The Invisible Connection: Why Mental Health Is Gut Health

I remember standing in an elevator in a New York City skyscraper, staring at seven different prescriptions in my hand.

I was finishing my cardiology fellowship at Lenox Hill Hospital. My life was a blur of sleepless nights, hospital cafeteria food, and constant stress. Somewhere along the way, my body started to break down. I developed severe allergies, Irritable Bowel Syndrome, and a heavy depression I couldn’t shake.

As a doctor, I knew something wasn’t right.

These medications weren’t healing me. They were painting the brown leaves green, silencing symptoms while the roots of the tree continued to rot.

That realization changed everything. It led me to Functional Medicine, where I discovered a truth that Western medicine is only now beginning to acknowledge:

Mental health is inseparable from gut health.

Your Second Brain: A Superhighway of Information

We tend to think of the brain in our skull as the sole command center for our emotions, thoughts, and mental health. But that view is incomplete.

Your gut contains its own vast and sophisticated nervous system, the enteric nervous system, often referred to as the second brain. In fact, the gut contains hundreds of millions of neurons and communicates continuously with the brain through the vagus nerve.

When the gut is calm and nourished, it sends signals of safety and balance.

When the gut is inflamed or irritated, it sends distress signals, often experienced as anxiety, irritability, low mood, or brain fog.

Your thoughts don’t just come from your head.

Many of them begin in your gut.

The Serotonin Factory

When someone is diagnosed with depression, the standard medical response is often an SSRI, medications designed to keep serotonin available in the brain for longer.

But there’s a crucial question rarely asked:

Where is serotonin actually made?

Between 80–90% of the body’s serotonin is produced in the gut, largely influenced by the microbiome. SSRIs may affect serotonin signaling, but they do nothing to repair the system that produces it.

If the gut is inflamed, damaged, or microbiome-depleted, serotonin production is compromised at the source.

A damaged gut doesn’t just affect digestion.

It affects motivation, resilience, emotional regulation, and joy.

The Broken Border: Leaky Gut and Mental Fog

I often call the gut the Achilles’ heel of modern biology.

Just beneath the gut lining lives nearly 80% of the immune system (the GALT). Modern foods—especially processed sugar, refined carbohydrates, industrial oils, alcohol, and gluten—can damage the tight junctions that hold the gut wall together.

When these junctions loosen, the gut becomes permeable, a condition commonly called leaky gut.

This allows bacterial fragments, particularly lipopolysaccharides (LPS), to escape into circulation, triggering systemic inflammation. That inflammation reaches the brain, disrupting neurotransmitter balance and stress hormones.

An inflamed gut creates an inflamed mind.

Healing the Mind by Healing the Gut: The Functional Medicine Approach

To heal mental health, we must heal the environment in which the mind operates.

In Functional Medicine, we use a framework known as the Five Rs. This is not theory, it’s a practical, repeatable system.

1. Remove: Eliminate the Irritants

Healing always begins by removing what is interfering with the body’s natural ability to regulate and repair itself.

In the gut, this means eliminating foods and substances that damage the intestinal lining, disrupt the microbiome, and trigger chronic immune activation. An elimination diet is not about restriction, it is about creating a temporary environment of safety so healing can begin.

Common dietary irritants include:

• Added sugars and refined carbohydrates, which feed inflammatory microbes and destabilize blood sugar
• Gluten and, for many people, dairy, which can increase intestinal permeability and immune reactivity
• Alcohol and excess caffeine, both of which irritate the gut lining and overstimulate the nervous system
• Ultra-processed foods and industrial seed oils, which promote systemic inflammation

When these irritants are removed, inflammation begins to settle. The immune system no longer needs to stay on high alert, and the gut is given the opportunity to calm down. Many people notice early improvements not only in digestion, but also in mood, energy, and stress resilience.

Reducing gut inflammation lowers inflammatory signals to the brain, a key driver of anxiety, irritability, and low mood.

2. Repair: Heal the Gut Lining

The intestinal lining renews itself rapidly, but only when it has the nutrients required to do so. Chronic stress, poor diet, and inflammation can deplete these building blocks, leaving the gut vulnerable and permeable.

