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28 October 2026 | Volume 21, Issue 2

Y-ECCO Interview Corner: Juozas Kupčinskas

Written by
Florian Tran

Y-ECCO Committee Member

Ask any gastroenterologist in Europe to name a leading voice in IBD and microscopic colitis research, and the name Juozas Kupčinskas quickly comes up. Head of the Department of Gastroenterology and Vice Rector for Research at the Lithuanian University of Health Sciences (LSMU) in Kaunas, Juozas has built one of the most versatile research profiles in the field, spanning IBD, microscopic colitis, genetics and the gut microbiome. He now brings that breadth of experience to ECCO's newly formed Working Group for Microscopic Colitis.
We sat down with Juozas for this edition of the Y-ECCO Interview Corner to talk in vitro models, faecal transplants and what he'd tell his younger self.

What first drew you to gastroenterology, and was there a particular moment or mentor that influenced your decision to pursue an academic career?

Portrait of Juozas Kupčinskas

Juozas Kupčinskas © ECCO

Very early on I learned to understand that gastroenterology is a very wide and versatile specialisation that allows you to combine clinical work, manual skills and research. Management of patients with gastrointestinal diseases like IBD can be very rewarding but at the same time there are a lot of unmet needs and potential areas for research. This unique combination sparked my curiosity. I must admit that I was also influenced by my family environment since my father is a gastroenterologist and he has always been a role model for me as a clinician and a researcher.

Looking back at your training and early career, what experience had the greatest impact in shaping you as a clinician-scientist?

I was exposed to the research environment very early in my life. As mentioned above, my father is a professor of gastroenterology, and my mom is a professor of biology. I remember that at the age of 15 years I was already spending time in my mom's lab working with her plant specimens, helping with molecular analysis and reviewing her scientific papers. Then later in my career I met a lot of excellent international mentors, including Professor Peter Malfertheiner, Professor Stephen Schreiber and many others who gave me insights into the fascinating life of a clinician-scientist, which is not easy but at the same time is very rewarding. I am also grateful to ECCO and the European Helicobacter and Microbiota Study Group, which provided an excellent networking environment for me as a young researcher.

Your research spans IBD, microscopic colitis, genetics and the gut microbiome. What scientific question currently excites you the most, and why?

I think the beauty lies in the complexity of these diseases. Using advanced omics technologies and large patient cohorts, the IBD Research Community has identified many interesting signals. The next step now is to delineate their actual role. At our Institute of Digestive Research at the Lithuanian University of Health Sciences in Kaunas we are focusing on patient-derived IBD organoid technologies. This platform allows us to capitalise on different omics hits and bring them to personalised organoid testing platforms. These experiments currently include bacteria-derived metabolites, bacterial cell wall components, food metabolites, novel therapies and other substances that we are testing under the Horizon Europe MiGut-Health project as well as contracted research. We hope that these approaches can lead to certain translatable solutions for IBD patients in the longer run.

We are seeing enormous interest in microbiome-based therapies, including faecal microbiota transplantation. Which developments do you believe are most likely to change clinical practice in the coming years, and which expectations may currently be overestimated?

We have seen very rapid and enormous success of faecal microbiota transplantation for the management of patients with refractory Clostridioides difficile infection. Clinicians expected that we would immediately be able to transfer FMT to IBD and other complex disorders; however, this approach has largely failed. I think that the future of microbiome therapeutics is great, but we are at the very early phases of it. The major breakthroughs will come through targeted bacteria-derived metabolite therapies, phage therapies or predefined consortia of bacteria that are already in clinical trials in different clinical settings. We are trying to implement some of these approaches in another Horizon Europe-funded project, PerPrev-Cid, together with the University of Kiel and other international partners.

Microscopic Colitis is increasingly recognised as an important cause of chronic diarrhoea, yet many unanswered questions remain. What do you see as the most important research priorities for the field over the next decade?

I am very happy that ECCO has decided to create a Working Group on Microscopic Colitis and I’m grateful that I had a chance to join it. I have been involved in Microscopic Colitis research for the last ten years, including clinical trials, clinical registries and basic research. I think that microscopic colitis clearly belongs to the spectrum of IBD. While classic IBD has received a lot of coverage in terms of basic/omics research, microscopic colitis needs much more of that in the future. We are currently running several wet lab studies looking at the microbiomes and immunity, trying to understand the underlying mechanisms in microscopic colitis.

In addition to leading a busy gastroenterology department, you serve as Vice Rector for Research at LSMU. What have you learned about leadership, and how do you build an environment that enables young researchers to thrive?

It is a real challenge to combine research and administrative tasks but I'm very happy to have strong teams around me, which makes this combination possible. I think that the main conditions for which researchers should strive are collaboration, international exposure, less bureaucracy and flat leadership. This is what we're trying to implement at our institution now.

Many young clinicians aspire to combine clinical work, research and international collaboration. What advice would you give to someone at the beginning of this journey?


First, you need a strong and devoted mentor who is prepared to guide you during the early days of your research. I also think that you need to dive deeply into a specific area or research niche in order to be successful. Thirdly, I would strongly recommend international research exposure early in your career; this can be achieved through a PhD, internships or postdoc positions at excellence centres abroad, all of which help in creating networks and friendships. Lastly, I would strongly advise all clinicians who are considering a clinician-scientist research pathway to spend some time in the wet labs—this will enormously enhance your chances of doing impactful translational research.

Finally, if you could give one piece of advice to your younger self at the start of your career, what would it be?

If I could go back, I would spend even more time doing a research sabbatical abroad.

Thank you, Juozas, for such a candid and energising conversation and for the reminder that behind every "unmet need" in IBD research is an opportunity waiting to be seized.