Beyond Ammonia: What You Need to Know about Neurotoxicity

by Aric Cox, DC

Neurotoxins are a clear and present threat to healing from Lyme disease.  But this threat does not stop at Lyme.  Neurotoxic load is also an issue with chronic pain syndromes, Fibromyalgia, dysautonomia, gastrointestinal imbalances (e.g. SIBO, IBS), neurodegenerative conditions, and chronic fatigue.

Ammonia is likely one of the better-known neurotoxins, especially in the case of Lyme Disease.  There is yet to be any peer-reviewed, published evidence indicating that the key bacteria involved with Lyme disease (Borrelia burgdoferi) actually excretes a toxin, or possesses toxins, in its cell wall.1,2 However, there is ample research on the action of urease and how bacteria can produce ammonia in our body as a result of its action.3,4 Clinically and anecdotally, practitioners and patients can attest to its presence as well as the associated problems with excess ammonia. 

Patients have reported smelling that unmistakable odor of ammonia emanating from their body.  Testing for ammonia (serum, genetic, et al) connects some dots as to its toll on the liver, kidneys, and brain.  Ammonia-metabolizing protocols have also shown symptomatic improvements. 

But we cannot just stop there.  There are potentially dozens of microbial neurotoxins that can cause equal, if not more, damage as that of ammonia toxicity.

We were made to live deeply connected lives with the microbes of our body.  It is when we tolerate imbalances in our lifestyle (e.g. diet, relationships, sleep, rest) that the microbes within our body, or even those foreign to us, foster imbalances in our health. 

On the spectrum of illness to wellness, the stressors of our lifestyle shift us into dis-ease and eventually to disease.  With more imbalances we, thus, become more susceptible to infections, toxins, conditions, and syndromes.

Like an overflowing barrel, symptoms and loss of function come to the surface once we have taken on too many stressors.  The path to wellness includes finding the appropriate way to drain the barrel (i.e. the process of detoxification).

Detoxification has become a well-known process for seeking health or maintaining health.  Damage to, or irritation of, the nervous system is a common thread between patients with Lyme disease.  The term neuroborreliosis is used to reference the neurological manifestation of Lyme disease in the central nervous system.

The nervous system is highly sensitive to any toxin.  But in the case of chronic Lyme disease, I want to focus on the specific intoxicants known as neurotoxins.  A neurotoxin is any biological, chemical, or physical agent that adversely affects the brain, spinal cord, or nerves.

Across most disease states or conditions, there are three main categories of neurotoxins: 

  1. Heavy metals – mercury, lead, cadmium, aluminum

  2. Biotoxins – produced by bacteria, viruses, fungi, and parasites

  3. Environmental toxins – synthetic compounds produced by man, e.g. dioxins, food preservatives, insecticides. 

All three areas connect to, and influence, Lyme disease. But, for the purpose of this article, I want to focus on biotoxins.  These biological toxins can be further separated into endotoxins, exotoxins, or antimetabolites. 

Endotoxins are non-secreted toxins in the cell wall of the bacteria.  These are typically only a problem when we have too many gram-negative bacteria in our bodies or when these bacteria die.

Lipopolysaccharide (LPS) is the prime endotoxin to stir up the inflammatory response.  Both death of the bacteria and a number of stressors (including antibiotic use) cause the release of this endotoxin.

If our biological terrain and detox pathways cannot clear this, its presence triggers a damaging inflammatory response, increases intestinal permeability (“leaky gut”), inhibits liver function, and disrupts the blood-brain barrier.5

Exotoxins, on the other hand, are toxins actually secreted by the microbes.  They can also be released upon death of the bacteria.

Much like LPS, exotoxins stimulate inflammatory and immune responses that are highly toxic to both the bacteria and our own cells.  This inflammatory signal can create the cascading domino effect into developing a bacterial allergy and overstimulation of our immune system.

Antimetabolites are molecules produced by the normal metabolism of yeast or bacteria that inhibits our normal metabolism.  Essentially, these are the result of microbes eating, breathing, and pooping in our body, which affects our ability to eat, breathe, poop, and more. With both LPS and exotoxins, self-destructive harm comes from the collateral damage as a result of our immune system’s reaction.  Macrophages and neutrophils release strong free radicals that increase oxidative stress, as well as other destructive acids and enzymes that further increase cell damage.

