When I first began my career as an internist & pediatrician, and eventually a functional medicine physician, my approach was clear — if you correct the body’s biochemistry, health will follow.

The deeper I went into practice, however, the more I realized that biochemistry doesn’t exist in isolation. Our psychological, emotional, and spiritual states play just as critical a role in shaping health outcomes. This understanding deepened during after joining The Guest House Ocala, a residential trauma and addiction treatment center, where I witnessed firsthand how addressing psychological trauma led to profound improvements in physical symptoms and biochemical imbalances.

Later, after completing my certification in psychological trauma through Spirit2Spirit Healing, under the guidance of Judy Crane, one of the pioneers in the field of psychological trauma and cofounder of The Guest House, it became even clearer: trauma and chronic stress don’t just leave emotional scars — they physically reshape the brain. This rewiring locks patients into a vicious cycle where altered brain structure reinforces patterns of stress, dysregulation, and chronic symptoms.

As practitioners, we often see patients struggling with symptoms of anxiety, hypervigilance, emotional dysregulation, memory issues, and even physical tension. These symptoms don’t just stem from how a person feels—they reflect real, measurable changes in brain structure and function caused by psychological trauma.

Understanding how trauma physically alters the brain—while integrating functional medicine testing and interventions—empowers us to better support our patients’ recovery. Let’s explore four key brain regions impacted by trauma and how functional medicine can guide personalized healing strategies, including the emerging role of hyperbaric oxygen therapy (HBOT).

The Amygdala: The Brain’s Alarm System

The amygdala is the brain’s fear center, responsible for detecting threats and triggering fight, flight, or freeze responses.

Trauma’s Impact on the Amygdala

Chronic or traumatic stress enlarges the amygdala and makes it more reactive. This heightened sensitivity means even neutral situations may feel threatening, leaving patients anxious, hypervigilant, or easily startled.

Functional Medicine Approach

To help regulate the amygdala, functional medicine strategies include:

• HPA Axis Testing: Salivary 4-point cortisol testing reveals whether a patient’s stress response is over-activated (often linked to amygdala hyperactivity).
• Adaptogenic Support: Adaptogens like ashwagandha can help modulate the stress response, indirectly calming amygdala overactivation.
• Mindfulness and Somatic Work: These practices help retrain the amygdala’s threat response.
• Hyperbaric Oxygen Therapy (HBOT): By improving oxygen delivery and reducing neuroinflammation, HBOT may indirectly reduce the amygdala’s chronic hyperactivity.

The Prefrontal Cortex: The Executive Function Center

The prefrontal cortex governs rational thinking, decision-making, emotional regulation, and impulse control.

Trauma’s Impact on the Prefrontal Cortex

Trauma shrinks this region, making it harder for patients to:

• Regulate emotions.
• Solve problems under stress.
• Override automatic fear responses triggered by the amygdala.

Functional Medicine Approach

Supporting the prefrontal cortex through functional medicine includes:

• Nutritional Support: B vitamins, omega-3 fatty acids, and magnesium are all critical for prefrontal cortex function and neuroplasticity.
• Circadian Reset: Encouraging consistent wake-sleep cycles with morning light exposure enhances prefrontal activity.
• Cognitive Training and Therapy: Tools like neurofeedback and cognitive behavioral therapy (CBT) enhance prefrontal processing.
• Hyperbaric Oxygen Therapy (HBOT): By increasing oxygen delivery to the brain and enhancing cerebral blood flow, HBOT may help restore prefrontal cortex volume and improve cognitive function in trauma-impacted patients.

The Hippocampus: The Brain’s Memory Processor

The hippocampus helps form, store, and retrieve memories while distinguishing between past and present experiences.

Trauma’s Impact on the Hippocampus

Trauma shrinks the hippocampus, interfering with:

• Memory formation and recall.
• Accurate time-stamping of memories (leading to flashbacks).
• Differentiating real-time safety from past threat triggers.

This can lead to intrusive memories, fragmented recall, and feeling stuck in the past.

Functional Medicine Approach

Hippocampal regeneration can be directly supported with:

• Physical Activity: Aerobic exercise has been shown to stimulate hippocampal neurogenesis.
• Nutritional Support: Polyphenols, omega-3s, and phosphatidylserine support memory formation and neuroplasticity.
• EMDR and Trauma Processing Therapies: These modalities help the hippocampus properly integrate traumatic memories into the timeline of life.
• Hyperbaric Oxygen Therapy (HBOT): Research shows that HBOT can stimulate hippocampal neurogenesis and reduce inflammation in hippocampal tissue, supporting better memory consolidation and cognitive recovery.

The Cerebellum: The Brain’s Sensory and Motor Integrator

The cerebellum, often overlooked in trauma discussions, plays a critical role in coordination, sensory processing, and autonomic regulation.

Trauma’s Impact on the Cerebellum

Emerging research shows that trauma can dysregulate cerebellar function, contributing to:

• Poor balance and coordination.
• Heightened sensory sensitivity (light, sound, touch).
• Disconnection between body awareness and emotional states.

Functional Medicine Approach

To support cerebellar health and regulation, consider:

• Sensory Integration Therapy: Functional medicine can collaborate with occupational therapists trained in sensory regulation techniques.
• Nervous System Reset: Practices like vagal nerve stimulation, breathwork, and trauma-informed movement reconnect body and brain.
• Targeted Nutrition: Magnesium, zinc, and DHA support cerebellar plasticity.
• Hyperbaric Oxygen Therapy (HBOT): By improving oxygen supply and reducing neuroinflammation in the cerebellum, HBOT may enhance coordination, sensory processing, and autonomic balance.

Functional Medicine Testing for Trauma Recovery

Functional medicine excels in providing objective data to guide recovery from trauma-induced brain changes. Key assessments include:

Salivary Cortisol Testing

This remains the gold standard for identifying HPA axis dysregulation, which often accompanies trauma. A flattened or exaggerated cortisol curve can reflect either hypervigilance (overactive amygdala) or blunted resilience (hypoactive HPA axis).

HRV (Heart Rate Variability) Monitoring

Tracking HRV offers real-time insight into nervous system flexibility, a key marker of trauma recovery.

Comprehensive Nutritional Testing

Checking for B vitamin status, omega-3 levels, and inflammatory markers can identify nutritional gaps affecting brain resilience.

Final Thoughts

Understanding how trauma physically changes the brain helps practitioners:
✅ Educate patients about why they feel the way they do.
✅ Shift the focus from self-blame to biology and recovery.
✅ Implement personalized, evidence-based strategies rooted in functional medicine and neuroplasticity.

The brain is remarkably adaptable. With the right testing, targeted nutritional support, nervous system therapies, trauma processing, and emerging tools like HBOT, trauma survivors can rewire fear responses, rebuild cognitive function, restore memory processing, and reconnect with their bodies.

Want to Master Your Functional Medicine Game?

Join our FMP Essentials Mastermind — a hands-on mentorship designed for functional medicine practitioners who want to:

✅ Master advanced lab testing and interpretation
✅ Learn proven strategies for complex cases — from HPA axis dysfunction to trauma recovery
✅ Get direct mentorship and collaborate with a community of forward-thinking practitioners

🔗 Learn More and Join Here

-Yousef Elyaman, MD, IFMCP

Founder of FMP Essentials

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    https://doi.org/10.4103/2045-9912.208514