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  • Writer's pictureTina Shiver

Why Functional Medicine Practitioners Order a Stool Analysis


When I meet with a new patient, they fill out an assessment form and a medical symptom questionnaire. The information they provide allows me to start to get to know their story and helps me to identify in balances in their body that is contributing to their gastrointestinal symptoms.

It is not unusual to find common symptoms on an assessment which include bloating, belching, gas, reflux, stomach pain, diarrhea, and constipation. The recommendations they have been given include the wrong supplements, a food plan that does not help and or medications that keep the symptoms low, but do not get to the root cause of the in balance.

Food records indicate that people are confused about what to eat. A person may be on medications which could be making their symptoms worse or could slow down healing their gut.

In my practice, I will often request a stool analysis. The stool analysis can be used as a foundational tool that helps me evaluate what is going on in their gastrointestinal world.

What is the stool analysis comprised of?

  • Digestion and absorption markers

  • Immune and Inflammation markers

  • Microbiome and it’s metabolic products

The stool test can detect microbes that are causing a microbial in balance or contributing to illness. I’m able to look at bacteria, fungi, virus and parasite in balances which can cause many different symptoms which include diarrhea, bloating and gas and sometimes reflux.

If there are pathogens present, the protocol in functional medicine is to use the 5R approach which includes:


  • Remove: Remove certain foods, bugs, and toxins.

  • Replace: Adding back the foods and or adding digestive enzymes or betaine or bile salts.

  • Reinoculate: Adding back pre and probiotics.

  • Repair: Adding L-glutamine and nutrients to help repair the gut wall lining.

  • Rebalance: The stool test looks at commensal bacteria where trillions of microorganisms are found in the intestine where they play an important role in a person’s health. Did you know that commensal bacteria extract’s nutrients and energy from the food we eat which helps us maintain a gut barrier function, produce vitamins and protect us from potential pathogens?

An example of a commensal bacteria is Bifidobacterium spp which is found in most probiotics and is also present in breast milk. It is colonized in the human GI tract at birth. It can thrive on a wide variety of prebiotic fibers.

The stool analysis provides you with information on any opportunistic bacteria as dysbiotic/overgrowth which is important because these bacteria can eventually cause leaky gut or small intestinal overgrowth.

Enterococcus faecalis is another opportunistic bacterium that may be found in high levels because of low stomach acid, PPI use, compromised digestive function or small intestinal bowel overgrowth.

The test also shows whether a person has high levels of candida spp. If you have candida some of the symptoms may be gas, bloating, constipation or diarrhea.

Some of the intestinal health markers include testing the pancreatic elastase I, steatocrit, which looks at the amount of fat in the stool, and whether you have maldigestion, malabsorption, bile salt insufficiency or celiac disease.

The test takes a look at how your immune system is responding and whether or not it is suppressed.

An important marker called calprotectin tests whether there is inflammation and distinguishes between IBD and IBS.

The stool analysis gives you enough information to begin to change the symptoms a person may have been having for years. It’s highly recommended in my practice especially if you have been diagnosed with IBS, IBD (Crohn’s or ulcerative colitis), unexplained diarrhea, gastritis, or any type of gastrointestinal disease.

As you can see, there is much that can be learned from a stool analysis. If you have been plagued with gastrointestinal issues, I would suggest speaking with your doctor or seeking out a Functional Medicine Practitioner who can order this test for you.

Until next time…eat healthy and move.


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