure, Carmen. We’ve been planning this interview for a while, and now it’s finally happening. To start, could you share something you believe about bioprocess development that most people might disagree with?

Carmen Jungo Rhême [00:03:28]:
Many people perceive bioprocessing as highly uncertain and lacking robustness. However, when bioprocesses are thoroughly characterized—meaning they are well understood and effectively controlled—they can be extremely robust. A typical bioprocess includes both upstream and downstream parameters, sometimes managing over 200 variables. This complexity highlights the need for comprehensive process characterization, which I believe is essential for enhancing robustness and minimizing variability.

David Brühlmann [00:04:16]:
Absolutely. I couldn’t agree more. That’s very well said, Carmen. We have several things in common and I actually I still remember that many, many years ago when we started studying chemical engineering at the EPFL in Lausanne, Switzerland, we met already at that time and then later on in our career our path have crossed several times again. But actually I'm getting ahead of the story. I would like you to draw us into the story. Tell us Carmen, how you first got started in the recombinant protein world and what were some interesting pit stops along the way that led you to now your role as a professor and leading the Biofactory Competence Center?

Carmen Jungo Rhême [00:05:01]:
Yes, I remember first of all when we were studying at EPFL, and I really remember the first day I saw you attending the classes. I would not have imagined at that time that we would also work in the same company, actually at Merck Serono, and especially that we would stay in contact. It’s really a pleasure.

So how did I arrive at the BCC? First of all, I would like to mention that during my studies at EPFL, I studied chemical engineering. I was inspired by the elegance of recombinant proteins—how you can take a gene, express it in a host cell, and produce something with therapeutic or industrial value.

Then my journey through companies like Lonza, Merck Serono, UCB Farchim, and CSL Behring was key before joining the Biofactory Competence Center. For example, at Lonza, I was immersed in the world of large-scale recombinant protein production, learning how to transfer and scale up from lab scale to manufacturing scale. At Merck Serono and UCB Farchim, I continued to strengthen my know-how in technology transfer, scale-up, and starting up new facilities. Finally, at CSL Behring, I expanded my experience in R&D.

What is also important is that I was able to develop a network in the pharma industry before joining academia. I think this is key—to have industry contacts to initiate projects and to stay aware of what’s happening in the field. At the BCC, I can continue to innovate in collaboration with industrial partners, and I can also share my experience with students, who represent the next generation of pharmaceutical scientists.

David Brühlmann [00:06:59]:
You make an excellent point, Carmen. Obviously, along our careers we learn a lot about science, but it’s not only about science—it’s really about developing a network. And I think especially at the stage we are in our respective careers, the network becomes increasingly important for collaborations, research projects, and so on. So if you’re listening and taking notes, Smart Biotech Scientist, put this at the top of your list: develop a network. That’s very important.

Carmen Jungo Rhême [00:07:32]:
Yes, I completely agree with you. That’s really key for your career—to develop a strong network. And often, when you have a question or a bigger challenge, you will go back to your network, and maybe someone will help you. You can do a lot of things with your network.

David Brühlmann [00:07:49]:
And I’ve heard some people say that your network is your net worth.

Carmen Jungo Rhême [00:07:54]:
Yes, I think that’s true.

David Brühlmann [00:07:58]:
Carmen, you are now tackling three massive challenges. Tell us what they are and what the common denominator between these is.

Carmen Jungo Rhême [00:08:07]:
I would say the three massive challenges at BCC are, first of all, antimicrobial resistance, sustainable food production, and digitalization. At first glance, these three topics might seem like separate challenges, but they are connected by a common factor: the need for smarter bioprocesses.

Antimicrobial resistance pushes us to rethink how we manage microbes—not just in medicine, but also in agriculture and food production. Secondly, sustainable food production demands that we use fewer resources, reduce waste, and maintain safety, all of which benefit from precise biological control. And third, digitalization is the enabler that ties it all together. By collecting and analyzing data from bioprocesses, we can better understand complex systems, predict outcomes, and make faster, more informed decisions. The common thread connecting these three topics is innovation at the intersection of biology and technology to develop smarter bioprocesses.

David Brühlmann [00:09:31]:
So let’s unpack this. How do we make bioprocessing smarter? I love that phrase because that’s the title of the podcast—Smart Biotech Scientist. So that’s excellent. Let’s start with antimicrobial resistance, because I think many of the listeners are not familiar with the challenges. And actually, how does a bioprocess look like to fight these “superbugs”? How does that work?

Carmen Jungo Rhême [00:09:58]:
First of all, it’s important to mention that the emergence and spread of drug-resistant pathogens challenges our ability to treat common infections with existing antimicrobials such as antibiotics. The World Health Organization lists antimicrobial resistance as one of the top challenges for humanity in the next decade.

Currently, several approaches are being explored by the scientific community. For example, the development of new vaccines, monoclonal antibodies, phage therapy, and also the use of recombinant proteins like endolysins to fight difficult-to-treat bacteria.

At the Biofactory Competence Center, we are working in collaboration with CHUV, the University Hospital in Lausanne, in the field of phage therapy. More precisely, we are collaborating with Dr. Grégory Rech from CHUV, who has been working in this area for more than 20 years, and with Dr. Jean-François Brunet from the Centre de Production Cellulaire in Épalinges, also part of CHUV.

