How Your Gut Health Affects Your Mental Health

It might be fair to say that we all would rather boost & keep our mood regulated - naturally - much more than we’d like to take medication. We want to feel our best! But oh, do we sometimes end up so far off track without realizing it. In this blog post, I’m going to share a lot of information for you to help highlight the ways that what we eat and what we are exposed to affect our mental health. Anxiety, depression, and other mental health disorders can often be completely reversed simply by changing our diet! Beware, this is a long one :-)


Let’s take a deep dive together.

Remember, I’m not a doctor, but I’m always stoked to share the information I learn and research in Functional Health. Take it or leave it! This isn’t my medical advice to you. If any of the below strikes you with inspiration, hop all in! If you want support in implementing any of these diet and lifestyle changes, I’m available for a free introductory call with you to see if Health Coaching is a right fit for you.






The Underlying Cause of Anxiety, Depression, and Mental Health Disorders - from a Functional Medicine Perspective: Inflammation

These issues are almost always primarily caused by inflammation
  • Potential causes of high inflammation include gut pathology/inflammation, diet, sleep deprivation, not enough exercise, too much exercise, and environmental toxins

  • When considering eliminating inflammation with regard to our diet, you’d basically just cut the “junk” food!

  • Excess sugar, caffeine (be sure to ween off, as stopping can cause withdrawal symptoms) and omega-6 fatty acids (industrial seed oils common in restaurants and packaged foods)

  • Avoid refined cereal grains, bread, flour, grain-based desserts, beer

  • Note: Gluten intolerance is exacerbated with pesticides sprayed on industrially grown grains (contributes to intestinal permeability)

  • Chemicals and preservatives found in highly processed and refined foods such as artificial flavors, colorings, etc., have been linked to behavioral problems and hyperactivity in children. They may also cause food allergy and sensitivity reactions that affect brain function.

  • Minimize or completely avoid these ingredients and stick to whole foods with little to no additives

  • Cook from scratch as much as possible for more control over what you eat

  • Environmental considerations with inflammation - avoid toxins!

  • Pathogens like mold or bacteria, heavy metals, and chemicals in cleaning and cosmetic products expose us to toxins that disrupt our cognitive function

  • Switch to natural cleaners and toxin-free cosmetics

  • Check your home for mold if mold exposure is suspected

  • Consider installing a high-quality air filter to reduce airborne toxins and pathogens


Gut Microbiome & the Brain

  • Chemicals, like cortisol, that bacteria produce in the gut have a significant impact on mood and brain function

  • Research on gut bacteria of animals and humans exposed to various stressors early in life show changes in brain function later in life

  • There are significant differences seen in the gut microbiome of patients with major depression compared to healthy controls

  • Consuming probiotics found in foods and also supplements can:

  • Reduce anxiety by lowering cortisol and decreasing stress response

  • Improve emotional and cognitive response and improve mental well-being

  • Disruptions in the gut microbiome and intestinal permeability lead to systemic inflammation, which we know is associated with mental health disorders including depression and anxiety

  • Endotoxins such as lipopolysaccharide provoke the release of inflammatory cytokines

  • Depression – the inflammatory cytokine model

  • Gut pathology via gut–brain connection stimulates production of inflammatory cytokines in the gut, resulting in systemic low-grade chronic inflammation

  • The cytokines travel through the bloodstream up to the brain, cross the blood–brain barrier, and suppress the frontal cortex, leading to major depressive disorder

  • SSRIs, the major class of antidepressant drugs, have been shown to have an anti-inflammatory effect, which may be how they help *when/if* they are effective

  • SIBO – is also associated with depression, anxiety, and mood disorders

  • 50% to 85% of irritable bowel syndrome (IBS) may be caused by SIBO

  • Disrupted gut microbiome causes/contributes to irritable bowel syndrome (IBS)

  • Can be an imbalance of good/bad microbes/pathogens or a pathological change in the function of the gut

  • Celiac disease and non-celiac gluten sensitivity

  • Associated with a variety of neurological and psychiatric complications

  • 22% of patients with celiac disease develop cognitive dysfunction

  • 57% of people with neurological dysfunction of unknown origin test positive for anti-gliadin antibodies

  • Neurological conditions associated with gluten sensitivity include seizure disorder, neuropathy, ADD, ADHD, autism, ataxia, anxiety, depression, and schizophrenia

