What foods promote a balanced microbiota?

Over the course of our lives, we consume around 60 tons of food. ¹ To ensure proper digestion, this food takes a long trip through our digestive tract, which measures roughly 5 meters from mouth to anus. ² The purpose of this trip is to break the food down into tiny pieces that can be absorbed by the body to provide it with all the necessary nutrients—the small building blocks that power our muscles, fuel our brain, maintain our bones, and much more.

To facilitate absorption, our digestive system is not only very long, but it also has a very large surface area, thanks to numerous folds (much like corrugated cardboard). Laid out flat on the ground, the surface area of the digestive tract’s walls would cover between 32 m2 (roughly half the size of a badminton court) ² and 250-400 m2 (similar to that of a tennis court). ¹ 

Throughout its journey, the food being digested encounters the trillions of gut flora microorganisms inhabiting the space between the lumen of the digestive tract and the protective mucus lining the digestive tract walls. The size and composition of the microbiota vary according to the parts of the digestive tract, with the number of microorganisms increasing from the stomach to the anus. There are estimated to be ³: 

• fewer than 1,000 bacteria/mL in the stomach, an environment too acidic for many species; 
• millions of bacteria/mL in the small intestine, an acid- and oxygen-rich environment where transit is rapid. Here, bacteria adapted to these conditions (e.g., Lactobacillaceae) predominate, growing rapidly and capable of attaching to the walls; 
• billions of bacteria per gram of digestive contents in the colon, where bacteria capable of fermenting undigested fiber (e.g., Prevotellaceae) live in an oxygen-free environment. 

These microorganisms help us to survive (protecting us from pathogens, regulating our immune system, etc.) ¹, but also help us to digest our food. For example, we are unable to digest dietary fiber, which thus arrives intact in the colon. There it encounters bacteria which, unlike us, are able to digest it, i.e., to use it as a substrate for their own metabolism, and to convert it, in particular, into short-chain fatty acids.
Our gut flora also provides us with essential nutrients, such as vitamins B12 or K, for example. ¹  

Our food isn’t sterile, and that’s a good thing. When we bite into an apple, a tomato, or any other fresh fruit or vegetable, we enrich our gut microbiota with bacteria and other microorganisms. Thus, biting into an apple introduces microorganisms beneficial to our health (bacteria, viruses, fungi), which temporarily colonize and enrich our gut microbiota. ⁵

Fermented foods, a source of good bacteria

Fermented foods are another source of bacteria and yeast. These foods include cheese, yogurt, kefir, and other fermented milk products, as well as fermented vegetables like sauerkraut, to mention just a few. If the foods are neither cooked nor pasteurized, the bacteria and yeasts stay alive, and can alter the composition of our gut microbiota, either temporarily (increasing immediately after consumption and then gradually decreasing), or even long-term, if the food is consumed regularly. ⁶

Because they are alive, the bacteria produce a wide variety of metabolites also found in the fermented foods in our diet, including: 

• organic acids (lactic acid in yogurt or pickles),
• bioactive peptides (bacteriocins in sauerkraut that inhibit competing pathogenic bacteria)
• and vitamins (vitamin K in nattō, i.e., Japanese fermented soybeans).

These bacterial metabolites can improve the functioning of our gut microbiota (strengthening the intestinal barrier, modulating inflammation, etc.), support our immune system, and provide health benefits for the host. ^6,7

Fermented Foods

Water also enriches our microbiota

Let’s not forget another major dietary source of microorganisms: what we drink. Bottled, tap, filtered, or well water: not all water is the same when it comes to chemical, mineral, and microbial composition, or the effect on our microbiota.

