Your Second Brain: Optimize Your Microbiome for Ultra-Trail

Introduction: Beyond the Legs, the Other Engine of Performance

I still remember that race. It was a few years ago, on the technical trails of an ultra in the Alps. My legs were there, in incredible shape. My mind, sharper than ever. But at kilometer 60, my stomach said stop. Violent cramps, bloating... a real betrayal. I had to slow down, walk, grit my teeth, and watch my hopes for a good time disappear. This frustrating yet foundational experience taught me an essential lesson: in ultra-trail, performance is not only determined by the legs or the mind. It is also, and above all, played out in our guts. That's where our "second brain" lies: the intestinal microbiota.

Hi, I’m Clara! As a former athlete and endurance enthusiast, I have spent years dissecting every aspect of performance. And if there’s one area that has revolutionized my practice and that of the athletes I coach, it’s understanding this fascinating ecosystem that lives within us. We often talk about VO2 max, pace management, gear... but we too often forget what happens inside. Yet, a healthy microbiota is the key to sustainable energy, a rock-solid immune system, and unyielding morale. On the field, it’s what makes the difference between a race endured and a race where we can fully express ourselves.

In this article, I won't drown you in indigestible scientific jargon. My goal is simple: to give you the keys, based on my experience and the latest research, to pamper your microbiome. We’ll talk concrete, practical matters, and most importantly, we will see how to transform your digestive system into a true ally for your ultras. Ready to explore your inner universe to unleash your full potential on the trails? Then follow me!

What is the Intestinal Microbiota and Why is it Our "Second Brain"?

Before diving into the strategies, it’s crucial to understand what we’re talking about. Imagine an incredibly dense and diverse rainforest, teeming with life. Your intestine is a bit like that! It houses billions of microorganisms (bacteria, viruses, yeasts, fungi) that live in symbiosis with you. Together, they form the intestinal microbiota. Far from being mere passengers, these tiny invisible beings work around the clock for you. It’s a true internal factory that weighs nearly 2 kg!

An Army of Microorganisms at Your Service

What’s fascinating is that each individual has a unique microbiota, a kind of microbial fingerprint. This community is not static; it evolves based on your diet, lifestyle, stress levels, and even your environment. These microorganisms do not just digest what you eat. Their functions are multiple and vital:

• Digestion and Absorption: They break down fibers that your body cannot digest alone, and in return, they produce beneficial compounds like Short-Chain Fatty Acids (SCFAs). Butyrate, for example, is the primary fuel for the cells in your colon.
• Vitamin Synthesis: Your microbiota produces essential vitamins, particularly vitamin K and some B vitamins.
• Defense Barrier: A healthy microbiota forms a protective barrier on the wall of your intestine, preventing pathogens and toxins from entering your bloodstream.
• Immune System Education: About 70% of our immune cells are found in the intestine. The microbiota acts like a conductor, teaching your immune system to distinguish friends from foes.

The Key Role of Microbiota for Endurance Athletes

For us ultra runners, these functions become even more crucial. An optimized microbiota is not a luxury; it’s a necessity. Here's why:

1. Energy Production: The famed SCFAs produced by the fermentation of fibers provide an additional energy source. They can supply up to 10% of our daily energy needs. Over several hours of effort, that’s significant!
2. Reduction of Inflammation: Ultra-trail is a sport that generates a lot of inflammation. A diverse and balanced microbiota produces anti-inflammatory compounds that help the body better manage this stress and recover faster.
3. Mental Health and Stress Management: The nickname "second brain" is not misplaced. The gut and brain communicate constantly via the vagus nerve. A healthy microbiota produces about 90% of our body’s serotonin, the well-being neurotransmitter. A good intestinal balance thus fosters a stronger mindset, better pain management, and less anxiety before the race. 🧠
4. Hydration and Electrolyte Balance: The microbiota plays a role in regulating the absorption of water and electrolytes in the colon, which is absolutely critical during prolonged efforts where dehydration is a constant threat.
5. Protection Against Digestive Disorders: This is the crux of the matter. A robust and resilient microbiota is the best assurance against cramps, nausea, or impromptu visits behind a bush...