Key nutrients that support gut repair include:

• L-glutamine, the primary fuel source for intestinal cells
• Zinc carnosine, which supports mucosal healing and tight junction integrity
• Omega-3 fatty acids, which reduce inflammation and support cell membrane health
• Polyphenols, found in plants and herbs, which protect the gut lining and nourish beneficial bacteria

Together, these nutrients help reseal the intestinal barrier, restoring its ability to selectively absorb nutrients while keeping inflammatory particles out of circulation.

A repaired gut wall reduces immune activation and inflammatory signaling to the brain, creating a calmer internal environment for neurotransmitter balance and nervous system regulation.

3. Restore: Support Digestion

Even with a healthy diet, digestion must function properly for healing to occur.

Many people today suffer from low stomach acid, insufficient bile flow, or inadequate digestive enzyme production, often as a result of chronic stress, aging, or years of inflammatory eating patterns.

Supporting digestion may include:

• Supplemental digestive enzymes to improve nutrient breakdown
• Bitters or bile-supporting nutrients to enhance fat digestion
• Mindful eating practices, such as slowing down and eating without distraction

Digestion is governed by the nervous system. When we rush meals or eat under stress, the body remains in fight-or-flight mode, and digestion shuts down. Simply slowing down activates the parasympathetic nervous system, the same system responsible for calm, repair, and emotional balance.

Proper digestion prevents partially digested food from irritating the gut lining and triggering immune responses that ripple outward into systemic inflammation and stress. 

Efficient digestion reduces inflammatory burden and stabilizes blood sugar, two major factors influencing mood, anxiety, and energy.

4. Reinoculate: Rebuild the Microbiome

A healthy gut depends on a diverse, balanced, and resilient microbiome. These trillions of microorganisms are not passive passengers, they actively shape digestion, immunity, metabolism, and emotional wellbeing.

Rebuilding this internal ecosystem requires more than simply adding bacteria. It means creating an environment in which beneficial microbes can thrive.

This includes the strategic use of targeted probiotics, along with an abundance of prebiotic fibers from vegetables, seeds, and resistant starches that serve as nourishment for healthy bacteria. Fermented foods can also play a supportive role when tolerated, helping to introduce beneficial organisms while enhancing digestive function.

The microbiome plays a direct role in the production and regulation of neurotransmitters, in modulating inflammation, and in shaping the body’s response to stress. When microbial balance is restored, communication along the gut–brain axis becomes clearer, often reflected in improved mood, emotional resilience, and a greater sense of calm.

5. Relax: Activate the Healing State

Chronic stress is one of the most powerful disruptors of gut health. When the body is under constant stress, digestion is suppressed, gut permeability increases, and the microbiome becomes imbalanced. The nervous system shifts into survival mode, leaving little energy for repair, regeneration, or healing.

True healing requires guiding the body back into its natural state of balance by activating the parasympathetic nervous system and the vagus nerve, the pathways responsible for rest, digestion, and renewal.

Some ways to do this are:

• Sleep
• Breathwork
• Meditation
• Gentle movement
• Time away from constant stimulation
• Time in nature

One particularly powerful practice is leaving at least 12 hours between dinner and breakfast. This allows the body to shift from continuous digestion into repair, detoxification, and cellular renewal. Giving the gut this daily rest can have a profound impact on inflammation, metabolism, and nervous system regulation.

Learn more about intermittent fasting and how giving your body the digestive break it needs can support both gut health and peace of mind.

Reclaim Your Vitality

You don’t have to wait for a diagnosis to begin healing. If you feel foggy, heavy, anxious, inflamed, or emotionally stuck, your body may be asking for support at the root level.

• Clean 21: A comprehensive 21-day gut reset designed to reduce inflammation and restore balance
• Clean 7: A powerful one-week breakthrough combining Functional Medicine, Ayurvedic wisdom, and intermittent fasting
• The Daily Ritual: Replacing one meal a day with a nutrient-dense shake reduces digestive workload and frees energy for repair and emotional stability
  

Your health doesn’t start in your head.

It starts in your roots.

Let’s start cleaning them.

To your health,

Dr. Alejandro Junger