GI-MAP Intestinal Health Markers: What Each Result Means

Most people who order a GI-MAP focus on the microbiome findings — the pathogens, parasites, and opportunistic bacteria — but the GI-MAP intestinal health markers are often where the most clinically actionable information is found.

These markers do not tell you which organisms are present. Instead, they tell you how well your gut is actually functioning: how effectively you are digesting food, how robust your immune defences are, how much inflammation is present, and whether you have leaky gut.

For many patients, abnormal intestinal health markers explain symptoms that the microbial section alone cannot account for. Persistent bloating despite no significant pathogens, fatigue, hormonal imbalances, food sensitivities, and skin problems all frequently trace back to findings in this section.

The GI-MAP measures eight intestinal health markers as part of the standard panel, with zonulin available as an add-on. This article explains what each one measures, what it means when levels are high or low, and how the markers work together to form a complete picture of gut function.

Key Takeaways

• These markers assess gut function, not just gut organisms. Digestion, immunity, inflammation, and barrier integrity are all measured independently of which bacteria or parasites are present.
• Low pancreatic elastase is one of the most commonly missed findings on the GI-MAP. Poor enzyme output explains why many patients do not respond to probiotics or antimicrobials until digestive function is supported first.
• Calprotectin is the gold standard for gut inflammation and distinguishes IBD from IBS, two conditions that feel identical to the patient but require entirely different treatment approaches.
• Beta-glucuronidase connects gut health to hormonal balance. Elevated levels can drive estrogen dominance and impair detoxification independently of any obvious gut symptoms.
• Low SIgA explains persistent infections. Without adequate mucosal immunity, pathogenic organisms and opportunistic bacteria can establish and maintain overgrowth far more easily.
• These markers rarely tell a complete story in isolation. The clinical value comes from reading them alongside each other and in the context of the microbial findings.

The Eight Intestinal Health Markers

1. Pancreatic Elastase-1 (Digestion)

Pancreatic elastase-1 is a digestive enzyme produced exclusively by the pancreas, making it a direct and specific marker of pancreatic exocrine function.

Unlike many digestive enzymes, elastase-1 remains stable through the digestive tract and survives in stool without degradation, which makes it reliable to measure.

It is also unaffected by pancreatic enzyme replacement therapy so patients who are already taking digestive enzymes will still get an accurate result.

Reference ranges:

• Above 500 µg/g: Normal pancreatic output
• 200–500 µg/g: Decreased pancreatic output
• Below 200 µg/g: Pancreatic insufficiency

Low elastase-1 means

The pancreas is not producing sufficient digestive enzymes to break down fats, proteins, and carbohydrates effectively.

This leads to malabsorption of nutrients and fat-soluble vitamins (A, D, E, K), explains symptoms like bloating, fatty stools, and persistent fatigue, and creates conditions in the gut that allow opportunistic bacteria to overgrow on undigested food substrates.

Common causes of low elastase-1 include hypochlorhydria (low stomach acid), H. pylori infection (which impairs acid production), cystic fibrosis, gallstones, SIBO and chronic stress on the pancreas. Low levels are also found in some vegetarians and vegans.

Clinical significance

Low elastase-1 is one of the most important findings to address before anything else on the test. Giving probiotics or antimicrobials to a patient with significant pancreatic insufficiency is unlikely to produce lasting results, because the underlying digestive dysfunction continues to fuel dysbiosis.

Treatment approach

Betaine HCl to support stomach acid, digestive enzyme supplementation (amylase, lipase, protease, pepsin), bile salts, taurine, digestive herbs and bitters. Identify and address underlying causes of why levels are low in the first place.

2. Steatocrit (Fecal Fats)

The steatocrit measures the amount of fat present in stool. Fats are normally emulsified by bile acids in the small intestine and absorbed efficiently, so fat appearing in significant quantities in stool indicates that this process has broken down.

Elevated steatocrit means

Fat malabsorption is occurring. This can be caused by pancreatic insufficiency (check elastase-1), insufficient bile acid production or flow, impaired small intestinal absorption, hypochlorhydria, celiac disease, or significant dysbiosis.

The consequences include malabsorption of fat-soluble vitamins A, D, E, and K, nutrients critical for immune function, bone health, vision, and cardiovascular health. Fatty, floating, or greasy stools are the most common symptom.

Treatment approach

Support stomach acid and digestive enzymes as for low elastase-1. Other options bile salts and taurine to support fat emulsification. Investigate underlying causes including celiac disease and liver/gallbladder function.

The StoolOMX add-on provides much more detailed insight into bile acid function when steatocrit is elevated and can help to guide the best way to treat fat malabsorption.

3. Secretory IgA (Mucosal Immunity)

Secretory IgA (SIgA) is the primary immune antibody produced in the intestinal lining.

It is the gut’s first line of immune defence, a coating that covers the mucosal surface and neutralizes pathogens, toxins, and food antigens before they can trigger systemic immune responses.

SIgA also plays a central role in regulating which bacteria can colonize the gut, making it a key determinant of microbiome balance.