  • Testing:

  • Standard testing with anti-gliadin antibodies alone is not accurate, likely resulting in an underdiagnosis of celiac/non-celiac gluten sensitivity

  • Recommend that you work with your practitioner for proper gluten sensitivity testing with Cyrex Array 3 – especially if you have neurological dysfunction

  • After testing: recommend that you do a 60-day complete gluten elimination





Malnutrition contributes to anxiety, depression, and cognitive disorders:

Inadequate macronutrients ratios (your protein, fat, and carbohydrates) is common in today’s world. We “just eat” without much regard to a good balance of these. And further, with our soil’s depletion of nutrients through over-agriculture and time, we aren’t getting the micronutrients we need either (more on micronutrients further on in this post).

  • Protein:

  • Too little or excess protein intake can exacerbate mood disorders because neurotransmitters are created from amino acids provided by protein in the diet

  • Make sure your diet contains all of the essential amino acids

  • Ideal protein intake: between 0.5 and 1 grams per pound of body weight or 1 to 2 g/kg of body weight per day

  • We don’t need to adjust protein as much as carbohydrates, and we’ll generally crave more if our brain needs more. Our brain has mechanisms for regulating protein consumption.

  • In general, aim for 10-30% of your daily calories coming from protein.

  • Don’t go above 35% of a day’s calories in protein because the body has a limited ability to metabolize protein. Once you’ve resolved the issue that puts you at 30-35% protein it’s suggested going back to a general health range.

  • Insufficient or excess micronutrients

  • One of the most common issues is excess intake of methionine, an amino acid that is found in muscle meats and eggs, which can lead to imbalance in the methionine-to-glycine ratio (excess methionine and insufficient glycine) = this leads to neurological symptoms. (Check out my other post that dives more deeply into amino acids and protein here)

  • The basic recommendation is to increase intake of glycine found in bones, joints, tendons, bone broth, cuts of meat such as chuck roast, brisket, oxtail, or shanks that have more collagen in them to protect against neurological conditions and improve brain function

  • May also help with sleep and anxiety by having better production of serotonin and melatonin


  • Carbohydrate intake:

  • Personalize carbohydrate intake based on your health, physical activity, and experience with high- and low-carbohydrate diets

  • Most people do well on a moderate carb intake. 15-30 percent of total calories in a single day coming from mainly starchy vegetables, tubers, and fruits… 200 grams for a 2600 calorie diet and 75-100 grams for a 2000 calorie diet

  • Higher carbs: Athletes, breastfeeding women, and children

  • Lower carb: elderly, sedentary people, insulin resistant/blood sugar issues, Alzheimer’s, or dementia

  • Initially, a low-carb diet can contribute to cognitive deficits (low mood and brain fog) as the body adjusts to using fat for fuel

  • This may not persist

  • If symptoms continue or worsen after a week or two = red flag, and add more carbs back in

  • Exercise caution in considering a long-term, very-low-carbohydrate diet

  • Especially in women and with any presence of HPA axis dysfunction (adrenal fatigue)

  • Carbohydrates have a big impact on sleep nutrition and mental health:

  • Based on clinical experience, both low-fat and low-carbohydrate diets seem to increase the likelihood of insomnia.

  • Carbohydrates help increase the production of serotonin and melatonin (both of which help you fall asleep). If you eat a low-carb diet, and struggle with falling asleep at night, try eating a few more carbohydrates, particularly with dinner. Even if you already eat a moderate carbohydrate diet, you can still adjust your carbs so that most are eaten later in the day.


  • Dietary fat and cholesterol - The human brain is made up of at least 60 percent fat, mostly saturated fat and cholesterol

  • Your total caloric fat intake will be the remaining percentage after determining your carbohydrate and protein intake needs.

