Complete Guide To the GI Map Test

Most people who come to us with chronic gut symptoms have already tried the basics: they have eliminated foods, tried probiotics, and had standard blood work done. 

Most have been told their results are normal. Yet the symptoms, bloating, unpredictable bowel habits, fatigue, brain fog, skin problems, persist. Even if you have had a colonoscopy or Endoscopy and told your results are normal these tests are only looking at physical problems and cannot identify functional gut issues.

The GI-MAP Test (GI Microbial Assay Plus) is one of the most accurate and comprehensive DNA-based stool tests available, and it has become the number one gut health investigation in functional medicine.

Rather than guessing which bacteria, parasite, or imbalance might be driving your symptoms, the GI-MAP measures the actual quantity of every relevant organism in your GI tract, from beneficial bacteria and fungi through to pathogens and parasites, using quantitative PCR technology that is significantly more sensitive than traditional culture-based laboratory methods.

Having used the GI-MAP with patients across a wide range of chronic conditions for the past ten years, The Complete Guide to the GI Map Test covers everything you need to know: what the test measures, the add-on panels, who should consider it, how it compares to alternatives, and how to get started.

Key Takeaways

• It measures quantity, not just presence. The GI-MAP uses qPCR technology to quantify how much of each organism is present, which is critical for determining clinical significance and tracking treatment progress.
• Add-on panels significantly extend what the test can tell you. StoolOMX (bile acids and short chain fatty acids), antibiotic resistance genes, fecal gluten peptide, and zonulin can all be added depending on your clinical picture.
• Symptoms well beyond the gut can have gut origins. The GI-MAP is relevant not just for digestive complaints but for skin conditions, mood disorders, autoimmune disease, hormonal imbalance, and more.
• You need an experienced practitioner to interpret it correctly. The value of the GI-MAP is in understanding the pattern of results as a whole, not reacting to individual markers in isolation.
• It is an at-home test that does not require a clinic visit. The kit is delivered to your door and the sample is collected at home and shipped back to the lab.

What is the GI-MAP Test?

The GI-MAP Test is a stool analysis test created by Diagnostic Solutions Laboratory that uses quantitative PCR (qPCR) technology to analyze a patient’s stool sample for bacteria, parasites, viruses, fungi, and key intestinal health markers. It is FDA-approved and has been one of the most widely used comprehensive stool tests in the US for a number of years.

What distinguishes it from older stool tests is the precision of qPCR technology. Rather than simply identifying whether a pathogen or organism is present or absent, qPCR determines the actual quantity of each organism’s DNA in the sample. This matters clinically: a small amount of a potentially pathogenic organism may have no significance, while a large amount demands attention. 

It also means the test is exceptionally useful for monitoring treatment, as a retest after an intervention will clearly show whether a pathogen has cleared, whether beneficial bacteria have recovered, and whether the overall microbiome has shifted.

Diagnostic Solutions Laboratory is the only laboratory in the United States exclusively using qPCR technology for comprehensive stool testing.

If you prefer to watch an introduction to the GI-MAP, the video below covers the essentials.

What Does the GI-MAP Test For?

The GI-MAP assesses the quantity of bacteria, parasites, viruses, fungi, and other intestinal health markers present in a stool sample. The full panel covers the following categories:

Commensal and Keystone Bacteria

These are the beneficial organisms that support gut function, immunity, and microbiome balance. Low levels of these bacteria are a common finding in chronic inflammatory and autoimmune conditions.

• Bacteroides fragilis
• Bifidobacterium spp.
• Enterococcus spp.
• Escherichia spp.
• Lactobacillus spp.
• Enterobacter spp.
• Akkermansia muciniphila
• Faecalibacterium prausnitzii
• Roseburia spp.
• Firmicutes phyla and Bacteroidetes phyla (including the Firmicutes to Bacteroidetes ratio)

The Firmicutes/Bacteroidetes ratio is worth paying attention to. A high ratio is associated with increased caloric extraction from food, impaired insulin sensitivity, fat deposition, and increased inflammation, making it a useful metabolic indicator alongside the other microbiome findings.

Opportunistic Bacteria

These organisms are considered normal at low levels but can cause problems when they overgrow, particularly in individuals with compromised immunity, reduced digestive function, or following antibiotic use.

• Bacillus spp.
• Enterococcus faecalis and Enterococcus faecium
• Morganella spp.
• Pseudomonas spp. and Pseudomonas aeruginosa
• Staphylococcus spp. and Staphylococcus aureus
• Streptococcus spp.
• Desulfovibrio spp.
• Methanobacteriaceae (family)
• Citrobacter spp. and Citrobacter freundii
• Klebsiella spp. and Klebsiella pneumoniae
• Mycobacterium avium subsp. paratuberculosis
• Proteus spp. and Proteus mirabilis
• Fusobacterium spp.
• Prevotella spp.

