I wrote a whole book about this — and most people assumed it was about metaphors. Gut Feeling — More Than Just a Saying. The title is the point. Because when I talk about gut feeling, I do not mean esotericism. I mean biochemistry. I mean a nerve that runs like a fiber-optic cable between your digestive tract and your brain. And I mean the trillions of bacteria living there that actively take part in the conversation — whether you notice it or not.

When my autoimmune illness knocked me flat in my late thirties, my gut was the last place I looked. I thought about the immune system, medication, thyroid values. But part of the answer was not in the blood work. It was about twenty centimeters below my breastbone — in a system everyday life often underestimates: the gut-brain axis.

What is the gut-brain axis?

The gut-brain axis is not just an idea. It is a physical, biochemical, real-time connection between your enteric nervous system — the “second brain” in your belly — and your central nervous system. Your gut contains around 100 million neurons. That is more than your spinal cord. This network receives stimuli, processes information and sends signals upward. Not metaphorically. Biologically.

The communication runs in both directions. Your brain tells the gut what to do — ramp up digestion, trigger diarrhea, reduce blood flow. But here is the important part: around 80 to 90 percent of the signals travel from the bottom up. The gut talks to the brain more than the other way around. When your stomach flips before an important moment, that is not only your head commanding your belly. It is also your belly telling your head: something is happening here.

The vagus nerve — the fiber-optic line

The most important cable in this system is the vagus nerve — the tenth cranial nerve, running from your brainstem deep into your abdomen. It is the longest cranial nerve in your body and a major route of the gut-brain axis. Through the vagus nerve, information about inflammation, nutrient status, microbiome composition and gut motility can reach the brain.

And this is where it becomes relevant for anyone dealing with chronic illness: low vagal tone — meaning weaker vagus nerve activity — is associated in research with higher inflammatory markers, poorer mood regulation and lower stress resilience. That does not make it a simple cause-and-effect switch. But if your vagus nerve is not signaling well, the body may have a harder time applying the brakes. Inflammation can keep running. The immune system may not receive a clear “downshift” signal. And you may wonder why things do not improve, even when you are doing so much.

The vagus nerve is like one of the brake lines of your immune system. When that line is weak, slowing down gets harder — and inflammation can keep rolling forward.

The microbiome talks too — whether you asked or not

Around 38 trillion microorganisms live in your gut. That is more than the number of human cells in your body. And these bacteria are not silent. They produce neuroactive compounds — including GABA, dopamine-related molecules, noradrenaline-related signals and, most famously, serotonin. Roughly 90 to 95 percent of the body’s serotonin is produced in the gut. Not in the brain. In the gut.

That means: when your gut flora is out of balance — dysbiosis, too few helpful strains, too many potentially problematic microbes — those bacteria can do more than produce inflammatory substances that influence signaling toward the brain. They can also affect which messenger substances circulate in your system. Research shows that people with depression often have measurable microbiome differences. People with autoimmune diseases can show them too. That is not proof of one single cause. But it is a strong hint that the gut-brain axis belongs in the conversation.

And it works the other way too: certain bacterial strains — often called psychobiotics — are being studied in relation to mood and stress processing. That is exciting. It is not a reason to turn them into a healing promise.

“Gut feeling” — taken literally

This is the connection that made me write a book. If your gut communicates with your brain through the vagus nerve — and your microbiome actively influences signaling — then what we call “gut feeling” is not a myth. It can be understood as an integrated neurocognitive assessment from two systems that are constantly talking to each other.

Your enteric nervous system registers stimuli that may never reach conscious thought: inflammatory markers, hormone levels, nutrient availability, microbiome signals. All of that feeds into a whole-body assessment that can arrive in awareness as a physical sense — as “intuition.” You feel that something is off before you can think it through. That is not magic. It may be your gut-brain axis sending data upward.

And when that channel is disturbed — through chronic inflammation, dysbiosis, stress — your “gut feeling” can become noisier too. You may read signals less clearly. Decisions get harder. Sleep becomes worse. Mood shifts faster. It is all connected. And for many people, part of that system begins in the gut.

Chronic illness and the gut

Here is the connection many people underestimate: for many chronic issues, the gut can be one relevant layer. Autoimmune diseases are often discussed alongside increased intestinal permeability — the so-called “leaky gut.” When the gut barrier becomes more permeable, substances may enter the bloodstream that do not belong there. The immune system reacts. Inflammation can rise. And through the gut-brain axis, an inflamed gut can signal danger to the brain. The brain responds with stress hormones, which may further strain the gut barrier. A loop can form.

I experienced part of that myself. My immune system was attacking me, and part of the background was a gut that had been burning for years — without anyone really looking. The blood values were there. The medication was there. But the question “How is your gut doing?” did not come up once.

What you can do

So, the gut-brain axis exists. The vagus nerve fires. The microbiome has a voice. But what does that mean in practical terms? These are the areas that can make a meaningful difference for some people — always with medical support when symptoms are strong, new or complex:

  • Stimulate the vagus nerve — Deep belly breathing, cold exposure, singing, humming, gargling, meditation. Anything that supports parasympathetic activity may help build vagal tone. Daily usually matters more than dramatic.
  • Feed the microbiome — Prebiotic fiber from vegetables, fermented foods if tolerated, diversity instead of dietary monoculture. Your microbiome responds to what you repeatedly eat.
  • Reduce gut inflammation triggers — Sugar, ultra-processed foods, alcohol and chronic stress are common gut stressors. Less of them can sometimes do more than another supplement.
  • Support the gut barrier — Glutamine, zinc and short-chain fatty acids such as butyrate from fiber are often discussed here. The barrier may get better conditions when you provide building blocks and reduce load.
  • Include stress regulation — Chronic stress can burden the vagus nerve, microbiome and gut barrier. If you ignore stress completely, an important part of the system is often missing.
  • See food as a signal — What you eat is not only fuel. It is information for your microbiome, your gut and, through that, your brain. Keto, intermittent fasting, anti-inflammatory nutrition — not magic diets, but possible intervention strategies for the gut-brain axis when they fit the person and the situation.

I am not a doctor. I am someone who had to walk this road myself. Someone who learned that the answer to chronic illness is not always only in the next medication — and not always only in lifestyle either. Often the better question is systemic: what is the gut doing, what is the nervous system doing, and how are they talking to each other?

Your gut feeling is not just a phrase. It can be a biological early-warning system. The only question is: are you listening?