Many of the aforementioned toxins are produced in the gut.  This fact further underscores the absolute necessity of addressing the gut terrain, as these toxins commonly find a way to disrupt the enteric nervous system, the nerves of the body, and the brain itself.

There is also the systemic inflammation that is generated from the imbalance of the biological terrain and microbiome.  No matter where they are coming from in the body, the release of these chemicals in the body exacerbates mitochondrial dysfunction.  This inhibits the metabolism and cellular machinery needed to detoxify poisons, regulate immunity, and stifles the energy to heal.

Systemic inflammation’s effect on the brain activates microglial cells (immune cells of the brain).  Microglia will then trigger increased neuron-to-neuron signaling via the neurotransmitter glutamate.  Higher amounts of glutamate promote lower thresholds to pain, brain fatigue, brain fog, depression, anxiety, and migraines.  Prolonged microglial activation brings on neurodegeneration.6

Basically, when our microbes are more burdensome than helpful, and our biological terrain can no longer take the garbage out, the nerves of our body are set on fire.  This fire significantly reduces our brain’s ability to function and regulate the systems of our body, causing us to feel more pain, and experience more depression and anxiety.  When left under fire for too long, our brain cells burn out and break down.

No matter the source of bacterial neurotoxic burden in the body, the toll on the brain and nervous system is severe.  Whether microbes have crossed the blood-brain barrier or reside in our gut, the chemicals they produce, as well as the chemicals we produce in response to their overpopulated presence, impair proper communication between brain and body.

Our detoxification pathways are adept at removing both endotoxins and exotoxins when all systems are balanced.  By applying correction, rebalancing, and support to the body through the lens of our BioRestorative Matrix, it makes a significant impact on the neurotoxic load.

If you are concerned about how neurotoxins are affecting you, please contact the Institute for Restorative Health.  For more on how you can reduce toxins, stay tuned.


  1.  Takayama, K., R.J. Rothenberg, and A.G. Barbour. 1987. Absence of lipopolysaccharide in the Lyme disease spirochete, Borrelia burgdorferi. Infect. Immun. 55:2311-2313.

  2. Fraser, C., S. Casjens, W.M. Huang, et al.  1997.  Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.  Nature.  11; 390(6660): 580-6.

  3. Kimoloi, S., Rashid, K.  2015.  Potential role of Plasmodium falciparum-derived ammonia in the pathogenesis of cerebral malaria.  Front Neurosci.  9: 234.

  4. Konieczna, I. et al.  2012.  Bacterial Urease and its Role in Long-Lasting Human Diseases.  Curr Protein Pept Sci.  Dec; 13(8): 789-806.

  5. “Chapter 4.2: Infections & Dysbiosis.” Inflammation Mastery: The Colorful and Definitive Guide toward Health and Vitality and Away from the Boredom, Risks, Costs, and Inefficacy of Endless Analgesia, Immunosuppression, and Polypharmacy, by Alex Vasquez, International College of Human Nutrition and Functional Medicine, 2016, pp. 404.

  6. “Chapter 5.1: Functional Inflammology Protocol for Metabolic Inflammation.” Inflammation Mastery: The Colorful and Definitive Guide toward Health and Vitality and Away from the Boredom, Risks, Costs, and Inefficacy of Endless Analgesia, Immunosuppression, and Polypharmacy, by Alex Vasquez, International College of Human Nutrition and Functional Medicine, 2016, pp. 934-935.

About the Author:

Dr. Aric Cox, DC completed his undergraduate work at the University of Kansas with a bachelor’s degree in anthropology. From there, he received his doctorate and graduated with honors from Cleveland University-Kansas City. While pursuing his doctorate, he also received certification in acupuncture and is a fellow in the Acupuncture Society of America. Dr. Cox holds certification in Chiropractic Plus Kinesiology through his training with Dr. Milton Dowty. For 5 years, he worked at the Hansa Center for Optimum Health advancing his certification in BioResonance Scanning while studying with Dr. David Jernigan. He also studied Biological Medicine with Dr. Thomas Rau, Medical Director of the prestigious Paracelsus Clinic in Lustmühle, Switzerland. Dr. Cox is certified in functional medicine through the Institute for Functional Medicine. Dr. Cox is one of the founders of the Institute for Restorative Health – 2307 N. Rock Rd. Suite 500, Derby, KS 67037

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