Several of these have documented associations with autoimmune conditions. Klebsiella, for example, is linked to ankylosing spondylitis and Crohn’s disease; Proteus with rheumatoid arthritis; Fusobacterium with systemic sclerosis and IBD. 

When intestinal permeability is also present, these organisms can escape the gut lumen and trigger or sustain autoimmune responses at distant sites.

Bacterial Pathogens

The more serious gut pathogens that are commonly associated with gastroenteritis and GI disease.

• Campylobacter
• C. difficile Toxin A and Toxin B
• E. coli (multiple pathotypes: EPEC/EHEC, Enteroinvasive E. coli/Shigella, Enterotoxigenic E. coli LT/ST, Shiga-like Toxin stx1 and stx2, E. coli O157)
• Salmonella
• Vibrio cholerae
• Yersinia enterocolitica

Not every positive finding requires treatment. Whether symptoms are present, the quantity detected, and other findings on the test all factor into clinical decision-making.

H. pylori and Virulence Factors

The GI-MAP provides a quantitative H. pylori load alongside a full virulence factor profile. These virulence factors help determine how pathogenic a given strain is and whether it carries elevated risk for ulcers or gastric cancer. 

Nearly 50% of the world’s population may carry H. pylori, but only a small proportion develop serious complications, and the virulence factors are key to assessing that risk.

Virulence factors tested: BabA, CagA, DupA, IceA, OipA, VacA, VirB, and VirD.

The standard panel also includes H. pylori-specific antibiotic resistance genes for clarithromycin, amoxicillin, fluoroquinolones, and tetracycline, which are critical for designing an effective treatment protocol if antibiotic eradication is required. 

At Planet Naturopath we focus on natural treatment strategies to eliminate H.pylori.

Viral Pathogens

• Adenovirus 40/41
• Norovirus GI/GII
• Cytomegalovirus (CMV)
• Epstein-Barr Virus (EBV)

A positive CMV or EBV result on the GI-MAP indicates active GI infection rather than past exposure. Both viruses have documented associations with autoimmune conditions (including rheumatoid arthritis, lupus, multiple sclerosis, and autoimmune thyroid disorders) and are found in a significant proportion of IBD patients.

Parasites

The GI-MAP tests for both protozoa and intestinal worms. Not all of these organisms are pathogenic at every level detected, and clinical context is essential when interpreting findings.

Protozoa:

• Blastocystis hominis
• Chilomastix mesnili
• Cyclospora spp.
• Dientamoeba fragilis
• Endolimax nana
• Entamoeba coli
• Entamoeba histolytica
• Giardia
• Pentatrichomonas hominis

Worms:

• Hookworms (Ancylostoma duodenale and Necator americanus)
• Roundworm (Ascaris lumbricoides)
• Whipworm (Trichuris trichiura)
• Tapeworm (Taenia spp.)

Fungi and Yeast

• Candida albicans
• Candida spp.
• Geotrichum spp.
• Microsporidia spp. (specifically Encephalitozoon intestinalis)
• Rhodotorula spp.

Intestinal Health Markers

A separate panel of functional markers covering digestion, immune function, inflammation, and gut barrier integrity. These intestinal health markers can help to guide the best way to treat infections.

Not all organisms identified on the GI-MAP require treatment. A core part of interpreting the test correctly is understanding the clinical context of the results as a whole: which organisms are elevated, which are depleted, how the inflammatory markers look, and what the patient’s symptoms are. Some findings require immediate treatment; others simply need monitoring.

You can read more about specific GI pathogens in the related article: GI Map Test — Bacterial Pathogens and Parasites.

Intestinal Health Markers

This section of the GI-MAP goes beyond the microbiome to assess how well the gut is functioning as a whole. These markers cover digestion, gut immunity, inflammation, and barrier integrity. For many patients, these are as clinically important as the microbial findings.

Pancreatic Elastase (Elastase-1) Elastase-1 is a digestive enzyme produced exclusively by the pancreas, making it a direct marker of pancreatic function. Low levels indicate the pancreas is not producing sufficient digestive enzymes, a condition called pancreatic insufficiency, which leads to poor breakdown and absorption of fats, proteins, and carbohydrates. 

This is commonly associated with H. pylori infection, low stomach acid (hypochlorhydria), and chronic digestive dysfunction, and explains why some patients experience persistent bloating, fatty stools, and nutrient deficiencies despite dietary changes.

