Inside your gut lies an unexpected world, teeming with microorganisms. This tiny universe, invisible to our eyes, plays an immense role in our health. In this article, we explain what the microbiota really is and why it deserves your full attention.

What is the microbiota?

Imagine your body as a vast galaxy housing billions of microorganisms: bacteria, viruses, fungi… These tiny inhabitants, invisible to the naked eye, form well-organized communities called microbiota, which are found in various parts of the body: nose, mouth, genital organs, skin, but most importantly… in our gut! If all of them were gathered together and weighed, they could total up to 2 kg (4.4 pounds)¹!

In this article, we will focus on the gut microbiota, a true cornerstone of our health. Did you know that 70 to 80% of the bacteria in our body live in the gut? They include hundreds of different species and play such essential roles².

Bacteria: friend or foe?

The word “bacteria” often has a bad reputation. However, not all bacteria are “bad”! Our body also hosts many beneficial bacteria that support our health. Each one has its own specificity, and the more diverse they are, the better they collaborate to protect us and maintain our body’s balance.

Why is balance so important?

A healthy microbiota is characterized by a wide variety and abundance of good bacteria. This balance is crucial to prevent ‘dysbiosis,’ an imbalance that occurs when good bacteria are depleted, harmful bacteria proliferate, or microbial diversity decreases. An imbalanced microbiota can have significant consequences on our health.

Our microbiota is threatened by our lifestyle

Unfortunately, our modern lifestyle disrupts the balance of our microbiota, making it more prone to dysbiosis. Just like the planet’s biodiversity is at risk, the diversity of our gut bacteria is also under threat. The more industrialized a society is, the less diverse its microbiota tends to be.

The main contributing factors?

• Highly processed foods that are low in fiber but packed with sugars and all kinds of additives
• Excessive hygiene, limiting natural exposure to microorganisms
• Frequent and sometimes excessive use of antibiotics, which wipe out both harmful and beneficial bacteria³.

The consequences are far from minor. When the diversity of our microbiota decreases or becomes imbalanced, it can trigger various digestive issues (constipation, diarrhea, abdominal pain, bloating) and, over time, raise the risk of serious chronic conditions like diabetes, obesity, autoimmune diseases, cardiovascular problems, and even certain neuropsychiatric disorders^4-8.

How is the microbiota formed?

It all begins at birth!

The story of our bacteria starts as soon as we enter the world. Before birth, a baby’s digestive tract is sterile, meaning it contains no microorganisms. During vaginal delivery, as the baby passes through the birth canal, they acquire their first “batch” of bacteria, primarily from the mother’s vaginal and fecal microbiota. In the case of a cesarean section, the baby’s microbiota is different: it is more colonized by bacteria from the hospital environment, the mother’s skin, and later from the father’s skin during skin-to-skin contact. This first exposure to bacteria is crucial because the first arrivals have the advantage over others: they settle in the best spots in the intestine. In other words, it’s a “first come, first served” rule ¹⁰.

Until the age of 3 to 5 years, the microbiota continues to evolve and diversify, influenced by various factors such as food intake, hygiene, medications, environment, and even genetics. Among these factors, breastfeeding, followed by the introduction of solid foods, plays a key role. Exposure to the environment—such as where we live, whether in the countryside or the city, or even contact with animals—also contributes to enriching and shaping the microbiota, which ultimately becomes unique to each individual¹¹.

The key role of diet and lifestyle

Just like fingerprints, the gut microbiota is unique to every individual. However, it is not permanent: less than 10% of our microbiota is influenced by our genetics, while the rest can evolve depending on external factors. It’s a dynamic ecosystem.
A recent study reveals a surprising fact: people living in the same house, even if they’re not related, share a more similar microbiota than family members living apart¹². This demonstrates that our diet and lifestyle have more influence than our genetic heritage! And that’s excellent news, as it means we have the power to directly impact our microbiota. Within just 24 hours, changes in dietary habits can begin to alter its composition¹³.

The superpowers of the microbiota

Although invisible to our eyes, the tiny organisms inhabiting our gut possess superpowers far beyond their size. Let’s explore the main benefits of these microscopic allies!

Production of really useful molecules

Our gut bacteria can produce essential vitamins for the body, such as B vitamins, which boost energy, and vitamin K, which is crucial for wound healing¹⁴.

The microbiota can also create remarkable small molecules called short-chain fatty acids (SCFAs) from the fiber of our diet. These SCFAs are true multitasking molecules¹⁵:

• They make the intestine slightly acidic, which slows the growth of harmful bacteria.
• They provide energy to intestinal cells, helping them regenerate quickly.
• They strengthen the intestinal lining, our protective barrier that prevents bacteria, toxins, and allergens from entering the bloodstream—a true defensive wall!

A guardian of our immune system

The gut microbiota acts as a natural shield, protecting our body through several mechanisms¹⁶:

• Physical barrier: The large number of beneficial bacteria forms a protective layer. Imagine an army of good bacteria lined up like a strong wall to defend our body—that’s our microbiota watching over us!
• Competition: When beneficial bacteria are abundant, they deprive harmful bacteria of nutrients, limiting their growth.
• Production of natural antibiotics: Our good bacteria produce “natural antibiotics” that inhibit the growth of harmful bacteria.

