The gut microbiota is linked to so many aspects of our health, and several studies have shown an imbalanced gut microbiota, also called dysbiosis, in conjunction with various non-communicable diseases such as obesity, diabetes, cardiovascular diseases and irritable bowel disease.

It is known that a diverse diet is best for gut health and promotes a balanced gut microbiota composition. In line with this, the Mediterranean diet seems to be the most beneficial compared to restrictive diets such as vegan, ketogenic, gluten free and low FODMAP diets, as well as the modern western diet. This is because the Mediterranean diet includes foods that contain components that are beneficial for the gut microbiota. Moreover, long-term elimination diets such as gluten free and ketogenic diets have been shown to decrease bacterial diversity in the gut.

A review by Rinninella and colleagues, in Nutrients, discusses new research about how certain diets, as well as food components and additives, affect the gut microbiota composition and pinpoints the following food components that play an important role:


Prebiotics are a type of fiber that serve as food for beneficial bacteria that can also produce beneficial short chain fatty acids (SCFA). Butyrate for example, is a SCFA that plays a major role in maintaining proper intestinal barrier and immune function.


Even though the gut microbiota can synthesize various B vitamins and vitamin K, other micronutrients consumed through the diet can also affect the gut microbiota’s composition.

For example, vitamin D can positively affects gut microbiota composition by increasing beneficial bacteria such as Lacnobacterium, which has been associated with modulating the immune response and asthma and allergic disease incidence.

The gut microbiome has also been found to play a role in beta carotene synthesis which thus regulates its antioxidant effects.

On the other hand, although sufficient levels of iron and zinc support physiological processes impacting gut microbiota, an excess amount of these minerals seems to promote the colonization of pathogenic bacteria in the gut, such as Clostridium difficile.


Besides vitamins and minerals, polyphenols found in thousands of plant foods such as fruits, vegetables, herbs, and cacao, promote a greater abundance of beneficial bacteria, and some polyphenols also exert prebiotic activity. Additionally, gut bacteria also increase the bioavailability of the beneficial polyphenols so they can exert their health benefits.

Essential fatty acids

Omega 3: These polyunsaturated fats are found primarily in fatty fish and have been found to increase the levels of beneficial bacteria that produce anti-inflammatory compounds and butyrate.

Omega 9: These monounsaturated fatty acids are for example, found in extra virgin olive oil, a staple of the Mediterranean diet. They do not seem to have an impact on diversity or richness, in particular between Bacteroidetes and Firmicutes ratio, but they do seem to have an impact at the genera level (in particular bacteria from the genera Parabacteroides, Prevotella, and Turicibacter).


Conclusion and Take Away

Unsurprisingly, eating a diet high in fiber, fruits and vegetables promotes a healthy gut and gut microbiota composition. Consuming a Western diet which is high in sugar, fat, salt and food additives can cause a decrease in beneficial bacteria which could increase intestinal permeability and inflammation.

Compared to restrictive and elimination diets, the Mediterranean diet appears to be the gold standard for supporting a healthy gut microbiota composition because it includes a balance between all food groups. Sticking to a non-restrictive diet that includes a variety of whole foods that are rich in fibre and nutrients is more important than focusing on a single nutrient for gut microbiota and overall health. In the future, microbiome analyses could determine personalized nutrition decisions in order to optimize gut and overall health.


Reference: Rinninella E. et al. Food components and dietary habits: Keys for a healthy gut microbiota composition. Nutrients; 2019: 11, 2393; doi:10.3390/nu11102393