Low SIgA means

The mucosal immune system is suppressed. This leaves the gut lining poorly defended against pathogens, opportunistic bacteria, and food antigens.

Patients with chronically low SIgA are more susceptible to recurrent gut infections, struggle to clear parasites and bacteria, and often develop food sensitivities because undefended food proteins cross the gut lining and trigger immune responses.

Common causes include chronic dysbiosis, chronic stress, overtraining, protein malnutrition, and immunocompromised states.

High SIgA means

The immune system is actively responding to antigens in the gut. This is typically driven by acute or chronic infection, dysbiosis, food sensitivities, or chronic stress.

It is not inherently a problem, it indicates the immune system is doing its job but persistently elevated SIgA alongside other findings suggests ongoing immune challenge and looking at the rest of the test can help to identify the trigger.

Treatment approach for low SIgA

Address any chronic gut infections. Support the microbiome and reduce dysbiosis. Manage chronic stress and support adrenal function. Colostrum, immunoglobulins, Saccharomyces boulardii, L-glutamine, Lactobacillus and Bifidobacterium probiotics, zinc, and essential fatty acids all support SIgA recovery.

Related article: Tips to Test and Balance SIgA

4. Anti-gliadin IgA (Gluten Reactivity)

Anti-gliadin IgA measures an immune reaction specifically to gliadin, the protein component of gluten found in wheat, barley, rye, and related grains.

This is a gut-level immune response, the antibody is produced in the intestinal lining, not the bloodstream and it does not necessarily correlate with blood antibody levels. A patient can have elevated fecal anti-gliadin IgA with normal celiac blood markers.

Elevated anti-gliadin IgA means

The gut immune system is reacting to gluten. This can occur in celiac disease, non-celiac gluten sensitivity, or as part of a broader food reactivity pattern driven by increased intestinal permeability.

For patients who believe they are already avoiding gluten, elevated anti-gliadin IgA points to hidden sources of exposure through cross-contamination or unlabelled ingredients.

Treatment approach

Consider gluten elimination for a trial period. If you are already gluten-free, investigate hidden sources including dairy, corn, oats, millet, rice, and yeast (which can cross-react with gliadin). Support the gut barrier with L-glutamine, zinc carnosine, and colostrum.

5. Eosinophil Activation Protein (EDN/EPX)

Eosinophil activation protein also known as eosinophil-derived neurotoxin (EDN) or eosinophil protein X (EPX), is released by eosinophils, the immune cells responsible for allergic and mast-cell-mediated inflammatory responses in the gut lining.

It is a direct, objective measure of chronic intestinal inflammation driven by allergic or immune-mediated pathways.

Elevated eosinophil activation protein means

Chronic gut inflammation is present, driven by immune or allergic mechanisms.

Associated conditions include IBD (where it can be used to evaluate disease activity and predict relapse), IBS, food allergies and sensitivities, eosinophilic esophagitis, acid reflux, functional dyspepsia, intestinal parasites, and IBS-related anxiety.

It is also useful for measuring whether a food elimination diet is actually reducing gut inflammation.

Treatment approach

Address the underlying driver and this can be infection, food sensitivities, or dysbiosis. Anti-inflammatory dietary interventions including curcumin, omega-3 fatty acids, aloe, and resveratrol. Remove identified food triggers.

6. Calprotectin (Gut Inflammation)

Calprotectin is the most studied and clinically validated marker of gastrointestinal inflammation on the GI-MAP. It is released by neutrophils which are white blood cells when they migrate into the gut mucosa in response to inflammation.

It is the gold standard marker for diagnosing and monitoring inflammatory bowel disease, and is used clinically to differentiate IBD from IBS.

This distinction is critical because IBD and IBS produce near-identical symptoms (diarrhea, cramping, urgency, bloating) but require completely different treatment approaches. IBS is typically associated with normal calprotectin; IBD produces elevated calprotectin.

A high calprotectin result in a patient previously told they have IBS warrants further gastroenterological investigation.

Elevated calprotectin means

Active gut inflammation is present. Possible causes include intestinal infections and pro-inflammatory dysbiosis, food allergens, NSAIDs and certain other drugs, IBD, polyps, diverticulitis, and colorectal cancer.

Persistently elevated calprotectin always warrants further clinical evaluation, usually with a colonoscopy.

Treatment approach

Address the cause of inflammation. Anti-inflammatory support: anti-inflammatory diet, curcumin, omega-3 fatty acids, aloe vera, and resveratrol.

Related article: How to Reduce Calprotectin Naturally

7. Occult Blood — Fecal Immunochemical Test (FIT)

The fecal immunochemical test (FIT) detects trace amounts of human blood in stool that are invisible to the naked eye.

It uses antibodies specific to human hemoglobin, which means dietary choices (red meat, for example) do not affect the result and false positives are minimized, a significant advantage over older guaiac-based methods.

Elevated occult blood means

Blood is present in the stool from somewhere in the digestive tract.

Causes range from minor to serious: hemorrhoids, anal fissures, pathogenic infection (including Giardia), bleeding ulcers, liver disease, upper GI infections, intestinal polyps, IBD, and colorectal cancer.