  • Cholesterol is a component of the myelin sheath, the insulation around the neurons in the brain

  • Inadequate or excess cholesterol can cause neurological impairments

  • Recommend mixed fat intake

  • Monounsaturated fats increase the neurotransmitter acetylcholine and blood flow to the brain

  • Choline improves memory and protects against cognitive decline (found in cholesterol-rich foods such as eggs and liver)

  • Medium-chain triglyceride and beta-hydroxybutyrate can improve cognitive function in older adults with memory disorders such as Alzheimer’s (found in coconut oil and butter)

  • Goal: Balance of essential omega-3 and omega-6 fats

  • Long-chain omega-3 fat DHA is particularly important

  • Vegetarians have 30% lower EPA and DHA levels

  • Vegans have 50% to 60% lower EPA and DHA levels


Micronutrients of Concern in Mental Health

  • B12 deficiency

  • In a typical lab reference range for B12 when you get panels drawn, the lower end is actually too low - Research suggests deficiency symptoms can begin as low as 450 pg/mL

  • B12 malabsorption is typically caused by: gut dysbiosis, leaky gut, inflammation, pernicious anemia, alcohol intake, medications, hypochlorhydria (which is low stomach acid), celiac disease, inflammatory bowel disease, and particularly Crohn’s (involves inflammation of the terminal ileum where B12 is absorbed)

  • Deficiency is common even in those consuming meat - Vegetarians (68% more) and vegans (83% more) are at much higher risk

  • Folate deficiency

  • Decreases serotonin synthesis, s-adenosylmethionine (SAM), and increases inflammatory homocysteine

  • Associated with depression, epilepsy, psychiatric conditions (especially in the elderly)

  • Possible link between folate and homocysteine levels and aging, dementia, and Alzheimer’s disease

  • B6 deficiency

  • B6 is required to make serotonin, a crucial neurotransmitter that regulates mood and mental health. B6 deficiency is less common in a well-rounded diet

  • Consider this especially if anxiety, mental health, and depression are an issue for you. Symptoms of B6 deficiency includes poor stress control, nervousness, anxiety, and mood swings

  • Zinc and copper

  • Ideal ratio of serum copper to zinc is 0.7 to 1

  • Both function as neurotransmitters in the brain

  • Excessive copper and deficiency of zinc can cause: hyperactivity, ADD and ADHD, behavioral disorders, depression, autism, panic disorders, and paranoid schizophrenia.

  • Vegetarians diets:

  • Often have high copper intake and low zinc intake

  • Might have adequate intake but inadequate absorption because vegetarian diets reduce zinc absorption by 35%

  • Inflammation:

  • Copper is an acute-phase reactant and will be elevated in an inflammatory response (such as if you’re highly stressed)

  • Oxidative stress and inflammation can reduce zinc levels and increase copper levels

  • Vitamin D

  • This is actually a hormone which is vitamin-like and it activates genes that release neurotransmitters such as dopamine and serotonin

  • Vitamin D receptors are located in regions of the brain linked with depression and deficiency is associated with depression, other mood-affective disorders and schizophrenia

  • Vitamin D supplementation has been shown to be more effective than light therapy in treating seasonal depression

  • Magnesium

  • Most commonly deficient nutrient in modern diet due to soil depletion and removal from drinking water

  • Stress and excess caffeine increases magnesium wasting

  • Excess calcium can interfere with magnesium absorption

  • Can aid anxiety, depression, irritability, restlessness, headaches, etc.

  • Protects against excess excitatory neurotransmitters

  • Suppresses the stimulation of cortisol by the HPA axis

  • This prevents stress hormones from crossing the blood–brain barrier into the brain

  • Magnesium is therefore helpful with regard to mitigating adrenal fatigue

  • Iron: Deficiency and overload can cause problems

  • Iron overload

  • Accelerates mitochondrial decay ➜ impairs mitochondrial function = major source of cognitive and mood problems

  • Iron is a catalyst for oxidative damage and increases oxidative stress in brain cells that can cause cognitive/neurological problems and neurodegeneration.

  • Iron deficiency

  • Common concern, particularly in menstruating females

  • Iron is crucial for oxygen delivery which is required by the brain

  • Low iron leads to compromised oxygen delivery to the brain, contributing to mood and cognitive disorders



So what can you do to help balance your gut and therefore any mental health challenges and disorders?

Here are some tips on therapeutic diets. Let me know how this lands for you/if you have questions!

