Cheese isn't just food—it’s a microbiome booster, study confirms

By Tarun Sai LomteReviewed by Susha Cheriyedath, M.Sc.Mar 3 2025

Scientists reveal that cheese isn’t just a tasty treat—it’s a microbiome modulator! Hidden bacterial players in cheese could enhance gut function and support metabolic health.

Study: Functional modulation of the human gut microbiome by bacteria vehicled by cheese. Image Credit: George Dolgikh / Shutterstock

In a recent study published in the journal Applied and Environmental Microbiology, researchers investigated the impact of cheese on the functional potential and taxonomic composition of consumers' gut microbiota.

Diet is recognized as a primary driver shaping the gut microbial ecosystem. It also serves as a vehicle for transferring food-related microbes to the gut, where they proliferate, modulate the microbiota, and influence host health. Fermented foods, including yogurt and cheese, are among the most widely consumed dietary components. Specific lactic acid bacteria in cheese microbiota can be transiently transferred to the human gut, exerting positive effects such as pathogen inhibition, bioactive compound synthesis, and epithelial function modulation. While studies have explored the health effects of cheese intake, its impact on gut microbiota composition and functional potential remains poorly defined.

The Study and Findings

Researchers evaluated the effects of cheese intake on gut microbiota composition and functional potential using an in vitro gut environment-simulating medium (GESM). This medium lacks host-derived factors like immune interactions and competition with native gut microbes, a key limitation for real-world applicability.

Fifteen cheeses were cultivated in GESM for 16 hours, followed by DNA extraction and sequencing. The microbial composition changed drastically with GESM cultivation, reducing the abundance of dominant species while increasing certain accessory bacterial taxa. For example, Hafnia paralvei in a cheese sample (L3) increased from 0.08% to 86% after cultivation.

Researchers conducted RNA sequencing and hierarchical clustering, identifying three expression clusters (EXC1–EXC3), with EXC2 being the most prevalent. Functional analysis of these clusters revealed 62 enzyme-coding genes (ECGs) related to oxidative stress protection, short-chain fatty acid (SCFA) biosynthesis, and vitamin production.

A gene back-tracking analysis identified Clostridium butyricum, H. paralvei, and E. hormaechei as key taxa-enriched post-GESM cultivation. Importantly, these functions were redundantly encoded across multiple taxa, suggesting ecological resilience in gut functional modulation.

Metabolomic analysis using liquid chromatography-mass spectrometry identified 1,787 signals, with 142 showing significant changes post-GESM cultivation. Among these, 45 had identifiable compounds. Notably, reductions in sterol lipids, such as glycocholic acid (a bile acid metabolite linked to pathogen resistance), suggested that cheese bacteria may indirectly support gut health.

Cheese-Related Bacteria in Consumer Gut Microbiota

To investigate cheese-derived bacterial presence in human gut microbiota, researchers analyzed stool samples from 13 individuals consuming three specific cheeses (CC1–CC3). While H. paralvei was detected via metagenomic sequencing in only one consumer, highly sensitive qPCR assays identified it in all five CC1 consumers, highlighting challenges in detecting low-abundance strains through standard sequencing methods.

Further, RNA sequencing of H. paralvei T10 cultivated in GESM revealed high expression of genes involved in antioxidant capacity, amino acid biosynthesis, and SCFA metabolism. Metabolomic analysis showed significant changes in oligopeptide derivatives and glycerophospholipids.

Conclusions

The findings illustrate that less abundant bacteria in cheese microbiota play a crucial role in modulating gut microbiota function. These effects may arise from functional redundancy across multiple cheese-derived taxa (e.g., Clostridium, Enterobacter, Hafnia), collectively expanding gut metabolic capabilities.

The presence of H. paralvei T10 in the consumer's gut contributed to the production of metabolites influencing host-microbe and microbe-microbe interactions. While the study’s in vitro model provides mechanistic insights, future research in humans is needed to validate whether these bacteria persist and interact with native gut microbes in vivo.

Overall, the results underscore the significance of fermented foods in shaping gut microbiota and promoting human health.