They have the first GMP manufacturing line in Switzerland for the production and purification of phages, and they have already started to test it on patients. We are working in collaboration with CHUV, have transferred their process to BCC, and are now performing a full characterization using a Quality by Design approach. This is very important when we talk about smarter bioprocesses—it’s critical to have a complete understanding of the process. Of course, you know all the process steps, but it’s very important to list all the process variables, including process parameters and material attributes, such as raw materials, chemicals, and filters.

We conducted a full risk assessment on each process variable to categorize them as critical or non-critical—for example, regarding product quality or yield. After this assessment, we are now characterizing the key and critical process parameters, collecting data to achieve full process characterization. Of course, this is already standard practice in industry for recombinant protein production, and we are now applying it to a phage production process.

Maybe I can also say a few words about bacteriophages for people who are not familiar. Bacteriophages are viruses that specifically infect and kill bacteria. For each bacterium, there is a specific bacteriophage in nature. They exist naturally all over the planet—they can be found in water, soil, and other environments—and were actually used to treat bacterial infections at the beginning of the 20th century. They were discovered in 1917, while antibiotics were discovered in 1928.

However, their use declined in favor of antibiotics after World War II, because antibiotics were easier to use. Some countries, like Georgia, Poland, and others in the former Soviet Union, continued to use phages because they didn’t always have access to antibiotics. In the last two decades, there has been renewed interest in phage therapy in Europe, the US, and other countries.

We are very proud to develop an innovative process and contribute to its characterization in collaboration with CHUV. Recently, we also started addressing phage formulation through lyophilization, because currently most formulations are stored in liquid form. Lyophilized formulations offer advantages for stability and storage.

David Brühlmann [00:14:15]:
That’s excellent. You’re making a big difference—solving a major problem for humanity. Looking at the production process itself, how does it differ from more established processes, such as mammalian cell culture or E. coli fermentation? Is it similar or very different?

Carmen Jungo Rhême [00:14:35]:
It’s actually very similar. In a process for recombinant protein expression, you have an upstream phase for expression, followed by purification and final formulation. The production and purification of bacteriophages is very similar. The same technologies are used: first, you grow the host bacteria, then add the corresponding phage to amplify it. After harvest, you have a clarification step, followed by purification steps, which are very similar to recombinant protein purification. So the expertise and technologies are very similar.

David Brühlmann [00:15:28]:
And now moving on to your second area, sustainable food production, which has some similarities but also differences. Tell us a bit about what you’re doing there, and how it ties back to digital transformation.

Carmen Jungo Rhême [00:15:42]:
Yes, as you said, we are also working on sustainable food production in the food sector. For example, we work on the valorization of whey permeate by cultivating microalgae on a whey-permeate-based medium. It’s important to mention that there is a lot of whey permeate in Switzerland, thanks to the cheese industry.

We also have experience producing recombinant proteins through precision fermentation using Pichia pastoris. Returning to microalgae, there is huge potential in cultivating microalgae for the sustainable production of proteins and lipids for the food industry. We can grow microalgae to produce specific proteins or lipids, then extract and purify them. I think we are only at the beginning of a major change in the food industry. More and more, food waste will be transformed into high-value nutrients using microalgae, bacteria, yeasts, or even fungi.

David Brühlmann [00:16:59]:
That’s excellent. Now, in academia, I imagine you have a bit more freedom than we would in the corporate world or even in the startup world. Well, in startups, you have freedom, but sometimes you don’t have the resources to fully explore. So what myth or challenge would you like to tackle in your current role?

Carmen Jungo Rhême [00:17:20]:
In bioprocessing, we have more freedom than in industry, so we can be more creative and sometimes explore ideas that we don’t know will work. I think that’s the main difference. We also have projects with our students where there isn’t necessarily a client behind them. When students work on a project, we have complete freedom, and sometimes we take the time to assess more possibilities and just explore.

I think that’s the main difference with startups or industry, where you have to be fast and results are expected in a short time. In academia, with bachelor or master projects that aren’t linked to an industry client, we have the freedom to test new technologies. Sometimes companies also come to us needing data to test prototype equipment, and this is something we can do more freely than in industry.

David Brühlmann [00:18:28]:
And that concludes part one with Carmen Jungo Rhême—from her industry journey to tackling antimicrobial resistance and sustainable food production. In part two, we’ll dive into the Biofactory Competence Center’s game-changing approach to process development and training.

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.

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About Carmen Jungo Rhême

Carmen Jungo Rhême is full professor at the Haute Ecole d’Ingénierie et d’Architecture de Fribourg (HEIA-FR) and Director of the Biofactory Competence Center (BCC). She has extensive experience (17 years) in the pharmaceutical industry with a proven track record in several biopharmaceutical companies manufacturing therapeutic recombinant proteins (Lonza, Merck Serono, UCB Farchim and CSL Behring). 

She specialized in bioprocess development, both in cell culture and in purification of proteins, scale-up, and technology transfer of marked products. Since her start at HEIA-FR in November 2023, C. Jungo Rhême has initiated several research projects in the field of antimicrobial resistance, one of them in the field of antimicrobial resistance, sustainable food production, and digitalization of bioprocesses.

Connect with Carmen Jungo Rhême on LinkedIn.

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

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