By Dr. Alejandro Junger, founder of the Clean Program
In medical schools around the world, students are taught about the body one organ at a time. Early in their studies, they begin considering which specialty to pursue—often choosing based on specific organs. Neurologists focus on the brain, gastroenterologists on the digestive system, cardiologists on the heart, nephrologists on the kidneys, and the list goes on.
A specialist becomes an expert in one organ, but the simple truth is that no organ functions in isolation. The body is a deeply interconnected system, and one of the most fascinating connections is the one between your gut and your brain, creating the gut-microbiota brain axis.
How Your Gut Influences Your Cravings
Imagine this: You suddenly think of a bagel. Maybe you had a subtle sensation of hunger before that, but you weren’t paying much attention. The moment the thought of a bagel pops into your mind, that hunger intensifies. Before you know it, you’re compelled to act—whether that means preparing one, buying one, or ordering it on an app. Once you eat it, the craving subsides.
What if I told you that this entire process might not be entirely your doing?
Science has now made it clear that certain gut bacteria can influence what you crave. These microbes communicate with your brain, nudging you toward certain foods—often the ones they thrive on. In a way, the bacteria in your gut can act like tiny puppeteers, shaping your desires to suit their needs.
The Role of Bacteria and Their "Poop"
How do they do this? We’re only beginning to understand the full picture, but here’s what we know so far:
Bacteria in your gut help digest food, and in the process, they release waste products—essentially, bacterial poop. But this isn’t just waste; these substances, known as postbiotics, can have profound effects on your body.
Depending on which bacteria dominate your gut, the postbiotics they produce can vary widely. Some may trigger intense sugar cravings, reinforcing a cycle of addiction to sweets. Others may enhance your immune system, making you more resilient to illness.
Your gut bacteria influence not only what you eat but also how you feel. Some microbes produce compounds that promote relaxation and happiness, while others can contribute to irritability, anxiety, or even depression.
The Gut-Brain Connection: More Than Just Chemistry
The relationship between your gut and brain isn’t just about chemicals circulating in your bloodstream. There’s also a direct, physical connection: the vagus nerve.
This nerve acts as a superhighway of communication between your gut and your brain. Signals travel back and forth, influencing digestion, mood, and even decision-making. This is why the gut is often called the "second brain"—it doesn’t just passively digest food; it plays an active role in regulating emotions, metabolism, and overall well-being.
In some cases, gut bacteria can affect muscle contractions in the intestines, leading to issues like constipation. Harmful postbiotics can damage the intestinal lining, contributing to leaky gut syndrome and systemic inflammation. This inflammation doesn’t stay confined to the gut—it can spread throughout the body, even affecting the brain and influencing conditions like anxiety and brain fog.
The Bigger Picture: The Gut-Brain Axis
When we talk about the gut-brain axis, we’re referring to this intricate web of connections between:
- The brain in your skull
- The "second brain" in your gut
- The gut itself
- The trillions of microbes that live there
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The neurotransmitters, hormones, and chemical signals that keep this system running
Every thought you have, every craving you experience, and even how you feel emotionally can be shaped by the bacteria inside you. It’s a reminder that we are not just individuals—we are ecosystems. And by taking care of the health of our gut, we are, in turn, taking care of our mind, our mood, and our overall well-being.
How Gut Health Impacts Mental Well-Being
Mental well-being is a vast topic, and perspectives on it vary widely. A psychiatrist might approach it differently than a meditation master. But from a Western medicine standpoint, we’re in a time of both exciting discoveries and overwhelming complexity.
The reality is this: gut health is mental health. They are not separate. Asking how gut health affects mental health is like asking how water affects rain—they are fundamentally connected.
Consider this: your gut contains more neurons than your brain. That’s right—there are more nerve cells in and around your intestines than in your skull, in what we traditionally (and only recently) started calling “the brain.” The neurotransmitter serotonin, widely known for its role in mood and well-being, is primarily produced in the gut. When the nervous system around the gut becomes inflamed or disrupted, it shifts from producing feel-good chemicals to prioritizing stress-response neurotransmitters—the ones that keep you on high alert, ready to fight or flee.
This gut-brain connection plays out in everyday life. Ever had a sudden urge to run to the bathroom before a big exam? That’s your gut responding to stress in real time.
But the gut’s influence extends beyond digestion and anxiety. It also affects something more intangible: intuition. We say “trust your gut” for a reason. Spiritual teachers often emphasize gut instincts, and those fluttery feelings in your stomach before a big decision are a real, physical response. But when the gut is compromised—when harmful bacteria take over, when the gut lining becomes damaged (leaky gut), or when inflammation spreads—intuition can become clouded. That inner compass we rely on may start leading us in the wrong direction.