A result of 10 µg/g or above is associated in the literature with potentially serious conditions including polyps or colorectal cancer and warrants follow-up investigation.

Treatment approach

Identify the source. Follow-up testing may include colonoscopy, upper endoscopy, or imaging and is recommended when occult blood is detected, particularly at higher levels or in patients over 45.

8. Beta-glucuronidase (Detoxification and Hormonal Balance)

Beta-glucuronidase is an enzyme produced by certain gut bacteria that interferes with one of the liver’s key detoxification pathways.

To understand why this matters, you need to understand glucuronidation: the liver conjugates compounds including estrogen, environmental toxins, and certain medications to a glucuronic acid molecule in preparation for excretion via bile and stool.

Beta-glucuronidase breaks that bond, freeing the conjugated compound to be reabsorbed rather than eliminated.

In practical terms, elevated beta-glucuronidase means that estrogen and other compounds the body has packaged for removal are being recirculated. This is one of the mechanisms connecting gut health to hormonal balance.

Elevated beta-glucuronidase means

Dysbiosis is present (this enzyme is produced by an imbalanced microbiome), the glucuronidation detoxification pathway is being impaired, and estrogen that should be excreted is being reabsorbed.

This can contribute to estrogen dominance, PMS, PCOS, endometriosis, and hormonal breast conditions. Extremely elevated levels are also associated with increased colorectal cancer risk. Overexposure to environmental toxins and drugs amplifies these effects.

Treatment approach

Address the underlying dysbiosis. Promote bacterial diversity through probiotics, fiber, prebiotics, and fermented foods.

Consider calcium D-glucarate and milk thistle for liver and glucuronidation support, particularly in patients on hormone replacement therapy or with elevated cancer risk. If there are no signs of dysbiosis on the GI-MAP, consider a SIBO breath test as an additional cause of high levels.

Add-on Marker: Zonulin (Intestinal Permeability)

Zonulin is available as an optional add-on to the standard GI-MAP panel. It is a protein that regulates the tight junctions between epithelial cells lining the intestinal wall, essentially the seals that control what passes through the gut lining into the bloodstream.

When zonulin levels are elevated, those junctions loosen and the gut becomes more permeable, allowing bacteria, toxins, and partially digested food particles to enter the bloodstream. This is what is commonly called “leaky gut.”

Elevated zonulin means

Intestinal permeability is increased. This can trigger immune activation, systemic inflammation, food sensitivities, and in susceptible individuals, autoimmune responses. It is particularly relevant for patients with autoimmune conditions, chronic food sensitivities, or inflammatory conditions that do not have an obvious cause.

It is worth noting that zonulin alone is not a complete picture of intestinal permeability. It correlates with increased permeability but should be interpreted alongside SIgA, calprotectin, anti-gliadin IgA, and the microbial findings.

The Vibrant Wellness Wheat Zoomer blood test additionally measures anti-actin antibodies and lipopolysaccharide (LPS) levels, which help confirm leaky gut from a different angle.

Treatment approach

Address dysbiosis and pathogen overgrowth. Eliminate gluten and address food sensitivities. Gut barrier support: L-glutamine, butyrate, essential fatty acids, aloe vera, probiotics, zinc carnosine, slippery elm, marshmallow root, and deglycyrrhizinated licorice (DGL).

Related article: Understanding Leaky Gut and Zonulin

How the Markers Work Together: Common Patterns

The real clinical value of the intestinal health markers section comes from reading the findings together rather than in isolation. Several patterns are particularly instructive:

Digestive dysfunction pattern

Low elastase-1 alongside elevated steatocrit points to pancreatic insufficiency as the primary driver. If Methanobacteriaceae or Streptococcus are also elevated on the microbiome section, this confirms that poor digestive function is creating downstream dysbiosis. Treatment sequencing matters here: supporting digestion first creates the conditions for the microbiome to recover.

Immune suppression pattern

Low SIgA alongside elevated calprotectin creates a paradoxical picture, the mucosal immune system is suppressed while gut inflammation is active. This is common in patients with longstanding gut infections, chronic stress, or overtraining. Targeting the infection alone is insufficient; mucosal immune recovery needs to be part of the protocol.

Leaky gut and immune activation pattern

Elevated zonulin alongside elevated anti-gliadin IgA, high eosinophil activation protein, and elevated calprotectin is a strong indicator of active gut barrier disruption driving systemic immune responses.

This pattern is commonly associated with food sensitivities, autoimmune conditions, and chronic inflammatory presentations.

Hormonal connection pattern

Elevated beta-glucuronidase in a patient with hormonal symptoms (PMS, estrogen dominance, PCOS) makes the gut a primary clinical focus, even when the presenting complaint appears purely hormonal. Treating the gut dysbiosis driving beta-glucuronidase elevation is often more effective than hormonal intervention alone.

Treating this pathway is the priority before taking supplements like DIM that support phase one and two of estrogen detoxification.

Frequently Asked Questions

For a complete overview of everything the GI-MAP measures, visit the Complete Guide to the GI-MAP Test. To order the test, visit the GI-MAP order page, or contact us to discuss your situation.