In the first Gut-Brain article in the series, we established there is a gut-brain axis (GBA) and the pathways through which the gut and brain are connected. In this article, we will cover:

  • Sources of inflammation
  • How inflammation hurts both your gut and your brain
  • Cognitive and emotional imbalances resulting from gut dysbiosis


Inflammation is the root of many undesirable symptoms and diseases in the body [1]. Inflammation in the gut does not stay in the gut, but can extend into all bodily systems, including the brain. So what causes this pervasive inflammation? External toxins, such as pesticides, genetically modified organisms, water & air pollutants, chemicals from plastics and endocrine disrupting chemicals [1, 2], just to name a few. In addition to the outside world affecting our internal world, internal toxins, those created or released inside the body (via various pathways such as digestion or detox), such as sugar, bacterial byproducts, heavy metals, some strains of fatty acids and gluten proteins, also trigger inflammation.



Let’s take a closer look at the toxins we are exposed to from the environment and how they create inflammation. Just within our food supply, toxins abound. Genetically modified organisms (aka GMOs) are foods that have had their DNA altered, which initially sounds like a benefit- no bugs destroying crops? Great! Larger fruits? Awesome! But altering the DNA of foods also alters our DNA once we eat it and not for the better [1]. Even one altered piece of DNA can create disease [3]. GMOs have become the staple ingredients in all of our meals; unless an item has the “NON-GMO Verified” or “organic” label, it contains genetically modified ingredients. What the “NON-GMO Verified” label doesn’t include is the validation that there are no pesticides used to grow / make the product. Oh, but they keep the bugs away right? WRONG.

Pesticides and herbicides are toxic chemicals sprayed over fields of crops that end up harming your gut, your endocrine system, your tissues, all of your organs and your brain. These chemicals don’t get excreted with the rest of the food you eat, they cozy up in different areas of your body and nestle in for life. In particular, glyphosate, the active ingredient in the herbicide Roundup, has been shown to disrupt liver enzymes, facilitate the buildup of gallstones, and interferes with the digestive enzymes responsible for breaking down fats and proteins. Glyphosate can even open the tight junctions of the gut wall and the blood-brain barrier (BBB) [4]. In addition, the pesticides chlorpyifos and organophosphorous have been shown to negatively affect the development of the brain [5]. Pesticides and GMOs create DNA mutations and misfolded proteins in the brain, increasing the risk of cancer and neurodegenerative diseases, like Parkinson’s disease [2].

Undigested proteins inflame the gut and can open the tight junctions in the lining of the intestines. Glyphosate also opens the blood-brain barrier (BBB), allowing toxins to enter the brain. Important to note, herbicides like Roundup are not just sprayed on fruits and vegetables, they are also sprayed on wheat, grains, legumes, oats, canola, sugar cane, coffee and tea, among others, and including on NON-GMO verified foods. Glyphosate hides in protein chains and can be found in many high protein foods, like soy, beans, and meat [4]. Glyphosate-based herbicides have been shown to induce behavioral changes, including mood alterations, and also change the microbiome composition, reducing many health-promoting bacteria species [6].


I could spend days covering the detrimental effects gluten has on the body, but let’s start with a brief overview. Gluten negatively affects the body in various ways, one of which is changing the bacterial species present in the gut, reducing the helpful strains and feeding the inflammatory strains. These changes occur within just 30 minutes of ingestion [16]! Related to this microbiome interference, gluten impedes the break down and absorption of nutrients. When gliaden, a gluten protein, makes its way to the intestines, it impacts the gut lining by loosening the tight junctions between cells, allowing inflammatory compounds and bacterial toxins into the bloodstream [17]. This raises the amount of LPS in the blood, further promoting inflammation.

Gluten proteins negatively impact digestive enzymes, which subsequently damages the intestines, liver, gallbladder and pancreas. And the damage doesn’t stop there, gluten’s inflammatory effects go all the way to the brain! Research shows that cerebrospinal fluid contains antibodies to gluten (and dairy), indicating the BBB has been disturbed. It doesn’t just cause a leaky gut, it creates a leaky brain! Multiple neurotransmitters are affected, including serotonin (happiness), dopamine (motivation), acetylcholine (learning) and epinephrine (stress).

Gluten ingestion has been linked to mental health disorders such as depression, autism, ADHD, schizophrenia, bipolar disorder and seizures [18,19]. An important piece of evidence is that schizophrenic patients who went on a gluten free diet demonstrated a disappearance of psychiatric symptoms and normalized brain function [17]. While this result cannot be expected to happen with everyone, it wouldn’t hurt to try eliminating gluten to see if improvement occurs. The link between gluten and mental health is not surprising given the research showing that gluten negatively impacts the function of the frontal lobe, regardless of if you are “gluten sensitive” [20].