Signs of Poor Gut Health
When something is off in the gut, the most obvious signs tend to be digestive: bloating, gas, stomach pain, indigestion, diarrhea, constipation, or even bleeding. Food is often involved, though pinpointing the exact trigger can be tricky.
But gut dysfunction doesn’t always manifest as digestive discomfort. Any symptom in the body—physical, mental, or emotional—could be linked to an unhealthy gut.
Some lesser-known signs of poor gut health include:
- Fatigue and brain fog
- Mood swings, anxiety, or depression
- Poor sleep
- Low libido and hormonal imbalances
- Autoimmune conditions
- Skin issues like acne or eczema
- Sugar cravings and difficulty maintaining a healthy diet
The gut-brain axis works as a feedback loop—it can keep you in a good cycle or trap you in a bad one. The bacteria in your gut influence your cravings, and your cravings determine what you feed them.
Take our Do I Need a Detox? Quiz to find out which reset program is right for you.
It’s true that you are what you eat, but it’s equally true that you eat what you are. If your gut is full of beneficial bacteria, they’ll push you toward real, whole foods that nourish you. If your gut is dominated by harmful microbes, they’ll make you crave what they thrive on—sugar, processed foods, and artificial chemicals.
The good news? It only takes about three days of consistent effort to shift from a bad loop to a good one.
Actionable Tips to Support the Gut-Brain Connection
Since the gut and brain are inseparable, taking care of one automatically benefits the other. When the gut is in balance, neurotransmitter production is optimized, inflammation is reduced, and the nervous system functions more smoothly—all of which contribute to better mood, mental clarity, and overall well-being. However, for many people, gut dysfunction is so deep-rooted that a few small dietary changes won’t be enough to create lasting improvements.
That’s why I highly recommend a structured gut repair program, like the 21-day Clean Program, which is designed to fully reset and restore balance across all systems in the body by addressing health at its core—the gut. The program eliminates processed foods, refined sugars, and inflammatory triggers that disrupt digestion, hijack cravings, and contribute to mood imbalances.
By focusing on whole, nutrient-dense foods and incorporating daily digestive rest, the Clean Program gives your gut the break it needs to repair, allowing beneficial bacteria to thrive and the gut-brain connection to recalibrate. As inflammation subsides and the immune system resets, you’ll likely experience improved digestion, more stable energy, enhanced mental clarity, and a more balanced mood.
Building a Clean foundation starts with a healthy gut—and when your gut is thriving, your mind and body follow.
But if you’re looking for simple, effective ways to start improving your gut-brain connection today, here are my top tips:
1. Eat real food. Prioritize whole, organic foods and avoid ultra-processed, chemical-laden products that disrupt gut bacteria.
2. Give your digestive system a break. The idea that we need breakfast, lunch, and dinner every single day is a modern myth. Eating less frequently, opting for easily digestible foods, or experimenting with fasting can give your gut time to heal.
Even small shifts in your diet and habits can have a profound impact on both your gut and your mind. Because when you take care of your gut, you take care of everything.
Start Improving Your Gut-Brain Axis
Your gut and brain are in constant communication. When your gut is out of balance, it can lead to brain fog, anxiety, fatigue, and poor decision-making. A structured reset can help restore harmony to your gut-brain axis improving both your physical and mental well-being.
We’ve designed full-body programs to support a healthier gut and in turn a more balanced, sharper mind:
Clean 21: A Full Comprehensive Gut Reset
Our 21-day program provides a deep gut reset by eliminating inflammatory foods, replenishing essential nutrients, and supporting a thriving microbiome. Clean 21 helps enhance digestion, boost mental clarity, stabilize mood, and improve overall energy levels. If you’re looking for a transformative approach to gut and brain health, this program offers a powerful foundation.
Clean 7: A Quick and Effective Detox
For those looking for a reset without a long commitment, Clean 7 offers a powerful yet flexible approach. In seven days, this detox helps rebalance digestion, reduce cravings, and support gut-brain communication. It’s a great way to kickstart healthier habits, experience more mental clarity, and feel more energized—fast.
By taking care of your gut you’re also taking care of your mind. Find a reset that fits your lifestyle and start healing from the inside out. Still not sure where to start? No worries. Contact one of our Clean-Certified Health Coaches or find the supplement that best supports your health goals for personalized guidance to discuss your individual mind-body needs.
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