But that’s not all! The microbiota also regulates our immune system, helping our white blood cells identify real threats, like certain viruses and harmful bacteria. This allows the immune system to focus its defenses on actual intruders, avoiding attacks on good bacteria or, worse, our own cells¹⁷!

A regulator of weight and metabolism

The gut microbiota influences how we store fat and gain weight. This might partly explain why some people are more susceptible to weight gain than others, even with similar eating habits^18,19.
Moreover, the microbiota affects our appetite and satiety. Depending on its composition, it can even influence cravings for fatty or sugary foods!

A key player in mental health

The microbiota plays a crucial role in communication between the gut and the brain, notably through the production of neurotransmitters (chemical messengers)^20,21. Did you know that 95% of serotonin, often called the “happiness hormone,” is produced in the gut thanks to the microbiota?

The gut microbiota and the brain maintain a constant dialogue, often referred to as the gut-brain axis. This connection is tangible: who hasn’t experienced a stomachache before a stressful event? But this dialogue goes far beyond fleeting emotions—it influences our mood, stress levels, and may even play a role in complex disorders such as anxiety or depression^22,23. Maintaining a balanced microbiota is therefore essential for our mental health.

Star foods for a healthy microbiota

Taking care of your microbiota starts on your plate. This precious ecosystem thrives on whole foods and fermented foods. Here are the must-haves to include in your daily diet!

Fiber

Dietary fiber is essential for your gut’s microbiota health. Yet, most of us consume far too little! In France, 89% of adults fail to meet the 25 g/day recommended by the WHO, and in the United States, this figure rises to 95%^24-26. However, getting enough fiber helps reduce the risk of strokes and diabetes²⁷.
Why is fiber so important? Since fiber isn’t digested by the stomach or small intestine, it makes its way to the colon intact, where it becomes a favorite food for gut bacteria. These bacteria ferment the fiber, producing short-chain fatty acids (SCFAs) that offer incredible health benefits.

Here are some foods to prioritize²⁸:

Vegetables	Garlic, artichokes, asparagus, beetroot, broccoli, carrots, chestnuts, endive, cabbage, fennel, green peas, corn,  onions, parsnips, leeks, sunchokes
Legumes	Beans, lentils, peas, fava beans,  chickpeas
Fruits	Avocado, bananas (not too ripe), dates, figs, kiwi, apples, nectarines, peaches, pears, prunes
Nuts	Almonds, peanuts, walnuts, hazelnuts, pistachios
Seeds	Chia, flaxseed, sunflower seeds, pumpkin seeds, sesame seeds
Grains and starchy foods	Oats, whole wheat, millet, barley, cooled potatoes, quinoa, brown rice, rye, buckwheat

Tips to boost fiber intake:

• Opt for whole fruits and vegetables. You can also eat the skin, as it often contains a lot of fiber—just make sure to opt for organic produce, since the skin can also concentrate pesticides.
• Limit fruit juices, which are low in fiber and normally high in sugar.
• Choose high-fiber grains like brown rice, buckwheat, oats, or quinoa, as they contain more fiber. Ideally, go for organic options, since the fiber is mostly in the outer layer of the grain, which also tends to concentrate pesticides.
• Add legumes to your meals at least twice a week²⁹: chickpeas, beans, lentils, fava beans – To make them easier to digest, soak them in water overnight before cooking, then rinse them 2 to 3 times.
• Use less refined flours and opt for whole grain or ancient varieties like spelt or rye. 
• Consume cold starches (like rice or potato salads). When cooled, they contain more resistant starch, a type of fiber that nourishes good gut bacteria³⁰.
• Sprinkle seeds on your meals: on salads, yogurt, or baked goods. Remember to soak flax and chia seeds in liquid before consuming them, as they are great for supporting transit!

Polyphenols

Polyphenols are natural compounds plants produce to defend themselves against external stressors like insects, mold, or UV rays. And what protects plants can also protect… your microbiota! These compounds stimulate the good bacteria in your gut and boost microbiota diversity³¹.

The richest food in polyphenols include red fruits (blackcurrants, blueberries, raspberries), artichokes, coffee, dark chocolate (at least 70% of cocoa), black and green tea, and spices like turmeric, cloves, and anise^32,33. By eating these foods regularly, you give your microbiota a real boost!

Organic Products

It’s better to choose organic fruits and vegetables, as they contain on average 20 to 70% more polyphenols than conventional ones³⁴. Eating organic food also helps you avoid exposure to chemical pesticides, which can weaken or kill certain bacteria in the microbiota. A double benefit!

Fermented Foods

Fermented foods, such as yogurt, certain cheeses (especially those made with raw milk)³⁵, kombucha, kefir, miso, tempeh, and lacto-fermented vegetables (like kimchi and sauerkraut), are a true treasure for your microbiota. These foods are packed with live beneficial bacteria that support the diversity and balance of the microbiota. They can be considered natural probiotics, contributing to both digestive and overall health^36-38.

