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Why Functional Medicine Practitioners Focus on Gut Health

Medically reviewed by 
Why Functional Medicine Practitioners Focus on Gut Health

Two thousand years ago, Hippocrates claimed that all disease begins in the gut. He didn't have the benefit of the advanced microbial and cellular testing we have now but made the assertion based on observation of patterns.

There is likely a lot of truth to this statement. Naturopathic Doctors have been treating the gut first for many years, and the concept is gaining more recognition as recent research supports connections between the gut microbiome, gut health, and many health conditions, from allergies to PTSD to cardiovascular disease. 

Many aspects of modern life do not promote optimal gut health, so it is worth paying extra attention to avoid or improve conditions linked to gut imbalances. This article will discuss gut health, its connection to other conditions, and how to test and treat gut dysfunction.


What is Optimal Gut Health?

Optimal gut health may look like having a healthy appetite, smooth digestion without discomfort such as bloating, and having 1-2 regular bowel movements daily. It also may look like metabolic health, the ability to maintain a healthy weight, lack of food sensitivities, lack of chronic health conditions, and generally experiencing a calm and positive mood and clear thinking.

On an ecological level, optimal gut health will be characterized by a healthy, diverse microbiome with low levels of unhelpful species, high levels of beneficial species, and a high diversity of gut microbes. There will be a healthy and intact mucosal barrier that can function well, protect from pathogens, and absorb nutrients.

In addition, as a high percentage of several neurotransmitters are made in the gut, a healthy gut will lead to healthy neurotransmitter levels. 95% of serotonin and up to 50% of dopamine is made in the gut. These are not primarily made by our cells but by certain microbes in the gut microbiome. 

What Causes Poor Gut Health?

Many things people may not have thought to associate with gut health can negatively impact it. For example, stress, lack of exercise, and poor sleep impact the gut mainly through the impact on the microbiome. Intense exercise can redirect the blood flow away from the gut, causing damage to the cells lining the gut, leading to increased permeability and leaky gut.

Eating foods one is allergic to or sensitive to will lead to low levels of ongoing GI inflammation, possibly causing leaky gut and a cascade of systemic inflammatory processes as a result. 

A diet high in sugar or unhealthy fats will shift the microbiome towards microbes that thrive in a high-sugar environment. However, these are generally not the ones that are beneficial to have at higher levels, so they are more likely to promote disease. 

Other factors that affect the gut are the genetic effect on the microbiome and the use of antibiotics, which can have a rapid and lasting impact on gut health and the gut microbiome.  

Imbalanced Gut Health Symptoms

Because gut health also influences systemic inflammation and neurotransmitter levels, a wide variety of symptoms can occur when the balance is disrupted. Some of the GI-focused symptoms may include: 

  • Bad breath
  • Abdominal cramps
  • Diarrhea
  • Constipation 
  • Acid reflux
  • Food intolerances
  • Gas/bloating
  • Nausea, upset stomach

Some more systemic symptoms could also include: 

  • Fatigue
  • Generalized inflammation
  • Achy body
  • Skin problems, such as acne, rashes, psoriasis, rosacea
  • ADHD or trouble concentrating
  • Mood issues, anxiety, or depression 

With prolonged gut dysbiosis, effects can become more deeply entrenched metabolically. Poor nutrient absorption may lead to micronutrient malnutrition despite an apparently adequate diet. An unhealthy gut microbiome can also negatively impact blood sugar regulation, increasing insulin resistance and the development of diabetes. That, in combination with altering hunger signaling, may lead to weight gain or obesity. 

Medical Conditions Associated with Poor Gut Health

Many medical conditions may arise from a long-standing gut imbalance because it leads to chronic low-level inflammation, a major driving factor in many chronic illnesses. 

Gut Conditions

Gut-specific illnesses associated with gut dysbiosis include Crohn's disease, ulcerative colitis (UC), colorectal cancer, gastritis, and gastric ulcers.

Metabolic Conditions 

Metabolic diseases associated with poor gut health include obesity, high cholesterol, and type 1 and type 2 diabetes.

Allergy and Immune Conditions

Seasonal and food allergies can both be impacted by poor gut health and dysbiosis because gut health is linked to immune health. Autoimmune conditions can also be worsened by poor gut health. The gut plays a significant role in the onset of autoimmune conditions, specifically Multiple Sclerosis (MS), rheumatoid arthritis, Celiac Disease, and ankylosis spondylitis. 

Cardiovascular Conditions

Cardiovascular disease risk is increased by poor gut health. In particular, coronary artery disease is strongly connected to the health of our gut flora.

Brain Conditions

Brain-focused conditions can often have a strong link to gut health. Conditions including autism, ADHD, anxiety, depression, and even PTSD can be significantly worsened by poor gut health and may respond positively to improvements in gut health as inflammation and neurotransmitters are re-balanced.

