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Stool Testing 101: A Complete Guide to the Top 4 Gut Health Tests

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Stool Testing 101: A Complete Guide to the Top 4 Gut Health Tests

Up to 70 million Americans suffer from digestive disorders, therefore it's vitally important for people to educate themselves and know when to seek help from a practitioner. Gut health is one of the first places we tend to look for root cause problems when things go awry. Multiple companies have comprehensive stool tests to help practitioners investigate and improve gut health. So, which one do you choose? With so many options, it can be hard to know which test is the best fit for you and your patient.

What to look for when comparing tests:

  • What markers they check for in their microbiome, digestion/absorption, and inflammation categories
  • The technology they use for microbiome testing
  • How much interpretation the report provides for you

Here is a quick and easy summary of some of the most popular gut health stool tests available today.

Genova Diagnostics
GI Effects
Diagnostic Solutions
Doctor’s Data
GI 360
Vibrant Wellness
Gut Zoomer
Insurance Coverage?
Medicare Coverage?
Microbiome Technology
PCR + Culture
PCR, MALD-TOFI, Microscopy
DNA Microarray Hybridization
~Number of Microrganisms tested
How much interpretation the report provides
Key Areas of  Focus
Digestion, Inflammation
Microbiome Analysis, Digestion, Inflammation
Microbiome Analysis
Microbiome Analysis, Inflammation
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‍‍GI Effects: Genova Diagnostics

GI Effects Stool Profile gives broad coverage of markers for inflammation, digestion/absorption, and the microbiome. It has options for many “add-on” markers allowing you to personalize your order for each patient and it comes with a patient-friendly report.

Here are some details on what you are getting when you order this test:

Gut Health Test Analysis

The GI Effects test uses PCR and Stool culture as dual methods for evaluating the microbiome. The PCR screens for 24 types of bacteria common to the GI tract and over 30 parasites. Of all the stool tests, the GI Effects has the narrowest microbial array and primarily screens for the commensal bacteria and parasites. However, it does offer a stool culture component to possibly catch other pathogens.

GI Effects also includes an analysis of the short-chain fatty acids produced by the colonic bacteria. This is a quick and easy way to see if you have enough helpful bacteria producing beneficial butyrate in the colon

Digestion and Absorption

Stool contains breakdown products of protein and fat from recent meals.  This test gives you a breakdown of fecal fat amount and subtypes as well as a total amount of broken down protein. By analyzing the type and amount of breakdown products, you can get a sense if someone is properly digesting their food.  You also get a measure of pancreatic elastase which can guide you to know if there is adequate production of pancreatic enzymes. Many practitioners use this information to see if digestion is a root cause problem for their patient and to decide whether or not specific digestive enzymes might help.

Inflammation and Immunology

‍GI Effects uses 3 powerful markers of inflammation within the GI tract: Calprotectin, Eosinophil protein, and Fecal Secretory IgA. Calprotectin is a widely accepted marker for inflammation in the GI tract. It is often used by gastroenterologists to help decipher between inflammatory and non-inflammatory bowel disease. Fecal Secretory IgA is an immunoglobulin secreted by the lining of the gut as a defense mechanism against infections.

While Calprotectin and Secretory IgA are common to almost all stool studies, the eosinophil protein X marker is unique GI Effects. This marker looks at IgE mediated inflammation of the gut which can be elevated in the setting of certain parasitic infections, food allergies, and some inflammatory bowel diseases.  

Using these three markers together, you can get a sense of whether or not someone has ongoing inflammation in their GI tract and gather some clues as to the possible source.

The Extras

‍Of all the options, GI effect is best known for the “Extras”.  They offer a proprietary “Functional Imbalance Score” that groups the results into easy to understand categories highlighting areas of focus and suggesting possible interventions. GI Effects has recently added an evaluation of “Dysbiosis Patterns” that takes the commensal bacteria profile and categorizes it into possible patterns that suggest root causes of dysfunction.

GI Effects also offers a wide array of “add-ons'' to better suit the needs of an individual patient. For example, you can add on specific bacteria tests such as H. pylori or Cdiff. You can also get a zonulin assessment or lactoferrin for additional metrics of inflammation.

What makes this test popular

  • Broad look at the three main elements of GI health
  • Ability to customize the test via add ons
  • Very patient friendly, visually appealing, and easy to understand reports. Reports offer assistance with both interpretation and suggest possible intervention

When should you consider this test?

