Various foods can trigger bacteriophage production, modulate the abundance of gut microbiota, and produce an antimicrobial effect, a study published in Gut Microbes suggests. Specific compounds in these foods, according to the study, may require further investigation to understand their role in suppressing harmful microbes and maintaining bacterial diversity in the microbiome.

Researchers tested the responses of 3 common gut bacteria species (Bacteroides thetaiotaomicron, Enterococcus faecalis, and Staphylococcus aureus) to 117 commonly consumed foods. Hot sauce, glycolic acid, toothpaste, citric acid, and vinegar held the strongest bactericidal effects. In most cases, antibacterial effects were shown with cinnamon, neem, licorice, and clove. In addition, antibacterial effects were demonstrated with coffee, stevia, and aspartame. Prebiotic effects were shown with cayenne, miso, cottage cheese, and fish sauce.

Foods and food products that most strongly induced phage production were honey, stevia, uva ursi, neem, and aspartame. The strongest inductor of B thetaiotaomicron was stevia, which correlated with a 410% increase in virus-like particles. In B thetaiotaomicron, propolis and clove also increased the number of virus-like particles by +115% and +185%, respectively. For E faecalis, the highest inducer was uva ursi, with a +842% increase in virus-like particles. Stevia was the highest inducer for S aureus, with a corresponding +321% increase in virus-like particles.

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Investigators also found that several foods suppressed virus-like particle production in the different tested strains compared with control. In B thetaiotaomicron, foods that reduced production of virus-like particles included pomegranate (−89%), grapefruit seed extract (−89%), toothpaste (−88%), and cinnamon (−88%). In E faecalis, kombucha was associated with a reduction in virus-like particles by 44%. Compared with control, foods associated with reductions of virus-like particles in all bacterial species included rhubarb (−62%), Fernet (57%), coffee Arabica (−49%), and oregano (−44%).

One limitation of the study was the fact that 1 strain of each bacterial species was tested, which the researchers said may limit the generalizability of their findings to other strains for each species.

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“As these ingredients are consumed by populations around the world,” the researchers wrote, “these mechanisms could further our understanding of how particular foods shape gut microbiomes.”


Boling L, Cuevas DA, Grasis JA, et al. Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome [published online January 13, 2020]. Gut Microbes. doi:10.1080/19490976.2019.1701353