Simply put, considering your microbiota as a training partner means giving yourself the means to be more performant, more resilient, and above all, to take pleasure in it all.

Dysbiosis: When Your Internal Ecosystem is Out of Balance

If a healthy microbiota is a super ally, an imbalance, called "dysbiosis," can quickly turn a race into a nightmare. Dysbiosis occurs when the diversity of microorganisms decreases and the "bad" bacteria take over the "good" ones. This state can be chronic or temporary, but in endurance athletes, the risk is particularly high.

The Tell-tale Symptoms on the Field

You have likely experienced one of these warning signals. They are the language of your gut telling you that something is wrong. In a race, these symptoms are exacerbated by the effort:

• Bloating and Gas: The feeling of having a stomach swollen like a balloon, making every step uncomfortable.
• Abdominal Cramps: Sharp pains that double you over and force you to stop.
• Nausea and Vomiting: Inability to eat, aversion to gels and bars, inevitably leading to hypoglycemia.
• Runner's Diarrhea: The most dreaded problem that can ruin a race and lead to severe dehydration.
• Persistent Side Stitches: Often linked to poor digestion and tension in the diaphragm.
• Unexplained Fatigue: Even with good training, a feeling of heavy legs and a lack of energy may be related to poor nutrient absorption.
• Frequent Infections: A lingering cold, general fragility... It’s often a sign of a weakened immune system, directly linked to a struggling microbiota.

Causes of Dysbiosis in Ultra Athletes

We trail runners put our bodies to the test. And our microbiota is on the front lines. Several factors specific to our sport can weaken it:

The physical stress of long efforts: During an ultra, the body is in "survival" mode. Blood flow is diverted from the digestive organs to the working muscles. This intestinal ischemia (lack of oxygenation) can damage the intestinal wall and disrupt the balance of bacteria. Additionally, the repeated shocks of running mechanically harm the intestines.

Nutrition During Effort: The massive and repeated consumption of simple sugars (gels, energy drinks) can feed bad bacteria and create a pro-inflammatory environment in the gut. Even slight dehydration thickens the intestinal protective mucus, making it more vulnerable.

Daily Diet: A diet low in fiber, too rich in ultra-processed foods, saturated fats, and added sugars is the best way to starve our good bacteria and give unwanted ones free rein.

Mental Stress: Pre-competitive anxiety, pressure to perform, everyday life stress... All of this has a direct impact on our gut via the gut-brain axis. Chronic stress can reduce microbial diversity and increase intestinal permeability (the infamous "leaky gut").

The Use of Non-Steroidal Anti-Inflammatory Drugs (NSAIDs): Many runners reflexively take ibuprofen for pain. This is a very bad idea, especially before or during a race. NSAIDs are known to irritate the walls of the stomach and intestines, increasing permeability and the risk of serious digestive disorders.

The good news is that we can act on most of these factors. Awareness of these threats is the first step toward building a protection and optimization strategy for your microbiota. That’s what we’ll cover now. 💪

Nourishing Your Good Bacteria: The Practical Guide Before, During, and After Effort

The most powerful strategy for shaping a champion’s microbiota lies in your plate. What you eat every day is far more important than any miracle supplement. The idea is simple: nourish the good bacteria so they can thrive and take over. Here’s how I proceed, both daily and around races.

Daily Nutrition: The Foundation of Everything

This is the foundational work, the one that happens 365 days a year. A resilient microbiota is not built in the week leading up to a race. It’s a long-term investment.

