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How to Start Using Comprehensive Stool Testing In Your Clinic

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How to Start Using Comprehensive Stool Testing In Your Clinic

More than 36 million people visit doctor's offices yearly with gastrointestinal (GI) complaints. The digestive process can be complex, involving numerous organs, enzymes, and processes. Comprehensive stool testing can give great insight into the GI tract by assessing many of those factors.

This article will discuss comprehensive stool testing, why it should be used, and how to set up a treatment plan with the results. Additionally, we'll discuss Rupa Health's top five comprehensive stool tests.


What is Comprehensive Stool Testing?

Comprehensive stool testing takes a deep dive into the digestive system. Recently, a large area of research has focused on the microbiome, a collective group of bacteria, viruses, and fungi that inhabit the large intestine. They function to digest and absorb food, synthesize vitamins for us to utilize, modulate hormone and immune cell production, and more. Comprehensive stool testing takes an in-depth look into the composition of the microbiome, showing the presence of commensal (beneficial), pathogenic (harmful), and opportunistic (beneficial in small amounts but potentially harmful in large amounts) microbes. In addition, comprehensive stool testing can show markers of inflammation and intestinal permeability, as well as estrogen metabolism, protein, fat, and carbohydrate metabolism.

Comprehensive stool testing is done in the comfort of the patient's home. Testing can vary from one to multiple samples over a single day to three days. Depending on the test, certain foods and supplements may need to be stopped prior to testing. Additionally, testing may need to wait until certain medications are ceased. The time of day is not of importance in comprehensive stool testing.

Why Use Comprehensive Stool Testing in Your Clinic?

Comprehensive stool testing can get to the root of many  symptoms by testing the following markers:

  • Maldigestion
  • Inflammation
  • Dysbiosis
  • Metabolite Imbalance
  • Infection

Who Can Benefit from a Comprehensive Stool Analysis Test?

Because of its comprehensive gut health analysis, almost every patient can benefit from a gut health assessment. Our gut is responsible for helping with detox, nutrient absorption, hormone metabolism, and neurotransmitter production, as well as hosting 70% of the immune system. Some conditions that warrant testing are:

How to Set Up an Individualized Treatment Plan Based Off Results from Comprehensive Stool Testing

Comprehensive stool testing often shows markers of digestion, giving insight into stomach acidity, breakdown products of proteins, fats, and carbohydrates, as well as levels of enzymes that aid in their breakdown. These results can assist in the formation of specific dietary or supplement recommendations.


A low FODMAP diet is also a common recommendation as a result of stool testing. FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These are short-chain carbohydrates that are poorly absorbed within the small intestine and can cause bloating, gas, belching, and more. Research has shown a low FODMAP diet can be effective in people with IBS and IBD. Additionally, the Specific Carbohydrate Diet (SCD), a diet low in carbohydrates such as pasta, bread, grains, and cereals, may also alleviate IBD symptoms. Markers on stool testing, such as carbohydrate digestion and microbiome composition, can help the practitioner decipher which diet is appropriate.

For high markers of inflammation, an anti-inflammatory diet may be appropriate. Anti-inflammatory diets often limit the intake of processed foods while focusing on fruits, vegetables, nuts, and fatty fish.

Prebiotic-rich foods may be indicated if there is a lack of diversity in the microbiome. Prebiotics are compounds that feed the bacteria of the microbiome, increasing the diversity and amount of microbes. Jerusalem artichokes, onions, and chicory root are examples of foods with high prebiotic content.

Complementary and Alternative Medicine

If markers indicating increased intestinal permeability are present, also known as "leaky gut," a protocol including digestive enzymes, glutamine, and zinc, among other nutraceuticals, can be helpful.

Any pathogenic microbes present will need to be eradicated. Oil of oregano and deglycyrrhizinated licorice root (DGL) are examples of antimicrobials that can remove harmful microbes.

Probiotics are supplements that contain strains of healthy microbes commonly found in the microbiome. Probiotics are not created equal: the number and type of strains and the total number of microbes can vary significantly from product to product. Comprehensive stool testing can tell you which beneficial microbes you may be lacking, which may aid in choosing a probiotic. In general, probiotics can increase the amount and diversity of the microbiome.

Rupa Health's Top 4 Comprehensive Stool Test

The following are the top five comprehensive stool tests that are ordered at Rupa Health:


GI-MAP, by Diagnostic Solutions, is a stool test using highly sensitive quantitative polymerase chain reaction (qPCR) technology to identify the DNA of different microbes. This test gives deep insight into the microbiome, showing pathogenic bacteria, viruses, and parasites, Helicobacter pylori and its virulence factors, opportunistic bacteria, and bacteria that may trigger an autoimmune reaction. In addition, markers of digestive functioning, immune reactions, estrogen metabolism, and inflammation are also shown.

GI Effects Comprehensive Stool Profile

GI Effects Comprehensive Stool Profile, by Genova Diagnostics, looks at both commensal and pathogenic microbes as well as numerous markers of GI functioning. Using a specific algorithm based on results, they compute a Functional Imbalance Score, which rates the need for support in five categories: maldigestion, inflammation, dysbiosis, metabolic imbalance, and infection. This makes the test easy to understand.

Comprehensive Stool Analysis and Parasitology-3 Day

In addition to evaluating various bacteria, viruses, and yeasts, the Comprehensive Stool Analysis and Parasitology-3 Day by Doctor's Data will test any positive pathogenic microbes against natural and prescription antimicrobials. This increases the chances of eradication of said microbe(s).

GI 360

GI 360, also by Doctor's Data, provides a Microbiome Abundance and Diversity score as well as a Dysbiosis score. Microbiome health is directly correlated with the amount and diversity of the microbes, so quantitating those attributes can be incredibly helpful in understanding the microbiome's health.


Comprehensive stool testing can be a valuable tool to assess GI functioning, affecting the GI system and numerous other body systems, such as the reproductive and immune systems. With a surplus of information from comprehensive stool testing, a targeted, personalized treatment plan, including diet and supplementation, can be made.

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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