Steatocrit (Fecal Fats) The steatocrit measures the amount of fat in stool, which is normally emulsified by bile salts and absorbed in the small intestine. Elevated fecal fats indicate fat malabsorption and can be caused by pancreatic insufficiency, insufficient bile acids, poor digestion, or conditions such as celiac disease. 

This marker helps identify why someone may not be absorbing fat-soluble nutrients such as vitamins A, D, E, and K, even when dietary intake appears adequate.

Beta-glucuronidase Beta-glucuronidase is an enzyme produced by certain gut bacteria that interferes with the body’s detoxification processes. Normally, the liver conjugates compounds including estrogen and environmental toxins in preparation for excretion, but beta-glucuronidase cleaves those bonds, allowing the compounds to be reabsorbed rather than eliminated. 

High beta-glucuronidase is associated with dysbiosis and can contribute to estrogen dominance, hormonal imbalances, elevated cancer risk, and impaired clearance of environmental toxins. It is one of the reasons the GI-MAP is relevant not just for gut symptoms but for hormonal presentations.

Occult Blood (FIT) The fecal immunochemical test (FIT) detects very small amounts of human blood in stool that are invisible to the naked eye. Unlike older methods, it uses antibodies specific to human hemoglobin so dietary choices do not affect the result, and false positives are minimized. 

Elevated occult blood can reflect causes ranging from minor (hemorrhoids, anal fissures) to serious (polyps, colorectal cancer, bleeding ulcers), and any meaningful finding warrants follow-up investigation.

Secretory IgA (SIgA) Secretory IgA is the primary immune antibody produced in the intestinal lining and represents the first line of immune defence against pathogens, toxins, and food antigens that enter the gut. It also plays a central role in regulating microbiome balance and protecting against food-derived antigens. 

Low SIgA indicates a suppressed mucosal immune system, increasing vulnerability to infection and dysbiosis; high SIgA suggests an active ongoing immune response, commonly driven by infection, dysbiosis, chronic stress, or food sensitivities.

Anti-gliadin IgA This marker measures an immune reaction to gliadin, the protein component of gluten found in wheat, barley, rye, and related grains. Elevated anti-gliadin IgA in stool indicates the gut immune system is reacting to gluten in the digestive tract, which can occur independently of celiac disease and does not always correlate with blood antibody levels. 

It is particularly useful for identifying gut-level gluten reactivity that may not show up on standard blood panels, and for patients who suspect gluten is contributing to their symptoms but have had negative celiac serology.

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 involved in allergic and inflammatory responses in the gut lining. 

Elevated levels in stool indicate chronic intestinal inflammation and are associated with IBD, IBS, food allergies, eosinophilic esophagitis, intestinal parasites, and acid reflux. It is particularly useful for monitoring disease activity in IBD and for assessing whether a food elimination diet is reducing gut inflammation.

Calprotectin Calprotectin is released by neutrophils (immune cells) when they migrate into the gut lining in response to inflammation, and it is the gold standard marker for gastrointestinal inflammation. It is used clinically to diagnose and monitor inflammatory bowel disease and to distinguish IBD from IBS, where calprotectin is typically normal. 

Persistently elevated calprotectin warrants further investigation, as it can indicate IBD, infection, polyps, diverticulitis, or colorectal cancer.

GI-MAP Add-on Tests

The core GI-MAP panel provides a comprehensive picture of the gut microbiome, but several optional add-ons can extend its diagnostic reach when a specific clinical question calls for it. These are not necessary for every patient, but in the right context they can add significant clinical value without requiring an additional sample collection.

Zonulin

Zonulin is a protein that regulates the tight junctions between cells lining the intestinal wall. When stool zonulin levels are elevated, it indicates those junctions have become too permeable, allowing bacteria, toxins, and partially digested food particles to pass into the bloodstream. 

This is what is commonly referred to as “leaky gut,” and it can trigger immune activation, systemic inflammation, and in susceptible individuals, autoimmune responses. Zonulin is the most direct available stool marker for intestinal permeability and is particularly relevant for patients with food sensitivities, autoimmune conditions, or chronic inflammation that does not have an obvious cause.

Fecal Gluten Peptide

The fecal gluten peptide add-on quantifies gluten immunogenic peptides in stool, which appear within two to four days of gluten ingestion. Because of structural similarities between gluten proteins, the test can also detect peptides from rye, barley, corn, and oat grains. 

This is clinically useful in two situations: confirming whether someone with celiac disease or non-celiac gluten sensitivity is maintaining a strict gluten-free diet, and identifying hidden gluten exposures through cross-contamination or unlabelled ingredients. Many patients believe they are avoiding gluten entirely but are still reacting, and this test removes the guesswork.

For more information on gluten testing and sensitivity, see the related article: Should You Be Gluten-Free? A Comprehensive Guide.