Fibers, the Superheroes of Your Gut

Fibers are the favorite food of your good bacteria. They are called **prebiotics**. By fermenting them, your bacteria produce the famous SCFAs, beneficial for your entire organism. The secret? Diversity! Don’t just stick to green beans. Aim for a rainbow on your plate. The goal I set and recommend is to try to consume at least 30 different types of plant foods each week (fruits, vegetables, legumes, whole grains, nuts, seeds).
My favorite sources: leeks, asparagus, onions, garlic (rich in inulin), oats, barley (rich in beta-glucans), unripe bananas, cooled potatoes (rich in resistant starch), lentils, chickpeas, flaxseeds, and chia seeds.

Polyphenols, the Colorful Protectors

Polyphenols are antioxidant compounds found in plants that give them their bright colors. They have a dual effect: they nourish certain good bacteria and exert a direct anti-inflammatory action. Think "color"!
My essentials: red fruits (blueberries, raspberries, blackcurrants 🍓), green tea, coffee (in moderation), dark chocolate (over 70%), walnuts, spices like turmeric and ginger.

Probiotics, the Direct Reinforcements

**Probiotics** are living microorganisms that, when ingested in sufficient quantities, strengthen the troops already present in your gut. The best sources are found in fermented foods. They bring new strains and increase diversity.
My allies: kefir (milk or fruit), natural yogurt (especially sheep or goat milk), kombucha, raw sauerkraut, kimchi, miso. I try to incorporate a small portion every day.

Good Fats and Quality Proteins

Let’s not forget omega-3s, essential fatty acids with powerful anti-inflammatory properties. They help maintain the integrity of the intestinal barrier. They are found in small fatty fish (sardines, mackerel), canola oil, flaxseeds, and chia seeds. Proteins are also vital, particularly glutamine (an amino acid) which is the main fuel for intestinal cells. We find it in eggs, meat, fish, and legumes.

Before the Race: Preparing Your Gut for the Challenge

The approach to a race, especially an ultra, requires nutritional adaptation. The goal is to rest the digestive system while maximizing energy reserves. This is a crucial phase to avoid nasty surprises.

In the 3 days leading up to the event (D-3), I change strategies. I drastically reduce foods that are excellent in everyday life but potentially problematic during effort. We set aside:

• Raw vegetables and legumes (too much fiber).
• Whole grains (we switch to white rice, white pasta, white bread).
• Very fatty foods (fried foods, charcuterie).
• Dairy products if you are sensitive to them.

We focus on easily digestible carbohydrates, lean proteins (chicken, white fish), and well-cooked tender vegetables (carrots, zucchini without skin). The idea is to line up at the starting line with a "calm" digestive system and glycogen stores bursting at the seams. It’s a fundamental principle to acclimatize your body. It’s akin to what I explain in my guide for training your digestive system in triathlon; the principle remains the same: gradually acclimate it to effort so it performs efficiently on the big day.

During the Ultra: Refueling Smartly

On race day, the golden rule is: **nothing new**. You must have tested and validated every food and drink during training. Digestion during effort is a challenge. The goal is to provide energy without overloading the system.

• Start Eating and Drinking Early: Don’t wait until you’re famished or thirsty. Start within the first hour, with small regular amounts (every 20-30 minutes).
• Vary the Pleasures (and Sources of Carbohydrates): Alternating sweet and savory is an excellent strategy to avoid saturation. Mix gels, compotes, bars, but also solid foods like chunks of potatoes, gingerbread, or crackers.
• Listen to Yourself: If you feel a hint of nausea, slow down and switch to clear water for a while before attempting liquid nourishment again (broth, diluted sports drink).
• Chew! For solid foods, take your time to chew well. Digestion starts in the mouth.

After Effort: Repair and Repopulate

The race is over, but the work for your microbiota continues. The recovery phase is essential for repairing the damage caused by effort and replenishing your armies of good bacteria.