One of the reasons people find it so hard to want to remove gluten from their diet is because it activates the opioid receptors in the brain, creating an addiction response and cravings. Wheat, just one source of gluten, has been shown to be highly excitotoxic. As mentioned earlier, excitotoxicity means that brain cells are damaged and /or killed and relates to neurodegenerative diseases like Alzheimer’s and Multiple Sclerosis, along with migraines and epilepsy [21].

According to Dr. Perlmutter, environmental chemicals in the air we breathe gets absorbed into our lungs; water contaminates, like chlorine, fluoride and pharmaceutical drugs [1, 7, 8], invade our entire body; plastics from bottles, cans and fish make a home in us [2] and microwave radiation affects our body on the cellular and DNA levels.  Antibiotics are given to meat and dairy animals, which are then taken into our body when we eat those products. They are also brought in via the water supply, if water is not appropriately filtered [1]. Antibiotics do not selectively target harmful bacteria, instead wiping out all bacteria, including the helpful species that protect our digestive health, neurotransmitter production and overall well being.
Toxins that are created or released inside the body, such as stress hormones, heavy metals, metabolic byproducts and gluten proteins, all create an inflammatory response in the body. We all experience stress from time to time, but chronic stress activates and wears out the immune system. When the immune system is in overdrive all the time, the body is creating unnecessary inflammation, as there is no real invader to fight off. This increases the risk for chronic disease, like heart disease, Parkinson’s, dementia, depression or cancer [1].


Heavy metals like mercury, lead, arsenic, cadmium and aluminum all contribute to brain inflammation. They often accumulate in the liver, intestines and brain tissue, settling in and releasing neurotoxic compounds that harm nearby cells, mutate DNA and can inhibit optimal brain function [9]. Heavy metals enter the body through the water supply, pharmaceutical drugs, meat, fish, dairy and aluminum foil [1, 2]. While some arsenic comes from rice, the main dietary sources are actually poultry and tuna.  Mercury is mainly taken in from seafood and fish oil supplements [2], but is also received from vaccines [10] and can be leached into the body from silver/amalgam dental fillings [1]. Dairy is the leading cause of lead contamination [2]. Pesticides, poorly filtered (or unfiltered tap) water and common cookware also contain heavy metals [11]. Heavy metals come in through food and water, but are released from their source in the body and make a home in various places. Heavy metals can also be inherited, primarily from the mother during gestation, and passed down for many generations [9]. Heavy metals have been correlated to many diseases, including depression, autism, bipolar disorder, Alzheimer’s, and those of the gut [2, 9, 12].


Bacteria in the gut contribute to inflammation via toxic compounds called lipopolysaccharides (LPS for short). LPS, if released into the bloodstream, creates a dramatic inflammatory response and can travel to the brain, creating deep brain inflammation [1, 13]. LPS decreases the brain-derived neurotrophic factor (BDNF), a hormone important for protecting neurons, maintaining balanced neurotransmission and neurogenesis. Elevated levels of LPS have been linked with conditions such as Alzheimer’s Multiple Sclerosis, Parkinson’s, autism, depression and inflammatory bowel disorders [1].


Inflammation is also created by proteotoxins, food components that cause a cascade of inflammatory responses [8]. These proteotoxins include sugar, artificial sweeteners, trans and saturated fats, short-chain fatty acids and dairy & gluten proteins, among others. Sugar spikes insulin and triggers inflammatory chemicals to be released in the blood, creating toxic compounds called AGEs (advanced glycation end products), which are really just deformed molecules that damage blood vessels and the brain, in a sense aging the body very quickly [1]. Artificial sweeteners, like aspartame (Nutrasweet, Equal) or Sweet ’n’ Low, are even more toxic and are associated with an increased risk of depression, irritability and poor cognitive performance [2]. Aspartame, along with MSG, is an excitotoxin, meaning it attacks your brain cells and overstimulates them into death [14, 24]. These toxins can be found in anything labelled “sugar free” or “natural flavors”, along with Chinese food, canned vegetables or soups, processed meats and even cereal and juice.

According to Green Med Info, trans fats have been linked with aggression and irritability, along with cancer and cardiovascular disease [15]. They inhibit the production of the beneficial omega-3 fatty acids [15] and are found in processed foods, meat and dairy [2]. Saturated fats are also linked to heart disease and are mainly found in meat, dairy, eggs and processed foods [2]. Saturated fats create toxic products when they are broken down in the body, causing wide-spread inflammation and are related to various diseases like diabetes, various cancers and almost evert major disease Americans suffer from [2].