Eat a balanced Paleo diet – this is a great starting place & usually a great option for ongoing maintenance after doing a short-term, more intense diet change.
  • Eating Paleo helps because it’s naturally anti-inflammatory – it removes many foods that can provoke gut permeability, such as gluten, dairy, and grains

  • Moderate protein: 15% to 25% of daily caloric intake

  • Moderate carbohydrate: 20% to 40% of daily caloric intake

  • Determine protein and carb needs FIRST and get rest of your calories from fat

  • Healthy fats: 35% to 65% of daily caloric intake

  • HIGH VARIETY of plant and animal foods

  • Dairy: avoid it initially and reintroduce as tolerated, pasture raised, full-fat, and fermented

  • Eliminates industrial seed oils from processed foods and emphasizes a “whole foods” diet approach

  • Consume probiotic-rich fermented foods like yogurt, kefir, sauerkraut, kimchi, etc., for increased beneficial gut flora/promoted good gut bacteria.

  • Eat a wide variety of prebiotic, fiber-rich foods like fruits, vegetables, and starchy tubers to feed your beneficial flora

  • Work with your practitioner to treat any existing gut infections

  • If you have significant gut issues, then interventions such as the low-FODMAP diet, GAPS, or specific carbohydrate diet can be helpful, at least in the short term, to get those under control

  • Low-FODMAP diet: as tolerated, and not for extended duration

  • This diet emphasizes fermentable fiber/prebiotics that stimulate the growth of beneficial bacteria. Examples: onions, Jerusalem artichokes, legumes or lentils, fruits and non-starchy vegetables and starchy plants

  • Consider especially if you have IBS

  • Involves elimination of high-FODMAP foods that can reduce overgrowth of pathogenic bacteria in the small intestine.

  • Note: No evidence that a low-FODMAP diet will successfully treat OR cure SIBO or other gut infections without an antimicrobial treatment, either botanical or pharmaceutical

  • A few studies show that a long-term low-FODMAP diet, where all of these FODMAPs are removed, leads to undesirable changes in the beneficial bacteria in the colon

  • Likely because many FODMAPs feed the beneficial bacteria

  • Ultimately it is recommended that you reintroduce as many FODMAP foods as you possibly can to support the beneficial gut bacteria

  • Also try other non-FODMAP fermentable fibers such as soluble fiber to feed the bacteria; most people are not universally sensitive to all of the FODMAPs – might be more or less sensitive to a couple of categories (such as fructans: garlic and onions) but not as much to some of the other FODMAP foods

  • GAPS or specific carbohydrate diet:

  • High-fat, high-glycine, and low-specific-carbohydrate diet

  • “Specific” because it is low in complex sugars – permits monosaccharides, simple sugars

  • Prohibits disaccharides and polysaccharides – more complex carbohydrates

  • Removes many potential food allergens and fermentable carbohydrates because they are the longer-chain polysaccharides

  • Can help clients with: gut dysbiosis, intestinal permeability, and reduce gut–brain symptoms. Benefits have been seen in children with autism spectrum and other mental/behavioral disorders (ADHD)

  • Important notes: Worth a try in autistic children or ADHD and in adults with this kind of constellation of symptoms, but it *can* worsen your condition

  • Not unusual to have an initial period of getting worse, but if it just continues to get worse, discontinue this strategy

  • Additionally, NOT recommended to remove all the longer-chain carbohydrates long term as they feed the beneficial bacteria in the gut

  • Ketogenic diet

  • Can improve energy metabolism in the brain and reduce inflammation in the microglia

  • Can be beneficial for clients with:

  • Cognitive neurological disorders: Alzheimer’s, Parkinson’s, dementia

  • Mood disorders: such as depression, brain tumors, traumatic brain injury, seizure disorders

  • Severe blood sugar disorders

  • Important note:

  • Ketogenic diet is not necessarily preventative (no data showing prevention in those with a family history of these conditions)

  • Very-low-carbohydrate diet can worsen certain neurological conditions

  • This is a restrictive diet that can trigger disordered eating

  • Preliminary anecdotal data from the American Gut Project indicating individuals on very-low-carb diets have different gut microbiota possibly associated with adverse health impacts

  • Recall: many foods that feed the beneficial bacteria are carbohydrates

  • Consider other options where low carb is not necessary to produce ketosis

  • Adding MCT oil in fairly large quantities

  • 100 g of carbohydrates (which is low) + low-protein intake + large amounts of MCT oil/coconut oil and ketogenic amino acids such as leucine



So what do you think of all this? Please, share your thoughts in the comments below!

Resources for this post include the exhaustive Functional Health content from the Kresser Institute ADAPT Certified Health Coaching Program, The Paleo Cure by Chris Kresser, and this Neurobiology of Disease article.


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