  • You have a patient with a GI issue, but you aren’t sure exactly what is going on and the differential is long - could be an infection, digestive issue, inflammation etc.  This test can help point you in the right direction
  • You are at the start of an evaluation and don’t mind ordering a second test if you find a new direction to go in
  • You want to hand the patient the report directly and would welcome some help in interpretation of the report from the company  

GI MAP: Diagnostic Solutions

The GI MAP test is a microbiome focused stool test. It uses quantitative polymerase chain reaction (qPCR) technology that is unique to the industry and captures low-level microorganisms. It screens for over 50 bacterial pathogens, viruses, worms, parasites, various yeast types, H-pylori and virulence factors.

Here are some details on what you are getting when you order this test:

Gut Health Test Analysis

GI Map is a microbial assay, the technology allows for strain-specific identification of microorganism.  The test does not directly measure toxins, but rather genetic potential which will help rule out more serious GI pathogens. GI MAP brings together many of the pathogens that a physician would order for a traditional evaluation of GI complaints combined with the less common pathogens and commensal bacteria that a functional medicine panel often evaluates. It offers one stop shopping for a serious microbiome stool evaluation.  

Digestion and Absorption

GI Map offers two markers for digestion and absorption:  Elastase and Steatocrit. Steatocrit is a marker that is used to detect significant elevations of fat in stools. Studies have shown this marker to be comparable to a 72 hr fecal fat test.

Elastase is a pancreatic enzyme and is commonly used to assess pancreatic enzyme quantity and can be helpful when you are trying to decide if pancreatic enzymes might benefit your patient.


The GI MAP includes calprotectin a standard marker of inflammation and Secretory IgA (SIgA) a marker of mucosal immune response.
*See the GI Effects section for more info on these two

The Extras

GI MAP includes anti-gliadin IgA and the GI markers β-Glucuronidase & Occult Blood - FIT. They also offer Zonulin as an add on option.

What makes this test popular

Gi MAP offers a comprehensive microbiome analysis that includes viruses and many common clinical pathogens. It will often spare you from having to order a second stool test from a more traditional lab. They also offer consultations and lab interpretations for practitioners as well as all of their webinar content is available on YouTube and social media for educational purposes.

When should you consider this test?

You are highly suspicious of infectious causes and want to know exactly what organism you are dealing with.

GI 360: Doctor’s Data

The GI 360 stool test combines a broad investigation into the three main areas of digestive health with a very detailed microbiome analysis. GI 360 also offers some proprietary analysis of the data with a “Dysbiosis Index” and a “Microbiome Abundance and Diversity Summary”. The report includes explanations for the markers and summary interpretations, making this a well-rounded and easy to use choice.  

Here are some details on what you are getting when you order this test:

Gut Health Test analysis

The GI 360 uses PCR, MALDI-TOF, and Microscopy to provide a highly sensitive evaluation of over 80 targeted analytes. The analyte list combines the most common pathogenic bacteria with an analysis of the broader commensal flora that can inhabit a healthy gut. GI 360 tests for viruses that can cause illness, parasites, worms, and even less common pathogens such as mycoplasma. There is no culture component to this stool analysis.

GI 360 also includes an analysis of the short chain fatty acids produced by the colonic bacteria. It provides a breakdown of all the subtypes of short chain fatty acids and their relative percentages.  

Digestion and Absorption

The GI 360 contains multiple markers for digestion and absorption. It looks for “muscle fibers” in the stool which are incomplete breakdown products of protein as well as “vegetable fibers” and “carbohydrates”. In general, you should not see undigested food matter in the stool so if these levels are elevated, it can flag problems with adequate digestion. This test also offers a “fat stain” for fecal fat analysis and gives a baseline level of pancreatic elastase.


The GI 360 offers 4 markers for Inflammation and Immunology. It offers the standard Calprotectin and Secretory IgA and two additional markers: lactoferrin and lysozyme.

Lactoferrin is similar to calprotectin as a generalized marker for GI inflammation that is often used to differentiate between inflammatory vs non-inflammatory bowel disease. Lysozyme is an enzyme secreted by immune cells (mostly intestinal granulocytes) and is a sensitive indicator of an active immunologic process in the gut.           

The Extras

GI 360 has two proprietary analyses that help summarize key takeaways of their microbiology assessment. They have the “microbiome abundance and diversity summary”, which compares the individual's microbiome analysis to a “normobiotic” reference population and gives the patient a sense of how their microbiome compares. They also have the dysbiosis index which gives someone a score from 1-5. The higher the score, the more the sample deviates from the normobiotic profile. These interpretive markers can be a nice add on to help patients understand their microbiome results.