Do you mainly drink well water, which naturally contains more diverse microbial communities? If you do, your gut microbiota is likely to be more diverse than it would be if you drank tap, filtered, or bottled water. ⁸

Fiber to nourish our gut microbiota 

But food isn’t just a source of bacteria. It’s also a source of nutrients that feed these microorganisms. Foremost among these nutrients are the famous dietary fibers—carbohydrates our body can’t digest, but which our gut microbiota relishes. Resistant to digestion, dietary fibers eventually reach our large intestine, where they feed our bacteria. They come in a wide variety ⁹ and include :

• fermentable dietary fibers such as inulin (found in chicory or Jerusalem artichokes),
• pectin (apples, lemon peel),
• and galactooligosaccharides (breast milk, legumes),
• as well as non-fermentable fibers, such as resistant starch in grains. 

The fermentation of fermentable fibers by bacteria produces metabolites, including short-chain fatty acids (SCFAs) such as butyrate, which has remarkable properties:

• beneficial effects on the microbial community (e.g., inhibition of pathogens);
• improvement of gut barrier function (stimulation of proteins that help tighten the cells of the gut wall, thereby reducing gut permeability; stimulation of protective mucus production);
• and direct metabolic (e.g., on satiety) and immunological effects on the host. ¹⁰

Probiotics, prebiotics, and postbiotics to rebalance the microbiota  

If your diet is no longer adequate or rebalancing is necessary (e.g., following antibiotic treatment), your healthcare professional may give your microbiota a little boost by prescribing: 

• probiotic capsules containing live microorganisms beneficial to your health. Probiotics have different modes of action depending on the strain, and no specific beneficial effect can be generalized from one strain to another. 
• and/or prebiotics, which specifically “feed” certain beneficial microorganisms in the gut microbiota. Prebiotics are equivalent to dietary fibers. 
• and/or postbiotics, which include the beneficial small molecules produced by probiotics (such as SCFAs), as well as dead probiotics and their fragments. 

Since our diet also nourishes our gut microbiota, it plays a key role in gut microbiota composition. ^1,11 The more you feed bacteria the foods they like and know how to make use of, the more they proliferate at the expense of other microorganisms. There may also be cooperative relationships between bacteria, with the molecules produced by some serving as food for others. ¹

Much like a fingerprint, each individual harbors within their gut a specific combination of a few hundred bacterial species from among the approximately 3,000 species identified in the human digestive system to date. ^12,13

This microbiota is the result of years of development and rebalancing, beginning at birth, in which diet plays an essential role:

• breastfed infants develop a wide range of Bifidobacterium spp. strains beneficial to their digestion and health,
• whereas infants fed formula have a different, more diverse flora,
• and undernourished infants have an immature, imbalanced (dysbiotic) gut microbiota that harbors more pathogens. ^1,12,13

How is this possible? Breast milk, the gold standard for infant nutrition, contains not only microorganisms beneficial to the child’s health but also—and most importantly—prebiotics. These prebiotics, known as oligosaccharides, aren’t digested by the baby, but instead nourish and promote the growth of beneficial bifidobacteria. ^13,14  They thus shape the baby’s gut microbiota, with lifelong implications for health (immunity, etc.). ¹⁴

A different gut microbiota at every stage of life 

The microbiota continues to develop during early childhood.

• Between 4 months and 1 year of age, dietary diversification goes hand in hand with the arrival and establishment—or otherwise—of new microorganisms, and the decrease of others. African children who consume diets rich in fiber and starch have a more diverse microbiota which produces beneficial fatty acids, whereas Western diets low in fiber reduce diversity and levels of these protective fatty acids. ¹
• Between the ages of 1 and 3, the composition of this community continues to diversify.
• By ages 3 to 5, a child’s gut microbiota isn’t yet fully comparable to that of an adult, but begins to resemble it closely. ^12,15  
• In adulthood, our gut microbiota is diverse and is generally dominated by Firmicutes and Bacteroidetes.  
• Starting at age 70, gut microbiota composition can be affected by biological changes (e.g., poorer digestion), as well as changes in dietary habits, which are often less diverse. The result is a decline in gut microbiota diversity, including a decrease in bacteria such as the beneficial Bifidobacterium spp. ¹²

