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Understanding Your Functional Medicine Stool Test

The digestive system is a complex network of organs, nerves, hormones, bacteria, enzymes, and other microorganisms that make up your microbiome. It consists of the liver, pancreas, gallbladder, mouth, esophagus, stomach, small intestine, large intestine, anus, and much more.

Digestion plays an important role in everyday health. It’s responsible for breaking down the various nutrients (fat, carbohydrates, protein, vitamins, minerals, water) for absorption inside the body. Once absorbed, these nutrients are utilized for energy, growth, cell repair, and more.

The waste products of digestion are made into stool, which is stored in the rectum until it’s ready to pass through the anus via a bowel movement. Normal bowel movements reflect overall health in the body, which is why a stool test is necessary when diagnosing digestive issues.

Understanding Your Functional Medicine Stool Test

So, what is a functional medicine stool test?

Functional medicine stool testing is one of the most popular tests used in functional medicine. They can provide a world of information regarding digestive health and the health of your gut microbiome, which is essential to detecting digestive issues and ultimately finding a solution.

In order to take the test, a patient must collect a stool sample in a clean container following a bowel movement. It’s important that you use latex gloves when collecting the sample to avoid contamination. Once collected, the stool sample is sent to the doctor or lab for further analysis.

After several days, your doctor will receive an in-depth report of the stool test. They’ll analyze and use that information, along with your various symptoms and medical history, to detect any issues happening in your digestive system — and eventually, determine a treatment plan.

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What Do You Learn From a Functional Stool Test?

Functional medicine stool tests can tell you a lot about the health of your body. Some of the most important biomarkers that it looks at include digestion levels, absorption levels, bacteria, yeast, and parasite presence, inflammation, and levels of prebiotics and probiotics in the body.

Let’s take a closer look at some of these biomarkers:


The body’s ability to break down food with the help of digestive enzymes and stomach acid. Without proper digestion, your body won’t be getting the nutrients it needs.


The body’s ability to absorb the nutrients that were just broken down. This process takes place in the small intestine and could impact the nutrients your body gets.

Bacteria, Yeast, Parasites

Your body needs a healthy balance of good bacteria and bad bacteria in order to function. The presence of parasites could impede gut health, as well.


A strong majority of your immune system is housed in the gut, which means your digestive system is vital to the overall function of the immune system.


Your stool test can show levels of prebiotics and probiotics, which are short-chain fatty acids that are important for colon health and the immune system.

When all is good, your stool test will give you the peace of mind that your gastrointestinal tract and digestive system as a whole are in working order. If your doctor finds anything alarming, they’ll need to determine a solution that can return your digestive system to normal function.

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Using a Stool Test for IBD & IBS

Two of the most common diseases and disorders involving the digestive system include inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Many patients suffer from them every year and the two can have similar symptoms and are hard to distinguish at times but are extremely different in their own right.

Inflammatory bowel disease can cause abdominal pain, fever, weight loss, and diarrhea. It either affects the lower parts of the GI tract or the GI tract as a whole. The two major groups of IBD are Crohn’s Disease and ulcerative colitis, which deal with inflammation along the digestive tract.

Irritable bowel syndrome can cause cramping, constipation, diarrhea, bloating, and gas. Issues with the gut-brain axis and stress are two common triggers for this disorder. Unlike IBD, those suffering from IBS don’t experience permanent damage in the GI tract by inflammation.

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When taking a functional medicine stool test, there are several biomarkers that can give your doctor a better understanding when differentiating between IBD and IBS symptoms, including:

  • Calprotectin – an immunomodulatory protein that’s important for neutrophil defenses and inflammatory pathologies. It’s one of the most important biomarkers in a stool test.
  • Alpha-1 Antitrypsin – a linear glycoprotein that’s mostly synthesized in the liver. It can show intestinal protein loss and permeability since it resists degradation in the gut.
  • Lysozyme – an enzyme that is very important to your antibacterial defense system in the GI tract. An elevated level of this enzyme could mean the patient has colonic IBD.
  • Secretory IgA – acts as an immune barrier that’s commonly known as the first line of defense of GI mucosa. Elevated levels could mean an upregulated immune response.
  • Albumin – the most abundant protein found in the blood. Elevated levels could point towards IBD, but lower levels could mean inflammation due to liver damage or kidney disease.
  • Beta-Defensin 2 – play an integral role in the immune system with their antimicrobial effects. Reduced levels of beta-defensins could be a biomarker for Crohn’s disease.
  • Bile Acids – synthesized in the liver, but secreted by the bile duct and reabsorbed into the liver. Too much presence of bile acids in your stool could be a biomarker for IBD.

It’s because of these biomarkers that your doctor might order a functional medicine stool test when trying to rule out or differentiate between IBD and IBS symptoms. Since the treatments for IBD and IBS are very different from one another, detection and diagnosis are very important.

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Are You Interested In a Functional Stool Test?

If you’re experiencing symptoms of IBD, IBS, or any other health problems with your digestive system (such as leaky gut, gut infection, food sensitivity, or gut dysbiosis), it might be time for a functional medicine stool test. It’ll help point your doctor in the right direction when trying to find a solution or treatment plan for reducing the symptoms you’re experiencing.

You deserve to take back control of your life and that’s exactly what Dr. Hagmeyer is dedicated to achieving. As a Certified Functional Medicine Practitioner, Dr. Hagmeyer is focused on finding the reasoning — the why, the root cause — behind your symptoms, that way you can work towards a better life.

When you’re ready to gain back control in your life, reach out to Dr. Hagmeyer today and contact us.

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