Beyond Repair: When Mental Illness Has a Hidden Cause: How Nutrient Deficiencies and Infections Can Change the Mind

In our practice, we often see patients whose mental or behavioral symptoms have been labeled as psychiatric disorders — but the root cause lies somewhere else entirely. Sometimes, it’s not a chemical imbalance in the brain that’s the problem; it’s a deficiency in vital nutrients or an undiagnosed infection that’s quietly changing brain function (Bodnar & Wisner, 2005; Miller et al., 2013).

Case Study: Schizophrenia and Functional Medicine

A middle-aged man presented to with a diagnosis of schizophrenia. His chief complaint at the first visit was “sores” on his body that would not heal. On examination, his affect was sad and flat, he had no motivation, and he expected a prescription for a topical skin medication.

During a thorough assessment, however, we found signs and symptoms of small intestinal bacterial overgrowth (SIBO) along with nutritional deficiencies. We implemented a functional medicine plan to correct these imbalances, including antimicrobial support for SIBO, dietary changes, and nutrient repletion.

At his 10-day follow-up, the difference was striking. His facial expression was no longer flat. He appeared happy, energetic, and motivated. Both he and his psychiatrist noted the improvements. He proudly told us he had changed his diet and was on his way to mow his mother’s lawn — something he had not felt motivated to do for a long time.

This case highlights the importance of addressing underlying gut dysbiosis and nutritional deficiencies in patients with psychiatric diagnoses. What seemed to be a purely psychiatric condition improved rapidly once the root causes were treated.

Rare Nutritional Causes of Psychiatric Symptoms

Some lesser-known nutrient-related triggers of mental illness include:

• Autoimmune B12 Deficiency (Pernicious Anemia) – psychiatric symptoms may appear before anemia (Lindenbaum et al., 1988)

• B12 Deficiency from Diet or Medications – common in vegan diets, metformin use, proton pump inhibitors, H2 blockers, nitrous oxide exposure, and long-term oral contraceptives (O’Leary & Samman, 2010; Valuck & Ruscin, 2004)

• Folate Deficiency – from poor diet, alcoholism, methotrexate, or anticonvulsants (Reynolds, 2002)

• Lithium Deficiency – low trace mineral intake linked to mood instability and suicide risk (Kapusta et al., 2011)

• Magnesium Deficiency – can cause anxiety, depression, and treatment-resistant depression (Eby & Eby, 2006)

• Zinc Deficiency – linked to mood disorders and cognitive decline (Nowak et al., 2005)

• Iron Deficiency (Low Ferritin) – associated with depression, ADHD-like symptoms, and fatigue (Beard et al., 2003)

Infectious Causes of Neuropsychiatric Symptoms

Sometimes infections directly impact the brain:

• PANDAS/PANS – pediatric autoimmune neuropsychiatric disorders linked to strep or other infections usually hidden in the gut, causing sudden-onset OCD, tics, and mood changes (Swedo et al., 2012)

• Neurosyphilis – can mimic dementia, psychosis, or depression (Ghanem, 2010)

• Lyme Neuroborreliosis – associated with depression, anxiety, and cognitive decline (Fallon et al., 1998)

• Viral Encephalitis (e.g., HSV, EBV, post-COVID) – can trigger personality changes and psychosis (Granerod et al., 2010)

• Toxoplasmosis – linked to mood and personality changes (Torrey & Yolken, 2003)

• CNS Fungal Infections – more common in immunocompromised patients (Perfect, 2017)

Testing for Underlying Causes

• Functional Stool Testing – to identify dysbiosis, pathogens, and gut inflammation markers

• Lab Tests – CBC, CMP, vitamin/mineral panels (B12 with MMA and homocysteine, folate, zinc, RBC magnesium, ferritin, copper/ceruloplasmin)

• Autoimmune Markers – anti-intrinsic factor and anti-parietal cell antibodies

• Infectious Panels – RPR/VDRL, Lyme serology, HIV, HSV PCR, EBV, Toxoplasma

The Takeaway

Not every psychiatric symptom originates in the brain. Sometimes, the brain is simply reacting to an inflamed gut, a depleted nutrient reserve, or a silent infection. When we treat the underlying cause, the 'psychiatric' illness often resolves — sometimes in a matter of days, as in this schizophrenia case. If you or your loved one have persistent mental health symptoms that don’t fully respond to medication, it may be time to look deeper. The answers might not be in the psychiatrist’s office alone — they may be in the lab results from a functional medicine workup.

References

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Bodnar, L. M., & Wisner, K. L. (2005). Nutrition and depression: implications for improving mental health among childbearing-aged women. Biological Psychiatry, 58(9), 679–685.

Cryan, J. F., et al. (2019). The microbiota-gut-brain axis. Physiological Reviews, 99(4), 1877–2013.

Eby, G. A., & Eby, K. L. (2006). Rapid recovery from major depression using magnesium treatment. Medical Hypotheses, 67(2), 362–370.

Fallon, B. A., et al. (1998). Psychiatric manifestations of Lyme borreliosis. American Journal of Psychiatry, 155(11), 1571–1583.

Ghanem, K. G. (2010). Neurosyphilis: A historical perspective and review. CNS Neuroscience & Therapeutics, 16(5), e157–e168.

Granerod, J., et al. (2010). Causes of encephalitis in England: a prospective study. The Lancet Infectious Diseases, 10(12), 835–844.

Kapusta, N. D., et al. (2011). Lithium in drinking water and suicide mortality. The British Journal of Psychiatry, 198(5), 346–350.

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Lindenbaum, J., et al. (1988). Neuropsychiatric disorders caused by cobalamin deficiency without anemia. NEJM, 318(26), 1720–1728.

Miller, A. H., et al. (2013). Inflammation and its discontents: the role of cytokines in depression. Biological Psychiatry, 65(9), 732–741.

Nowak, G., et al. (2005). Effect of zinc supplementation on antidepressant therapy. Polish Journal of Pharmacology, 57(6), 799–804.

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Perfect, J. R. (2017). The antifungal pipeline: a reality check. Nature Reviews Drug Discovery, 16(9), 603–616.

Reynolds, E. (2002). Vitamin B12, folic acid, and the nervous system. The Lancet Neurology, 1(1), 43–50.

Swedo, S. E., et al. (2012). Modifying the PANDAS criteria to describe PANS. Pediatric Therapeutics, 2(2), 113.

Torrey, E. F., & Yolken, R. H. (2003). Toxoplasma gondii and schizophrenia. Emerging Infectious Diseases, 9(11), 1375–1380.

Valuck, R. J., & Ruscin, J. M. (2004). Proton pump inhibitors and vitamin B12 deficiency in older adults. Journal of Clinical Epidemiology, 57(4), 422–428.