Skin, lungs, and vagina also influenced by diet 

However, it would be wrong to think that our diet only affects our gut microbiota. Through the gut flora, it may influence other microbiomes as well. Take, for example, our skin microbiota, with various common skin conditions, such as acne, atopic dermatitis, psoriasis, and rosacea, having been linked to gut dysbiosis. ^16,17  

In the case of acne ^17,18: 

• a diet high in sugar, common among adolescents in developed countries, may lead to an imbalance in the gut flora;  
• disrupted gut bacteria may produce molecules capable of entering the bloodstream, reaching the skin, and altering various skin functions (inflammation, cell proliferation, lipid metabolism, etc.), thereby indirectly causing dysbiosis of our skin microbiota; 
• this skin microbiota imbalance may result in an overproduction of sebum, oil, and skin cells, thereby promoting the development of acne.  

This appears to be a two-way process, with acne in turn affecting the composition of the gut microbiota. This may result in a vicious cycle. ¹⁸ Thus, the gut and the skin are closely linked via a communication channel known as the gut-skin axis. ¹⁷ 

The same is true of the lung microbiota, which is part of a two-way gut-lung axis:  

• the gut microbiota may contribute to lung diseases, with gut dysbiosis often going hand in hand with winter respiratory infections ¹⁹ or asthma ²⁰;  
• conversely, lung conditions may influence the composition of the gut microbiota. ¹⁹

Diet may also influence the urinary microbiota, with gut dysbiosis potentially increasing susceptibility to urinary tract infections, although some findings in this area appear contradictory. ²¹

The same is true for the vaginal microbiota: reduced consumption of alcohol and animal proteins, and a higher intake of linolenic acid—typical of plant-based foods—can have a beneficial impact on the vaginal environment by maintaining a microbiota where protective Lactobacilli predominate. ²²

In both these cases, the interactions between microbiota are most likely linked to the proximity of the anus (gut microbiota), the vaginal opening (vaginal microbiota), and the urethral opening (urinary microbiota), such that bacteria of intestinal origin have little distance to travel to colonize the vagina or bladder. 

Thus, diet is clearly one of the most powerful levers for changing the composition and activity of the gut microbiota. Broadly speaking, a plant-based diet rich in fiber promotes protective bacteria, whereas a diet high in sugars, animal proteins, and saturated fats leads to a more inflammatory profile. ^16,23,24

Nutrients

Mediterranean diet: the gut microbiota’s friend 

Therefore, a plant-based diet, or the famous Mediterranean diet (which prioritizes fruit, vegetables, seeds, legumes, fish, nuts, and olive oil, while limiting sugar and meat), are healthy choices.

Scientific research seems to confirm this: a study conducted over the course of a year examined the effects of a Mediterranean diet on older adults in the United Kingdom, France, the Netherlands, Italy, and Poland. The study found a change in their gut microbiota, with an increase in bacteria associated with reduced frailty, improved cognitive function, and lower inflammation. ²⁵

Which beverages are beneficial to the gut microbiota? 

When it comes to beverages, the polyphenols in wine (part of the Mediterranean diet) ²⁶ and tea ²⁷ are also associated with a more diverse and healthier microbiome.

On the other hand, having a taste for sugary drinks (especially if consumption exceeds two glasses per day) has serious consequences for the gut microbiota: regular consumption appears to deplete populations of various beneficial bacteria, such as Bacteroides pectinophilus. This bacteria feeds on pectin but can’t process the sugars in soda, and thus its population declines when sugary drinks are consumed. ²⁸ 

Diseases linked to poor diet 

As seen previously, the gut microbiota varies greatly from one person to another depending on age, lifestyle, diet, etc. These variations are normal and can help the body adapt to its environment. But at times, the gut flora undergoes profound changes, which can be the cause and/or consequence of health problems. ^12,30

Various intestinal conditions ^12,30 appear to be linked to dysbiosis:  