When the bacteria in your gut break down fiber, different forms of short-chain fatty acids (SCFAs) are produced as metabolic byproducts. Two of them are beneficial for the gut, having anti-inflammatory effects, whereas another is harmful. Propionic acid (PPA) weakens the tight junctions of the gut lining, going into the bloodstream itself and also allowing other harmful compounds into the bloodstream. The immune activation because of this affects how cells communicate and impacts the brain’s ability to use energy. Protein and DNA damage occurs, while reducing levels of supportive omega-3s and antioxidants. What determines if the helpful for hurtful SCFAs are produced? What species of bacteria are populating your gut [1].


When toxins enter the bloodstream, by passing through the mucous membrane of the intestinal wall [22], the immune system releases inflammatory compounds called cytokines to attack the invaders. Cytokines, along with elevated blood sugar, create inflammation in the bloodstream which can travel anywhere and everywhere in the body [1]. Bad bacteria in the gut eat heavy metals for food and then release ammonia gas and neurotoxins into the bloodstream [9]. Another type of inflammatory compound, LPS, a combination of fat and sugars, is also then moving around in the bloodstream and creates a cascade of inflammation [1]. LPS molecules can even cross into the brain and trigger deep brain inflammation [13]. LPS isn’t the only molecule that gets into the brain; inflammatory cytokines increase the permeability of the BBB, further contributing to anxiety, depression and memory loss [23]. Even if toxins don’t travel immediately up to the brain, they disrupt liver and gallbladder function, hindering the removal of toxins, and reduce digestive enzymes [4]. When the liver can’t detox the daily toxins the body is exposed to, those toxins are stored in fat cells, especially the brain [24]! Gut and lower organ inflammation still gets gets transmitted to the brain via the vagus nerve, contributing to mental health imbalances [25, 26]. Environmental chemicals from pesticides and meat block hormone receptor sites, creating hormone imbalances [1]. All of this inflammation triggers oxidation of cells (like rust on your car), which is what damages DNA, ages the body and creates disease [27, 2], along with lowering the body’s immunity, increasing susceptibility to disease [27].


About 16 million Americans suffer from at least one depressive episode each year [2], so it’s very likely someone you know is familiar with this debilitating struggle, if you haven’t experienced it yourself. A direct causal link between inflammation and depression has been shown by numerous studies [1, 2, 23, 28, 29, 30]. Elevated levels of LPS are seen in people suffering from depression and the higher the levels, the worse the depression [1]. Similarly, one study found that infusing endotoxins into non-depressed people increased inflammatory cytokine production and made them depressed! Interestingly, infusing cytokines by themselves did not elicit depressive symptoms, showing that it is toxin-induced inflammation that triggers mood changes [23]. Glyphosate has been investigated for its effects on mood and results show exposure creates behavioral changes and increases anxiety and depression-like behaviors [6]. Arachidonic acid, a pro-inflammatory compound found in chicken and eggs, triggers neuroinflammation and significantly contributes to depression and even risk of suicide [2]. Depression has been linked to low levels of vitamin B12 [1] and lower levels of beneficial bacteria in the Lactobacillus and Bifidobacterium families [29], along with other species [48]. Supplementing with probiotics, vitamin B, vitamin D3, and omega-3s has been shown to reduce depressive symptoms and improve quality of life [31].  In fact, probiotics can improve symptoms as well as the common antidepressant Celexa and anti-anxiety medication, Valium [23].


Anxiety, worry, nervousness, mind chatter and stress are all characterized by an overactive nervous system. As we have seen, this can be caused by gut bacteria imbalances and inflammation. In support of this, studies show that the presence of good bacteria can normalize anxiety-like behavior and psychological distress by increasing vagal tone, which is calming and turns on the rest-and-digest part of the nervous system and also by increasing BDNF in the brain, which facilitates healthy neurons and communication [30, 32]. Probiotics also reduce social withdrawal [33] and when beneficial bacteria were transplanted into mice that were more shy and withdrawn, they became outgoing. The opposite effect was also observed- when mice that were socially outgoing were given bacteria that contribute to anxiety, they became shy and less likely to interact [1]. Probiotics have a supportive effect on the immune system, enhancing how immune cells communicate with the brain and show a protective effect against less desirable brainwave changes [33]. Hurtful microbiome changes can be perpetuated by perceived stress and anxiety, contributing to gut inflammation, changes to bacteria composition and increased gut permeability [1, 28]. In addition to the foods discussed below, stress management practices, good quality sleep and meditation are helpful for maintaining gut health.


