Gut Health and Gut Instincts: The Science of the Second Brain

The Gut–Brain Connection

When we talk about a “gut instinct”, we are not being metaphorical. The gut is often referred to as our second brain because of the enteric nervous system (ENS)—a vast network of over 100 million neurons lining the digestive tract. This system communicates bidirectionally with the brain through the vagus nerve, neurotransmitters, hormones, and immune signals.

The gut is also home to trillions of microorganisms—the gut microbiome—that produce neuroactive chemicals like serotonin, dopamine, and gamma-aminobutyric acid (GABA). In fact, around 90–95% of the body’s serotonin is synthesized in the gut, not the brain. This means our emotional state, clarity of thought, and intuitive decision-making are profoundly influenced by what is happening in our digestive system.

When your gut is healthy, the signals sent to your brain are balanced, reliable, and stabilizing. This can amplify your ability to sense subtle cues, weigh decisions intuitively, and act with confidence. Conversely, when the gut is inflamed, imbalanced, or dysregulated, the communication becomes distorted, leading to anxiety, low mood, brain fog, and impaired intuition.

How Gut Health Shapes Gut Instincts

  1. Neurochemical Balance

    • A diverse gut microbiome produces neurotransmitters that stabilize mood and sharpen perception. This helps your “inner compass” work accurately.

    • Dysbiosis (imbalance in gut bacteria) can lead to distorted signaling—making instincts feel unreliable or clouded.

  2. Stress and the Vagus Nerve

    • The vagus nerve is the direct “superhighway” between gut and brain. Stress, poor diet, and chronic inflammation reduce vagal tone, which blunts your intuitive sensitivity.

    • Strengthening vagal tone (through breathwork, humming, yoga, or meditation) sharpens your ability to “read” signals from within.

  3. Interoception

    • Interoception is the brain’s ability to sense internal states. A calm, balanced gut improves interoceptive accuracy, which enhances emotional intelligence and intuitive decision-making.

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Improving Gut Health to Strengthen Gut Instincts

Here are evidence-based ways to align your biological gut health with your intuitive wisdom:

1. Nutrition for a Balanced Microbiome

  • Eat diverse plant-based foods (30+ varieties of vegetables, fruits, herbs, nuts, seeds, legumes per week). Microbial diversity enhances emotional balance and resilience.

  • Prioritize fermented foods (kimchi, sauerkraut, kefir, miso) which introduce beneficial bacteria.

  • Choose polyphenol-rich foods (green tea, dark berries, cacao, extra virgin olive oil) that feed “good” gut bacteria.

  • Limit processed foods, refined sugars, and alcohol, which encourage inflammatory bacteria.

2. Stress Regulation

  • Practice daily breathwork, meditation, or yoga to calm the nervous system and improve vagal tone.

  • Schedule regular relaxation and restorative sleep, as sleep disruption alters the microbiome and weakens intuitive clarity.

3. Mindful Eating

  • Eat slowly, chew thoroughly, and bring awareness to meals. This optimizes digestion and signals safety to the brain, strengthening gut–brain harmony.

  • Avoid eating in a stressed or rushed state, as it distorts gut signals.

4. Supplements (When Needed)

  • Probiotics: can be helpful, but should be strain-specific and ideally tailored after a microbiome test.

  • Prebiotics: fibers like inulin, resistant starch, and pectin feed beneficial bacteria.

  • Omega-3 fatty acids: reduce inflammation and support brain–gut signaling.

5. Building Interoceptive Awareness

  • Practice body scans and mindful attention to internal sensations.

  • Keep a gut journal—notice how different foods, emotions, and environments affect your digestion and decision-making clarity.

Conclusion

Your “gut instinct” is not mystical—it is biological intuition, rooted in the health of your microbiome, the activity of your vagus nerve, and your brain’s ability to interpret internal signals. By cultivating gut health through diet, lifestyle, and mindful awareness, you not only enhance your physical wellbeing, but also sharpen the very instincts that guide wise, aligned decisions in life and leadership.

My learning from the perspective of Dr. Tara Swart, neuroscientist, physician, and executive coach, who bridges brain science, psychology, and wellbeing.

Health, Wellbeing, Staying Healthy, awareness, health and healing, Self-CareDina Khalilgut health, intuition, gut brain axis