This test also provides a comprehensive write up about the various abnormal bacteria in a sample. This can help direct a practitioner into where to look up more information about a specific pathogen and what type of research may exist on various health implications.

What makes this test popular

  • GI 360 is the kitchen sink of stool tests. It is hard to think you would miss something with this stool test
  • Proprietary summaries that help patients to compare their data and explanations of various markers  

When should you consider this test?

  • Your differential of what could be going on is quite broad and you want as much information as you can get your hands on
  • You would welcome some additional information relating to the microbiome results and want a hefty report to go over with the patient.

Gut Zoomer: Vibrant Wellness

Gut Zoomer by Vibrant Wellness is a stool test that uses a proprietary DNA microarray hybridization platform to screen for over 300 microorganisms. Although the exact details of this method are proprietary, DNA microarray techniques are a well-established method for identifying microorganisms in the stool. Vibrant Wellness has released their own analysis of this technique and report a 99% specificity and a 98% sensitivity of their test - making this the most accurate microbiome test on the market. ‍

Gut Health Test Analysis

With over 300 microorganisms tested, the Gut Zoomer offers an incredibly comprehensive analysis of gastrointestinal bacteria, bacterial toxins, parasites, helminths, and viruses. There is no culture component, but with a list this exhaustive, it is hard to imagine that there would be much to miss. For each microorganism tested, they provide information on any potential associations with a clinical condition. They also group their microbiome results into helpful categories such as “Gut Bacteria and Autoimmune Health” bringing together various bacteria that may be associated with a unifying issue.

Last but not least, the Gut Zoomer also provides an analysis of the colonic short chain fatty acid breakdown and levels of Beta Glucuronidase enzyme.

Digestion and Absorption

For an assessment of digestion, Gut Zoomer offers a complete breakdown of fecal fat into triglycerides, cholesterol, long chain fatty acids, and phospholipids. It also detects improperly digested vegetable and protein fibers in food and Pancreatic Elastase.


The Gut Zoomer offers a comprehensive inflammation assessment with 8 inflammatory markers. They include the standard Calprotectin and Secretory IgA and then bring in all of the other inflammatory markers used by their competitors: Lysozyme, Eosinophil Protein X, and Lactoferrin.

Beyond that set, Gut Zoomer has three unique inflammatory markers - MMP 9, S100A12, and Beta Defensin 2. Beta Defensin 2 is part of the GI tract’s innate defense system and gets turned on in the presence of certain microorganisms and inflammatory cytokines. This protein is expressed in inflammatory bowel disorders such as Ulcerative Colitis and in some functional GI disorders such as IBS. MMP 9 is an inflammatory marker that correlates with the degree of mucosal inflammation in disorders such as Ulcerative Colitis. Fecal S100A12 is another inflammatory marker that is highly specific to inflammatory bowel disease such as Ulcerative Colitis and Crohn's disease and is often used as a noninvasive screening test for these conditions.

The combination of all eight markers will give you a broad and detailed sense of the level of gastrointestinal inflammation.

The Extras

  • Bile acid metabolites: Gallbladder dysfunction can be a cause of uncomfortable gastrointestinal symptoms, and the Gut Zoomer is the only stool test that pulls in a quantitative analysis of bile acid metabolites
  • Fecal zonulin is included in their analysis and can be a potential indication of intestinal permeability
  • Fecal Anti gliadin is also included and is a specific but not sensitive analysis of wheat sensitivity
  • Calculated diversity indexes for the microbiome offering an insight into the overall microbial diversity of a sample. They include both Shannon’s and Simpson’s diversity index
  • They provide a breakdown of microbiome by Phyla
  • They precalculate and highlight key rations such as the Firmicutes: Bacteroidetes and Prevotellaceae: Bacteroidetes ratios

What makes this test popular

  • Over 300 microorganisms tested in their DNA microarray platform
  • Report includes descriptions of all of their markers and clinical associations for many of the microorganisms
  • Hits all the bases of digestion/absorption, microbiome analysis, inflammation assessment

When should you consider this test

  • You need an extremely comprehensive microbiome analysis because you are worried about unusual pathogens
  • You want as much information as you can get in a single stool test
  • You feel comfortable with their proprietary methods for microbiome analysis
  • You appreciate and welcome interpretation of the data for yourself and the patient
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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