As a registered dietitian and gut health expert, I often get a lot of questions about comprehensive stool analysis. Some common questions often include – what is this test all about? Who is the right candidate for the test? What exactly will it tell me about my gut microbiome? To end your confusion and to answer all your questions, let’s dive right into this topic and talk about all things comprehensive stool analysis. 

What is a comprehensive stool analysis? 

An Imbalanced gut and poor digestive health can be a root cause for autoimmune conditions, weight challenges, weakened immune system, diabetes, and even many neurological conditions. A comprehensive stool analysis provides in depth information about your gut microbiome and overall gut health beyond just a standard stool culture. It does this by taking a candid picture of your entire gut in order to help you uncover the root causes of your gut problems and so you can develop the right treatment plan to repair and heal your gut.

What can a comprehensive stool analysis tell me about my gut?

A comprehensive stool analysis helps detect how well you are digesting foods and absorbing nutrients. It also detects inflammation in your gut and any underlying gut infections like parasite infection, yeast infection, or H. pylori infection. The test also helps detect any missing beneficial species of microbes from your gut, which may help determine the right probiotics for you. Now please note that this test does not rule out small intestinal bacterial overgrowth (SIBO) so you may need to take an alternative test to test for SIBO, such as a breath test.  

How do I complete the test?

A comprehensive stool analysis can be done from the comfort of your home. Some labs require you to collect a two day or even a three day stool sample, and others require you to collect just a one day stool sample. After you collect the stool sample you mail it back to the lab and it typically takes anywhere between two to four weeks for your results to come in. 

Should I take a comprehensive stool analysis?

Good candidates for a comprehensive stool analysis include folks who are struggling with:

  • Food sensitivities
  • Skin rashes like eczema or dermatitis
  • Autoimmune diseases 
  • Leaky gut 
  • Frequent constipation and/or loose bowels 
  • GERD 
  • Low energy and fatigue 

These are all signs and symptoms that indicate gut dysbiosis and microbial imbalance and would be appropriate qualifiers to take a comprehensive stool analysis. 

Wooden dummy sitting on a toilet to represent the process of taking a comprehensive stool analysis.

What lab results are measured?


Most labs measure various inflammatory markers such as:

  • Calprotectin
  • Lysozyme
  • S100A12
  • MPP9

These inflammatory markers can help determine the root cause of your inflammation and GI infections. If you have elevated inflammatory markers, it is recommended to:

Other strategies to reduce inflammation include treating the infection if there is one (i.e. bacterial pathogens, parasite infection, or yeast overgrowth). If you are using NSAIDs regularly, then you may want to stop using them as it adds more inflammation into your body. 


Comprehensive stool analysis measures various markers of malabsorption, such as pancreatic elastase, which is an enzyme that is produced in your pancreas. A low level of pancreatic elastase indicates that pancreas are not producing enough of this enzyme and the food you eat is not being efficiently digested as a result. Another marker of malabsorption that is also measured is fat malabsorption. High levels of fat in your stool sample can indicate fat malabsorption as your body is not able to absorb fat efficiently. Other possible signs of fat malabsorption include weight loss, diarrhea, and nutrient deficiencies specifically for fat soluble vitamins like vitamin A, D, E, and K. 

Short Chain Fatty Acids 

Another important parameter most labs cover in a comprehensive stool analysis are short chain fatty acids. Short chain fatty acids play an important role inside our gut as they are the preferred fuel source for the cells that line the large intestine. They promote growth of new cells and repair the cells that are damaged. The good bacteria in the large intestine also like to chew on insoluble fiber and at the end of the chewing processes they produce short chain fatty acids. If the test shows suboptimal levels of short chain fatty acids, it could be an indicator of low “good” bacteria in the gut. To promote more short chain fatty acids in the gut, you can increase your intake of dietary butyrate and butyrate supplements which can help improve the total number. 

Fecal Zonulin

Some labs also cover what is called fecal zonulin which is a protein that regulates the reversible permeability of intestinal tight junctions. High levels of fecal zonulin suggest increased intestinal permeability, or what is commonly called a leaky gut. 

A person holding up a cooking that is shaped like stool to represent comprehensive stool analysis.

Fecal Gliadin

One other marker that some labs cover under this test is fecal gliadin. Gliadin is a protein unique to wheat gluten which is a known autoimmune trigger in celiac disease. It has direct interaction with intestinal zonulin to drive the zonulin signaling cascade and thus The Fecal Antigliadin Antibody tests for immune system reaction to gluten in the diet. It enables direct and quantitative assessment of gluten exposure early after ingestion and could possibly aid in the diagnosis and clinical management of non responsive celiac disease.

Final Thoughts 

In conclusion, a Comprehensive Stool Analysis helps to uncover the root cause of your gut health issues and determine the best course of action to solve your gut health puzzle and bring you some relief and healing. If you are interested in learning more about comprehensive stool analysis, are curious if it is the right test for you, and are looking for one-on-one support for your digestive issues we can help get to the root of your issues and provide some relief!


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