The great phage escape: How a breakthrough in dairy cultures could transform fermentation in dairy and beyond

As many dairy producers know, bacteriophages – otherwise known as ‘phages’, the viruses that infect bacteria – remain one of the most costly and disruptive challenges in manufacturing cheese, yogurt, and other fermented dairy products.

These viral infections require careful monitoring and management to prevent them from slowing or stalling fermentations, compromising quality, and sometimes even spoiling entire batches.

Our joint brand-new research demonstrates that phage mitigation involves not only controlling phages but also utilizing the natural defense systems of the bacteria themselves. Read on to find out why our results could transform dairy production and beyond.

A groundbreaking study from dsm-firmenich, APC Microbiome Ireland, and INRAE

Our scientists carried out this study in partnership with APC Microbiome Ireland, a world-leading Research Center at University College Cork, and the French National Research Institute for Agriculture, Food and Environment (INRAE).

Together, we discovered how Lactococcus lactis – the primary bacterial species used in dairy fermentation – uses newly identified defense systems to protect against phage infection.

Published in Proceedings of the National Academy of Sciences (PNAS), our research offers fresh insight into how these bacterial defenses function, how phages evolve to escape them, and how those adaptations are countered.

These discoveries create new opportunities to design more resilient cultures, create more secure fermentation conditions, and ultimately enable more consistent, efficient large-scale production of dairy and other foods.

Our discovery process: Mapping the bacterial anti-phage arsenal

In recent years, research has revealed that bacterial defenses against phages are far more diverse and complex than once imagined. Yet for many systems, the molecular details remained unknown.

For this study, we investigated 13 newly discovered resistance systems in Lactococcus lactis. These included Rhea, Kamadhenu, Rugutis, Audmula, PARIS, type II CBASS, Septu, and several abortive infection (Abi) families. We also analyzed 66 ‘escape’ phages to identify 15 viral genes involved in their evasion of the bacterial resistance systems. Our results revealed overlapping sensing mechanisms, modes of action, and vulnerabilities across the resistance systems, as well as unique features.

And one breakthrough finding was the defense mechanism of Audmula, one of the new defense systems. Unlike traditional abortive infection systems, which halt phage replication by inducing cell death, we found that this system modifies the bacterial cell wall, trapping phages inside. This prevents them from spreading throughout the fermentation.

This is the first time this mode of action has been observed. As such, the discovery greatly broadens the known spectrum of bacterial anti-phage defenses and opens new potential routes to improving dairy cultures’ resilience.

From discovery to dairy application

Together, these insights build a more complete picture of bacterial anti-phage defenses and how they interact with phages during dairy fermentation. This knowledge will enable dairy producers to strengthen culture performance – especially for cheese and other fermented dairy products – using:

• Phage-robust starter cultures designed with complementary defense systems
• Smarter rotation schemes that anticipate phage escape strategies
• Tailored solutions to protect yield and consistency across production environments

“We’re now finally beginning to understand how bacterial antiviral defenses function – and how viruses manage to evade them,” explains Prof. Douwe van Sinderen from APC Microbiome Ireland, senior author of the study. “In practical terms, these findings pave the way for next-generation starter cultures designed to withstand the phage challenges facing today’s dairy fermentations.”

Translating unparalleled science into real-world impact

These results clearly show how cutting-edge microbiology research can be translated into end-to-end solutions that address genuine industry challenges faced by producers.

As Dirk Lippits, Executive Vice President Ingredient Solutions, Taste Texture & Health, summarizes, “These findings demonstrate the power of combining our in-house scientific excellence with world-class research partnerships to solve real industry challenges. By applying these insights to our culture development, we’re adding to the unique depth and breadth of our dairy portfolio, and strengthening our ability to deliver more resilient and reliable fermentation performance for dairy producers worldwide.”

“By decoding the complex relationship between cultures and phages, we’re turning cutting-edge science into competitive advantage,” adds Noël van Peij, Principal Scientist at dsm-firmenich. “These findings empower us to develop highly-resilient cultures and enable producers to take control of fermentation – whether in dairy, plant-based products, or probiotic applications.”

Shaping the future of fermentation

While the immediate benefits of this work are clear for dairy, its implications reach further. A deeper understanding of bacterial antiviral systems could also advance biotechnology, probiotics, and biomedical innovation.

At dsm-firmenich, we are proud to be shaping the future. With more than 50 years of experience in microbial innovation and a strong record of industry partnerships, we continue to combine science, application, and collaboration to help producers deliver safe, sustainable, and consistently high-quality fermentation products – batch after batch.

To find out more about how new insight into anti-phage defenses could enable improved dairy cultures and more, read the full study – and learn more about our dairy solutions here.