Recent research published in Applied and Environmental Microbiology by Milani et al. (2025) has unveiled compelling insights into how bacteria found in cheese can actively modulate the human gut microbiome. The findings highlight a new dimension of functional foods—particularly fermented dairy—showing that cheese is more than just a nutrient-dense food; it is also a microbial vehicle with potential health-promoting benefits.

Key Takeaways:

1. Cheese as a Vector for Functional Microbes

While cheese is already valued for its flavour, nutrition, and heritage, this study shows it also serves as a vehicle for live bacteria that can colonize and influence the gut microbiome. Importantly, the bacteria that drive this change are not the dominant ones typically associated with cheese (like Lactobacillus or Streptococcus) but rather the lesser-known, low-abundance species such as Hafnia, Clostridium, Enterococcus, and Bacillus.

2. Beyond Probiotics: Functional Contributions of Cheese Microbiota

Using a sophisticated simulated gut environment and multi-omics techniques, the researchers found that these minor cheese microbes actively express genes involved in the production of:

• Short-chain fatty acids (SCFAs)
• Vitamins (e.g., folate, riboflavin, biotin)
• Amino acids (e.g., arginine and glutamate)
• Antioxidants (e.g., glutathione)
  These compounds are known to contribute to metabolic health, immune modulation, and protection against pathogens.

3. Evidence of Microbial Transfer from Cheese to Humans

Through fecal sampling of cheese consumers, the study traced specific cheese-associated bacterial strains in the human gut. Most notably, Hafnia paralvei strain T10 was confirmed to survive gut conditions and express health-relevant metabolic genes. This validates the concept of horizontal microbial transmission from food to host—supporting a broader view of dietary microbes as functional symbionts.

4. Implications for Cheese Manufacturers and Functional Food Developers

The evidence suggests that raw milk cheeses and possibly selected cultured dairy products can be tailored or formulated to enhance their microbial contributions to gut health. This opens up new opportunities in:

• Designing cheeses with targeted microbial compositions
• Promoting the gut health benefits of traditional cheeses
• Collaborating on clinical studies for health claims

5. Why This Matters in Food Innovation

In a market increasingly driven by consumer interest in gut health and clean-label functional foods, cheese has untapped potential as a bioactive food matrix. This study offers a robust scientific basis for positioning artisanal and raw milk cheeses not only as gourmet foods but as natural contributors to microbiome diversity and human health.

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Full Credit
This blog is based on findings from:
Milani, C., Longhi, G., Alessandri, G., et al. (2025). Functional modulation of the human gut microbiome by bacteria vehicled by cheese. Applied and Environmental Microbiology, 91(3). https://doi.org/10.1128/aem.00180-25. This work is licensed under the Creative Commons Attribution 4.0 International License.