Should You Get a Stool Test? A Closer Look At Stool and Gut Microbiome Testing

July 20, 2023
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In Naturopathic Medicine, a primary philosophy is the vital role the gut plays in overall health and well-being. “All disease starts in the gut” is often associated with naturopathic medicine although it’s originally attributed to Hippocrates, the Greek physician widely regarded as the father of modern medicine.  

Maintaining a healthy digestive system is essential because the gut is responsible for processing food, absorbing nutrients, and eliminating waste. It also plays a critical role in immune function and hosts a complex community of microorganisms, known as the gut microbiome, which interacts with the rest of the body in numerous ways.

Naturopathic medicine takes a holistic approach. It puts a strong emphasis on gut health because it considers the whole person rather than just their symptoms and disease. By using diet, exercise, stress management, and natural remedies to promote gut health it can have wide-ranging effects on overall health.

The gut, particularly the gut microbiome — the diverse ecosystem of microorganisms living in our digestive tracts — plays a vital role in numerous bodily functions. Here are several reasons why maintaining a healthy gut can contribute to overall well-being:

  • Nutrient Absorption: The gut is where your body breaks down food and absorbs most of the nutrients that you consume. Keeping your gut healthy ensures that your body can effectively extract and utilize these nutrients.
  • Immune Function: Roughly 70% of our immune system is housed in the gut. A healthy gut microbiome can help to regulate immune responses and prevent inflammation.
  • Mood and Brain Health: The gut and brain are connected through the gut-brain axis. The gut microbiome produces various neurotransmitters, like serotonin and dopamine, which can influence mood and brain function. Recent research also suggests a potential link between gut health and neurological conditions like Parkinson’s and Alzheimer’s diseases.
  • Heart Health: Certain types of bacteria in the gut can influence heart health by impacting factors like inflammation and cholesterol levels.
  • Weight Management: The gut microbiome can influence body weight and metabolism. Research suggests that the composition of the gut microbiome may play a role in obesity.
  • Digestive Health: A healthy gut can prevent issues like constipation, diarrhea, bloating, and heartburn, as well as more serious conditions like irritable bowel syndrome or inflammatory bowel disease.

Microbiome Stool Testing 

Fortunately, there are microbiome stool tests that can provide valuable insights in the health of your gut microbiome. It is a type of  fecal lab test used to identify microbial imbalances such as bacterial, viral, parasitic, and/or yeast overgrowth. 

Stool tests help health practitioners assess the cause of gastrointestinal symptoms and a person’s overall health. The insights provided by these tests can help guide dietary and supplement plans, offering patients relief from their symptoms. 

However, like all medical tests, stool tests have their strengths and weaknesses. They can provide essential information, but they are not perfect. In the following sections, we will delve into what the test measures, why it’s important, who should get tested, and the cons of stool testing, providing a balanced perspective that can help you make informed decisions about your health.

Key Points: 

  • What does the test measure 
  • Why is the test important 
  • Who should get comprehensive microbiome stool testing
  • Disadvantages of Stool Testing 

What does the test measure?

  • Commensal bacteria 
  • pathogenic/ opportunistic microbes 
  • Functional markers of intestinal inflammation 
  • Markers of malabsorption or digestive insufficiency
  • Microbial by-products such as short-chain fatty acids 
  • Hormone metabolism 

Why is this test important? 

  • A stool test can help detect acute or chronic illnesses that stem from the gastrointestinal tract 
  • Having dysbiosis or an imbalanced gut microbiome can lead to various chronic conditions and disease 
  • Approximately 70% of the immune system resides in the gut microbiome 
  • The gut, often referred to as the “second brain”, produces the majority of the neurotransmitters. Around 90-95% of the body’s total serotonin is produced in the gut. Serotonin plays a crucial role in mood regulation, digestion, appetite, and pain sensitivity 

Who should get comprehensive microbiome stool testing? 

  • Gas and bloating 
  • Indigestion 
  • Acid reflux/ GERD 
  • Food sensitivities/ intolerances
  • Diarrhea 
  • Constipation 
  • Abdominal pain 
  • Irritable bowel syndrome
  • Inflammatory bowel disease 
  • History of antibiotic use 
  • Fatigue 
  • Autoimmune condition 
  • Acne 
  • Eczema 
  • Mood disturbances 
  • Insomnia 
  • Brain fog 
  • Chronic sinusitis
  • Chronic yeast infections 
  • Chronic ear infections

Cons of Stool testing 

While stool testing is a valuable diagnostic tool, it is not without its downsides. For example, a  change in diet can change the gut microbiome within 24 to 48 hours. Stress can also alter the gut microbiome. Thus, the gut microbiome is similar to a moving target because test results can change from week to week, if exercise, diet, stress, supplements, and medications all change. 

Another barrier is that most comprehensive microbiome stool tests are costly and often not covered by insurance. They often also need to be ordered by a health practitioner which makes them not accessible for most people. 


A stool test is a valuable tool in the naturopathic practitioner’s toolkit to assess and enhance gut health. While comprehensive microbiome stool tests can be costly and may not be covered by insurance, the potential benefits they offer in terms of identifying imbalances and guiding tailored interventions are significant. As research evolves, the utility of these tests is expected to improve, with more precise, cost-effective solutions likely on the horizon.

It is important to remember that while stool tests provide a wealth of information, they are not a standalone solution. True health care is multi-faceted and should encompass lifestyle changes, regular check-ups, balanced nutrition, stress management, adequate sleep, and regular exercise. 

written by:


  • Dr. My Tang

    As a licensed Naturopathic doctor, I am here to support you in uncovering what is holding you back from living a healthy and vibrant life. I have found that in order to break through any unhealthy patterns, we often have to also dive deep to identify any limiting beliefs or any mental, emotional, or spiritual blocks. The body is highly intelligent and has an innate ability to lean towards healing. Through our work together, we are assisting, supporting, and allowing space for that healing.

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