1. The Metabolic Window: In the 30 to 60 minutes following your finish, have a recovery drink that combines carbohydrates (to replenish stores) and proteins (to repair muscle and intestinal fibers).
2. Rehydration: Drink water, broths, herbal teas to restore your hydration status.
3. Post-Race Meal: Opt for an easily digestible meal. Mashed potatoes with white ham, rice with white fish, vegetable soup.
4. Return to Normal: In the days that follow, gradually reintroduce fiber-rich and probiotic foods to help your microbiota rebuild and strengthen. Anti-inflammatory foods (turmeric, ginger, omega-3s) are your best friends. 🌿

Optimizing Your Microbiota: A 360° Approach

If nutrition is the central pillar, taking care of your microbiota requires a more holistic view. Your lifestyle has an equally powerful impact. Simply put, we cannot expect to have a healthy gut if the rest is neglected. It’s an ecosystem that reacts to everything: your sleep, your stress, your training.

Stress Management: Calming the Brain to Soothe the Gut

The gut-brain axis is a two-way highway. Mental stress sends negative signals to your gut, and a disturbed gut sends alarm signals to your brain. It’s a vicious circle, especially before a race. Learning to manage stress is as important a skill as managing your pace on climbs.

• Heart Coherence: This is my favorite tool. 5 minutes, 3 times a day. Inhale for 5 seconds, exhale for 5 seconds. This simple technique regulates the autonomic nervous system and has an almost immediate soothing effect on the digestive system.
• Mindfulness Meditation: Focusing on your breath, your bodily sensations, without judgment. This helps create distance from anxiety and reduces the production of cortisol, the stress hormone.
• Contact with Nature: Our sport has this immense advantage. Enjoy your outings to disconnect, listen to the sound of the wind, the singing of birds. Simply being in the forest ("forest bathing" or shinrin-yoku) has proven beneficial effects on stress.

Sleep, the Ultimate Repairer (For Your Bacteria Too)

We often neglect it, yet sleep is when the body regenerates deeply. And this includes the intestinal wall and microbiota. Chronic lack of sleep is associated with a decrease in microbial diversity and an increase in inflammation. During heavy training periods, sleep is not an option; it’s an integral part of preparation.

Aim for 7 to 9 hours of quality sleep each night. Establish a ritual: no screens an hour before sleeping, a cool and dark room, regular hours. A good night’s sleep guarantees a calmer digestive system and better recovery. 😴

Smart Training: Avoid Overtraining

More is not always better. Overtraining is one of your microbiota’s worst enemies. A body pushed beyond its recovery capacity enters a state of chronic inflammation. This can lead to intestinal hyperpermeability, or "leaky gut." The intestinal barrier becomes porous, allowing substances that should not enter the bloodstream to do so, triggering an immune response and cascading disorders.

How to avoid it?

• Plan Your Season: Alternate between load and recovery cycles.
• Listen to Your Body: Persistent fatigue, irritability, decreased performance, disturbed sleep... These are signs that you need to slow down.
• Respect Rest Days: They are just as important as your long sessions. It’s during rest that you progress.

By integrating these three pillars – stress management, quality sleep, and smart training – into your nutritional strategy, you create an overall environment conducive to the flourishing of your microbiota. It’s a holistic approach that will make you stronger, not only on the trails but in your everyday life.

My Personal 4-Week Protocol to Pamper Your Microbiota Before a Goal

Now that we’ve covered the theory, let’s move on to practice. Here’s, in very concrete terms, how I organize the four weeks leading up to an ultra to ensure that my "second brain" is in top form on the big day. This is not a magic formula but a framework to adapt according to your own feelings and experiences. Listening to yourself remains key!

Week 4 (D-28 to D-21): The "Cleaning" Phase and Reinforcement

This is the time to establish good habits and provide your microbiota with everything it needs to diversify and strengthen.

• Diversity Goal: I challenge myself to consume 30 different plants per week. I keep a small list to have fun: each fruit, vegetable, herb, spice, legume, nut counts. It encourages creativity in cooking!
• Daily Probiotics: I incorporate a source of probiotics every day. A glass of milk kefir in the morning, a spoonful of raw sauerkraut with my salad at lunch, natural yogurt as a snack... Consistency is key.
• Zero Ultra-Processed: I clean out the cupboards. Say goodbye to prepared meals, sodas, industrial cookies. I cook as many raw products as possible. It’s the best gift you can give your gut.
• Maximum Hydration: I make sure to drink at least 2 liters of water a day, outside of training. I also include herbal teas (ginger, peppermint) that are excellent for digestion.