• in irritable bowel syndrome (IBS), the loss of microbial diversity is thought to weaken the functions of the epithelial barrier and to alter the inflammatory response, which explains in part the symptoms of this condition. 
• in inflammatory bowel disease (IBD), even though a direct causal link has not been proven, microbial imbalances (particularly a decrease in butyrate-producing bacteria) are thought to contribute to the severity of the disease. 
• in celiac disease, dysbiosis appears to create an inflammatory environment and may prevent the intestinal mucus layer from protecting against the invasion of harmful antigens and pathogens. 
• in colorectal cancer, a reduction in beneficial butyrate-producing bacteria and an increase in opportunistic pathogens may contribute to tumor development. 

Gut dysbiosis is also implicated in numerous metabolic disorders: ^12,30,31,32

• in the case of obesity, gut dysbiosis increases the body’s ability to extract energy from food, promoting fat storage and inflammation. 
• in the case of type 2 diabetes, patients exhibit an increase in Betaproteobacteria (associated with elevated blood sugar) and a decrease in beneficial butyrate-producing bacteria such as Roseburia spp. 

The gut-brain axis is also affected: ¹²

• in Alzheimer’s and Parkinson’s diseases, a dysbiosis (e.g., an increase in Escherichia/Shigella for Alzheimer’s) appears to be associated with a peripheral inflammatory state that may contribute to these conditions. 

Adopting healthy habits for your microbiota  

While diet is one of the most powerful ways to influence our gut microbiota, it is by no means the only way. Exercise, when practiced in moderation (at less than 50% of VO2max), facilitates intestinal transit, improves the quality of the mucosa lining the digestive tract’s walls, and boosts our gut microbiota by promoting the establishment of a rich and beneficial flora. ³³ 

As with everything, perfect is the enemy of good: sixty minutes of high-intensity endurance training (at 70% of VO2max) can lead to abdominal pain, nausea, and diarrhea. ³³ And in case you need further convincing, 30% to 50% of athletes suffer from digestive problems, which rises to 90% for those who take part in ultra-endurance events. ³⁴

Lastly, good habits also require us to be mindful of our environment in the broadest sense of the term.
Or more precisely, to be mindful of the exposome—the set of environmental factors to which we’re exposed throughout our lives, and which influence our microbiota and our health.

Diet is certainly part of the exposome, but the exposome is far from limited to diet.
British epidemiologist Christopher P. Wild, who coined the concept, defines the exposome as a complex and dynamic representation of the exposures to which a person is subject throughout their life, incorporating the chemical, microbiological, physical, recreational, and pharmaceutical environments, as well as lifestyle, diet, and infections.

Spend as much time as possible in nature, let children play among plants and animals, avoid self-medication—especially antibiotics—and eliminate sources of microplastics: these are just some of the healthy habits that, together with a nutritious diet, will improve gut health and, by extension, general well-being. 

In practice, what do people actually do for their microbiota? 

However, from theory to practice, the gap remains wide. According to the 2025 Biocodex Microbiota Observatory, awareness may have improved, but “good” behaviors are struggling to keep pace: awareness of microbiota-linked health issues continues to grow, but the number of people taking action remained flat over the last year.
Specifically: 

• a large majority (83%) report eating a balanced and varied diet to ward off a microbiota imbalance; 
• around 3 in 4 respondents said they took part in physical activity (78%) and avoided smoking (77%) to limit the risk of a microbiota imbalance; 
• around half of those surveyed reported consuming probiotics, and around 40% prebiotics, for the benefit of their microbiota; 
• only a quarter of people received key information about the microbiota after being prescribed antibiotics, despite the impact of antibiotics on our gut flora. 

How can awareness be raised among the public about the importance of a balanced microbiota for health?
Recognized as trusted authorities, healthcare professionals may hold the key to encouraging behavioral change.
Stay tuned for updates in our future editions of our Observatory!