To fully benefit from their effects, it’s essential to consume these foods raw or unpasteurized, as heat destroys the live bacteria.

The enemies of a healthy microbiota

Now that we know why and how to take care of our gut microbiota, let’s review its worst enemies.

Antibiotics

Antibiotics are designed to eliminate bacteria responsible for infections, but their mode of action is non-selective: they also destroy many beneficial bacteria of the microbiota. Like a bomb, the explosion will eliminate harmful bacteria but also causes collateral damage by killing “friendly” bacteria.

This phenomenon can have significant consequences, especially for children under three years old, whose microbiota is still developing. At this age, disrupting this delicate ecosystem can increase the risk of long-term health problems, such as asthma, food allergies³⁹, diabetes, obesity⁴⁰, and chronic inflammatory bowel disease⁴¹. In cancer patients, studies suggest that antibiotics may even reduce the effectiveness of chemotherapy and immunotherapy⁴².

While antibiotics are indispensable in certain situations, particularly for bacterial infections, it’s crucial to use them only when necessary, follow your doctor’s advice, and avoid self-medication.

Ultra-processed foods

Packed with added sugars, saturated fats, and various additives, ultra-processed industrial foods can disrupt the microbiota.

Research indicates that certain food additives, such as emulsifiers, sweeteners, and colorings, can deplete and destabilize the gut microbiota while weakening the intestinal barrier. When this protective barrier becomes more permeable, harmful substances can enter the body, triggering a “silent” yet persistent inflammation.

Over time, this chronic inflammation can weaken the body and increase the risk of developing chronic conditions, such as allergies, certain autoimmune diseases (like Crohn’s disease), or even some cancers^43-49.

Lack of physical activity

Spending too much time inactive can harm the microbiota, reducing its diversity and weakening the intestinal barrier, which allows undesirable substances to pass through⁵⁰.

On the other hand, physical activity enhances microbial richness and diversity, boosting the production of SCFAs (short-chain fatty acids)—valuable multitasking molecules^51,52. It’s a win-win relationship: physical activity stimulates the microbiota, which in turn produces substances that increase our energy and physical performance, encouraging us to move even more^53,54.

No need to run a marathon—the key is to stay active every day with simple, regular activities!

Chronic stress

Prolonged stress disrupts the microbiota by increasing the production of cortisol, a hormone that promotes inflammation and destabilizes the gut. Additionally, stress often intensifies cravings for sugary or fatty foods, which feed “bad” bacteria and exacerbate inflammation. This can create a vicious cycle: the more we are stressed, the more we tend to adopt poor eating habits, and the more inflammation increases, further aggravating the situation⁵⁵.

To break this cycle, it’s essential to take time each day to relax—whether through meditation, a walk in nature, or simply by a few minutes of deep breathing.

Excessive hygiene

In the pursuit of disinfecting and sterilizing everything, we risk weakening our microbiota and especially for children, whose microbiota and immune systems are still in development. Overprotecting them from environmental microbes restricts their microbiota and their immune system from learning to differentiate between beneficial and harmful bacteria, leaving them more vulnerable later on.

A little bit of contact with germs is actually beneficial, as it helps the body learn how to make the difference between bad and good bacteria. Studies show that in populations with less strict hygiene practices, microbiota diversity tends to be higher—a key factor for better overall health⁵⁶ !

Of course, maintaining hygiene is important, but it’s important not to become overly obsessive about it.

Not enough sleep

A lack of sleep or an irregular sleep schedule can disrupt the balance of our microbiota. Just as our bodies are designed to be active during the day and rest at night, the microbiota is the same. Our microbiota loves regularity!

Even a slight disruption to this rhythm—such as staying up too late or getting too little sleep—can lead to an imbalance in the microbiota. Over time, this imbalance may contribute to the development of various chronic diseases⁵⁷.

In summary: 10 keys to a healthy microbiota

Now that you understand the importance of the microbiota for our health, here are 10 essential tips to remember:

	Let children explore their environmentEncourage them to spend time outdoors, interacting with nature and animals. A little bit of “dirt” helps their bodies prepare better for real threats.
	Limit antibioticsUse them only with a doctor’s prescription and avoid their use as much as possible in young children with fragile microbiota.
	Diversify your dietEat a wide variety of foods rich in fiber and polyphenols (fruits, vegetables, legumes), and include fermented foods.
	Opt for less processed foods as possibleAvoid ultra-processed foods and opt for homemade meals made with raw, organic, and seasonal ingredients.
	Include at least one different fruit or vegetable in every mealVariety is just as important as quantity!
	Choose whole grains over refined onesThey are richer in fiber and better for your microbiota.
	Incorporate legumes into your mealsAdd them to your menus at least twice a week.
	Stay active!Even 10-15 minutes several times a day can make a difference.
	Take care of your sleepGo to bed at regular times, aim for 7 to 9 hours of sleep per night, and limit screen use in the evening, stopping at least an hour before bedtime.
	Prioritize mental well-beingIf you work in front of a screen, take 5-minute breaks every hour. Dedicate at least 10 minutes a day to meditation or deep breathing exercises.

Source: Yuka.io