Week 3 (D-20 to D-14): Optimization and Testing

We continue in the momentum of week 4, but we add a crucial dimension: testing race nutrition.

• The Big Test: On my long weekend run (the longest before the race), I simulate the conditions of the ultra. I set off with the gels, bars, compotes, and drinks I’ve planned for the big day. I test everything: tastes, textures, quantities, and especially, digestive tolerance. This is the moment to note what works well and what doesn’t. Better to have issues in training than at kilometer 80!
• Inflammatory Focus: I boost my intake of anti-inflammatory foods to help my body manage the training load. On the menu: fatty fish, canola oil, nuts, plenty of turmeric in my dishes (always with a bit of black pepper for absorption) and fresh ginger in my herbal teas.
• Maintaining Routine: I, of course, keep up the dietary diversity and probiotics. Consistency pays off.

Week 2 (D-13 to D-7): Listening and Adjusting

Training decreases (tapering phase), but attention to nutrition and well-being increases.

• Review of Tests: I evaluate the test from the previous week. If a product caused issues, I rule it out permanently. I finalize my refueling plan.
• Start Reducing Fibers: If I am particularly sensitive in the digestive area, I begin to slightly reduce the most "aggressive" fibers: fewer legumes, fewer cruciferous vegetables (cabbages, broccoli). I prefer cooked vegetables.
• Priority to Sleep and Relaxation: The fatigue from preparation can be felt. I safeguard my sleep nights and practice heart coherence daily to lower the pressure.

Week 1 (D-6 to Race Day): The Digestive Tapering Phase

The final stretch! The objective is simple: to arrive at the starting line with a perfectly calm gut and top energy reserves.

• D-3, D-2, D-1: The "Pre-Race" Diet: This is when we apply the fiber discharge diet. No more raw vegetables, whole grain bread, lentils. Hello white rice, pasta, potatoes, white bread, fruit compotes, lean proteins. It’s a bit frustrating to set aside all those good vegetables, but it’s for the right cause!
• Hyper-Hydration: I drink a lot of water throughout the day to be perfectly hydrated. I monitor the color of my urine, which should be very clear.
• The Last Meal (Eve): Simple, tested, and approved. For me, it’s often white rice with a bit of grilled chicken and cooked carrots. Light and energy-giving.
• The Breakfast on Race Day: Again, a classic that I’ve tested dozens of times. No surprises. I take it at least 3 hours before the start to allow time for digestion.

This protocol may seem constraining, but it brings incredible peace of mind. Knowing you have done everything possible at the digestive level allows you to focus on the essential on race day: to run and enjoy. Taking pleasure above all starts with a happy gut!

Conclusion: Ultra-Trail, an Inner Adventure

Throughout this article, we have explored together this fascinating universe that is our microbiota. We have seen that it is much more than just a player in digestion. It’s a true performance partner, a conductor influencing our energy, our immunity, our morale, and our ability to endure thousands of meters of elevation gain.

Taking care of your second brain is not a matter of restrictive diets or magic formulas. It’s a philosophy, a holistic approach that integrates a living and diverse diet, good stress management, restorative sleep, and training that listens to one’s body. It’s a continuous dialogue with oneself.

On the field, I have learned that the greatest victories are not those of times or rankings, but those we win against ourselves. And overcoming the challenges of an ultra with a cooperating digestive system is a beautiful one. A happy gut is the freedom to express oneself fully, to savor every moment, from the starting line to the last aid station, to the finish arch.

So, the next time you prepare your bag for a long outing, think not only of your shoes and your flask, but also of the billions of little allies working for you. Feed them well, listen to them, and they will repay you a hundredfold on the trails. Simply. Happy running, and may joy be your main driver!