Autism Spectrum Disorder (which will be referred to as autism for simplicity) rates have drastically risen over the last decade or so and show no signs of declining in the near future unless some major changes are made to reduce toxin exposure and optimize health. Research now shows that children with autism have very different gut microbiome compositions than children without. The Clostridial bacteria species is much higher in children with autism and this bacteria puts the immune system into overdrive, creates inflammation and increases LPS levels. Studies where this bacteria was killed off demonstrated major improvements in the children’s behavior and communication skills. These improvements were only seen while the treatment was being used to keep the bacteria at bay; when the bacteria were allowed to flourish, the symptoms came back. There is also a correlation with SCFAs (short chain fatty acids), particularly the detrimental form PPA. PPA is toxic to the brain, loosens tight junctions in the intestinal wall and triggers widespread inflammation. Injections of PPA yielded immediate symptoms of autism and while children are not injected with this harmful compound, it is produced in the body from the Clostridial bacteria species, among others, and the subsequent breakdown of sugars [1]. Candida bacteria species may also contribute to autism symptoms, as the increase of Candida albicans increased autistic behavior in children on the spectrum [23]. The specific changes in bacteria composition seen with autism, correlates to the severity of the disease [25]. Promising research shows that establishing healthy bacteria ratios in the gut yielded improvements in social behavior [26]. Besides using probiotics and rebalancing the microbiome to begin healing, cruciferous vegetables contain the healing compound sulforaphane, which in just a few weeks demonstrated positive effects on social interaction, abnormal behavior and verbal communication in boys with autism [2].


ADHD is very common in both children and adults, with many people taking stimulant drugs on a daily basis to improve functioning. What if you could use nutrition to lessen the symptoms? You can. ADHD can be related to a lack of GABA in the brain, which is produced by Bifidobacterium and Lactobacillus. Inside the gut, vitamin B6 and zinc are needed so that these bacteria can synthesize an adequate amount of GABA. Probiotics containing these species, combined with omega-3s, show improvements in ADHD equal to that of Ritalin, a common pharmaceutical given for ADHD [1]. ADHD symptoms have also been linked to sugar-sweetened drinks, with a dose-dependent relationship meaning that more sugar = increase in symptom severity [34].


Dementia and Alzheimer’s disease are neurodegenerative conditions many people are worried about as they age and take a large toll on the family and friends of those who suffer. While there is no known cure, both of these conditions are increasingly being seen as preventable, with balancing nutritional components as an important piece [2]. Dietary cholesterol is consumed mainly from meat and eggs, but is exclusively found in animal products. The danger with cholesterol is not just blood cholesterol or heart disease, but with Alzheimer’s. Cholesterol increases plaque in the arteries of the brain and acts as a base for the amyloid plaques characteristic of this disease, so much so that a direct correlation is seen between the amount of cholesterol and the amount of amyloid buildup [2]. Dementia is also linked to animal fat, particularly saturated fat, which negatively impacts cognition and memory. Research shows that vegetarians have a 50% reduced risk of dementia [2]. People with dementia have elevated levels of LPS and lower levels of vitamin B12, which is crucial for brain and cellular health [1, 17]. In addition, trans fats contribute to irritability and aggression [15], which are not exclusive to Alzheimer’s and dementia, but are often symptoms.


To conclude, let’s take a look at the beneficial effects of probiotics on different areas of brain function. Probiotics have been shown to increase connectivity between the brainstem and prefrontal cortex, which would relate to cognition, motivation, mood and emotional balancing. Consumption of probiotics also yields decreased activity in the insula, which is responsible for processing bodily sensations related to strong emotions and the experiences of empathy, compassion, anger, disgust and pain. This means that area is more flexible and can respond to stressors more appropriately, while experiencing less emotional upset. Overall probiotics help to decrease brain excitability in cognitive, emotional and sensory processing areas, allowing for balanced thinking and emotional flexibility [1]. To summarize a quote from Dr. Mayer, a researcher at UCLA, there are studies showing that what we eat changes the composition of the microbiome and people with fiber-based diets high in vegetables have a different composition than those eating a diet focusing more on fats and carbohydrates … now we know that this affects not only metabolism, but brain function [1- p83].


Understanding why health and nutrition are essential to optimal brain function, longevity and overall wellness can serve as a great motivator to make changes. This article has detailed many foods, and poisons masquerading as foods, that are detrimental to our physical, cognitive and emotional health. Inflammation is a major driver of imbalance, but the good news is it can be reduced and eliminated. Taking out some of the aforementioned sources of inflammation is the best start to supporting all dimensions of your health. Coming soon in a third gut-brain article, we will include the practical information you need in terms of what to eat for your health, including choosing a good probiotic, how to remove sources of suffering and bring your body and mind back into balance!

Article by:
Heather Hill
Peak Neurofitness LLC
Neurofeedback Specialist, Client Care Manager


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