Fighting infections with the power of the microbiome

A balanced gut microbiome not only contributes to digestion, but is also an important protective factor against infections.

Researchers at the Helmholtz Centre for Infection Research (HZI) led by Prof. Till Strowig, scientist in the German Center for Infection Research (DZIF), want to harness the power of the microbiome to prevent serious infections. 

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They have discovered that bacteria of the species Klebsiella oxytoca can displace pathogenic bacteria from the gut and want to develop a living biotherapeutic based on this finding. The DZIF is now providing 2.2 million euros in funding for product development until the first tests on humans.

Disrupted balance

The balance of the hundreds of different types of bacteria in the gut can be disrupted by broad-spectrum antibiotics. The protective microbiome can then become a source of infection if pathogenic bacteria colonize niches that have become vacant.

“Many infections throughout the body start in the gut. Pathogenic bacteria can form a reservoir there and spread to other organs. For the first time, we want to create a way to eliminate this reservoir before an infection develops by ridding the gut of harmful bacteria,” says Dr Lisa Osbelt-Block, project leader and DZIF scientist who is working as a postdoc in Till Strowig’s department.

“Instead of developing new antimicrobial substances - which are also indispensable, but always damage parts of the microbiome - we are pursuing a microbiome-based approach.”

Displacing pathogens

In laboratory tests and mouse models, the researchers were able to show that Klebsiella oxytoca can displace various pathogens, such as Salmonella and Klebsiella pneumoniae, from the intestine. Klebsiella pneumoniae alone causes around 800,000 deaths every year, and the pathogen is increasingly resistant to common antibiotics.

On the one hand, K. oxytoca targets the same nutrients as the pathogenic bacteria. On the other hand, K. oxytoca alters the gut environment in such a way that the community of beneficial bacteria can recover. This restores the balance in the microbiome.

From the lab bench to the capsule

“A major challenge is that we are developing a living biotherapeutic (LBP),” says Prof. Till Strowig, head of the HZI department “Microbial Immune Regulation”, where the project was developed under the name DeKox.

“Unlike probiotics, which are freely available for sale, an LBP is a drug and must be clinically tested and approved as such,” adds Strowig, who is also a group leader in the DZIF research areas “Healthcare-Associated Infections” and “Community-Acquired Infections at Mucosal Interfaces” as well as coordinator of the DZIF bridging topic “Microbiome”.

With the help of funding from the DZIF FlexFund, the scientists aim to initially identify the best product candidates for further development. They are also developing processes for the production and quality control of their product.

“Our goal is to eventually have a capsule in our hands that contains the freeze-dried bacteria instead of an antibiotic active ingredient. We would then enter the first phase of a clinical trial,” says Osbelt-Block, explaining the aim of the project. In particular, patients with persistent K. pneumoniae colonization due to immunodeficiency may be treated with the LBP later.

Clinical partners

On the clinical side, the HZI team is working closely with the “Clinical Microbiome Research” research group headed by DZIF scientist Prof. Maria Vehreschild at the University Hospital of Cologne. Vehreschild, an infectious disease specialist, specialized in the research and development of microbiome-based therapies. 

Prof. Katharina Schaufler, head of the department “Epidemiology and Ecology of Antimicrobial Resistance” at the HZI site Helmholtz Institute for One Health (HIOH), is also involved in the project and will conduct virulence tests on the product candidates to demonstrate their safety.

Josef Penninger, Scientific Director of the HZI, is impressed by the development of the project: “DeKox is emblematic of the translational approach that we want to pursue at the HZI. Within a very short time, the project has developed from a basic research question to the preparation of a clinical study! I congratulate all colleagues involved on the DZIF funding and wish them continued success.”

The development of DeKox to date has been supported by the GO-Bio initial initiative of the Federal Ministry of Research, Technology and Space (BMFTR), by the HZI translation fund and by Helmholtz innovation programs. As part of the Helmholtz Enterprise spin-off program, the team is aiming to eventually spin off its project under the name “Arvalus Therapeutics”. The DZIF funding started on August 1, 2025, and runs for 40 months.