Functional Medicine Labs to Test for Root Cause of Gut Health Issues

Functional Medicine labs can provide insight into many aspects of gut health. Labs can help us answer the following questions: How is the microbial balance? Is gut permeability increased? How well are nutrients being absorbed? These tests can also analyze factors that affect gut health, such as stress, toxins, and allergens.

Gut Health Testing

A GI-MAP test can give a thorough look into the microbiome's health. This test analyzes the DNA of the microbiota to provide detailed information about the microbe diversity and balance while also giving information on gut permeability (leaky gut). 

A microbiome panel may be useful for additional insight into the microbiome's health. This test, in particular, gives some nutrition, lifestyle, and supplement guidelines to help practitioners guide treatments based on the test results.

A stool test for H. Pylori may be beneficial since H. Pylori is a common cause of Upper GI discomfort and pain. 

SIBO breath testing may also be indicated if symptoms such as bloating or belching are present. But, it can also be helpful for individuals with IBD, pancreatitis, hypothyroidism, rosacea, restless leg syndrome (RLS), diabetes, Parkinson's disease, or coronary artery disease since all of these conditions have been linked to SIBO.  

Nutrient Testing

Regarding nutritional status, a complete blood count (CBC) can show if there is anemia from GI bleeding or poor absorption (or low iron/b12/folate intake). 

A cellular micronutrient assay (CMA) can assess micronutrient deficiencies resulting from longstanding gut health issues or poor diet. 

Hormone & Neurotransmitter Testing

Stress impacts the gut, and the gut also affects the HPA axis. Testing the cortisol response throughout the day can give insight into how well the stress hormone systems are functioning.

Neurotransmitter tests can also provide insight into psychological or neurological conditions. Since neurotransmitters are mostly manufactured in the gut, this can be used to help determine overall gut health status. 

Toxin Testing

Many toxins impact the gut. In certain situations, testing and tracking their presence in the body may make a lot of sense throughout the healing process. Some labs that can give information on toxin levels are urinary mycotoxins, environmental toxins, and heavy metals.

Allergen Testing

Allergies can contribute to and result from poor gut health. Avoiding known allergens can allow the gut to repair itself and heal from systemic illnesses. If environmental or food allergens are suspected, testing both may provide useful insights. 

How To Balance Gut Health

What does it mean to balance gut health? It means restoring a healthy microbial balance, increasing healthy gut flora, and decreasing or eliminating unhealthy or pathogenic gut flora while increasing the microbe diversity. It also means addressing any gut inflammation leading to a damaged (leaky) gut wall.

Due to the wide variety of systemic effects, optimizing gut health is often among the first steps in a functional medicine plan. Having this in balance can cause other problems to simply resolve with no further treatment. But in cases where further work is needed, having addressed gut health first removes some of the noise.

Functional Medicine practitioners focus on balancing gut health with a whole foods nutrition plan, gut healing supplements, and lifestyle adjustments. The following are some of the most common functional medicine recommendations: 


At least initially, a gut-healing diet should exclude all known allergens, as well as gluten, which has been shown to increase gut permeability, even for those without celiac or gluten sensitivities. 

Sugar should be significantly limited or avoided as it leads to excess growth of unfavorable microbes. 

Foods likely to contain Glyphosate (i.e., GMO wheat), which is an herbicide that can damage the gut lining, potentially leading to negative impacts on the gut microbiome, should be avoided.

A high-fiber diet provides the substrate to grow bacteria that create short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate, which are the fuel sources for our gut lining cells. Butyrate is particularly anti-inflammatory.

Supplements & Herbs

Many supplements may play a role in restoring optimal gut health, depending on what imbalances are in place. 

A broad gut health-supporting protocol could include L-glutamine, an amino acid that aids in the repair of the gut lining, and natural anti-inflammatories such as omega-3 fatty acids and curcumin to reduce inflammation that leads to a leaky gut.

Probiotics and prebiotics help restore microbial balance, and zinc helps to restore an impaired gut lining. 

Antimicrobial herbs treat any pathogens such as H. Pylori or SIBO that have been identified. Lotus seed resistant starch (RS) has been effective in studies showing changes in the gut microbiome to reduce food allergies.

Complementary and Alternative Medicine

Any activity like yoga or meditation that helps regulate the stress response will benefit gut health. As acupuncture, massage treatments, and exercise can also help to reduce stress, they may be a supportive part of restoring GI health. 



Gut health is central to determining our overall health. It can be impacted by many factors common in modern life, like high stress, poor nutrition, and taking antibiotics for an infection. If one wishes to optimize overall health, paying attention to gut health, using functional medicine testing, and holistically treating the gut to restore optimal function is an instrumental first step.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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