Antibiotic Resistance Genes (Universal Panel)

The standard GI-MAP already tests for H. pylori-specific antibiotic resistance genes, which helps determine the most appropriate antibiotic protocol if H. pylori is present. The Universal Antibiotic Resistance Gene Panel add-on significantly broadens this, detecting 55 resistance genes across 10 antibiotic classes across the wider microbiome. 

An important principle here is that because microbes can rapidly share DNA with each other under stress, the presence of a resistance gene in any organism is reason to avoid that antibiotic class, regardless of which specific microbe carries it. This add-on is particularly relevant for patients with a history of repeated antibiotic courses, recent hospitalization, or chronic infections that have not responded to treatment.

StoolOMX (Bile Acids and Short Chain Fatty Acids)

StoolOMX is the newest and most clinically expansive add-on, introduced in 2025 and I think it is one of the most important add-on tests. It measures 25 bile acids alongside 9 short chain and branched chain fatty acids (SCFAs) using LC-MS/MS technology, providing a detailed look at gut metabolism that the standard microbiome panel cannot capture. 

Short chain fatty acids (primarily acetate, butyrate, and propionate) are produced by gut bacteria during the fermentation of dietary fiber. Butyrate is the primary fuel source for colonocytes (the cells lining the colon) and plays a central role in gut barrier integrity, immune regulation, and inflammation control. Low butyrate is associated with IBD, leaky gut, and metabolic dysfunction. 

The ratio of straight-chain SCFAs to branched-chain fatty acids (BCFAs) also provides insight into dietary patterns and whether the microbiome is fermenting fiber effectively, or fermenting protein instead, which can produce harmful byproducts such as ammonia and biogenic amines.

Bile acids, produced by the liver from cholesterol and released into the small intestine to assist with fat digestion, have a more complex role than most people appreciate. Around 95% of primary bile acids are reabsorbed after digestion and recycled. The remaining 5% reach the colon, where gut bacteria convert them to secondary bile acids. A high proportion of secondary bile acids relative to primary bile acids generally indicates a healthier, more diverse microbiome. 

An imbalanced bile acid profile can contribute to bile acid diarrhea (which affects an estimated 30% of patients diagnosed with IBS-D but is frequently misdiagnosed), malabsorption, motility disorders, and dysbiosis. Interpreting StoolOMX results alongside the GI-MAP findings, particularly calprotectin, elastase, steatocrit, and the Firmicutes/Bacteroidetes ratio, gives a substantially more complete picture of gut function than either panel alone.

When added to the GI-MAP, StoolOMX is particularly valuable for patients with IBS, IBD, unexplained chronic diarrhea or constipation, bile acid diarrhea, or where metabolic health is a factor.

Who is the GI-MAP Stool Test For?

The GI-MAP is an ideal test for those experiencing symptoms such as:

1. Constipation
2. Diarrhea
3. Bloating
4. Acid reflux
5. Diabetes and weight concerns
6. Brain fog
7. Mood disorders, depression, anxiety, and chronic fatigue
8. Stomach pain
9. Irritable bowel syndrome (IBS)
10. Inflammatory bowel disease (IBD)
11. Autoimmune conditions
12. Skin problems such as acne and psoriasis
13. Leaky gut syndrome
14. Joint pain

It can be done at any age. The test has been used with patients from 12-month-old infants through to people in their 80s, and digestive optimization is relevant at every stage of life.

It is also a valuable test for those dealing with hormonal imbalances. The GI-MAP measures beta-glucuronidase, an enzyme produced by certain gut bacteria that can interfere with estrogen detoxification.

When beta-glucuronidase is elevated, the body reabsorbs estrogen that should have been excreted, along with environmental toxins that have undergone phase one liver detoxification.

This can contribute to estrogen dominance and its associated symptoms, which is why the GI-MAP is often relevant well beyond a purely digestive presentation.

If you are not sure whether this test is right for your situation, book a consultation and we can help you work out the best path forward.

GI-MAP Benefits

The GI-MAP helps identify the specific factors driving gut dysfunction rather than relying on trial and error. It takes the guesswork out of diagnosis and allows for a targeted, evidence-based treatment plan rather than a generic protocol applied to everyone with similar symptoms.

This matters particularly for complex or chronic cases. Someone with persistent IBS who has already tried probiotics, dietary changes, and basic gut supplements may simply need a clearer picture of what is actually happening in their gut before the right intervention can be applied. The GI-MAP provides that picture.

I see this many times in clinic when people think they have parasites and have done a number of treatments only for the testing to show depleted levels of beneficial bacteria, or other intestinal health issues and no parasites.

It is important to work with a practitioner who is experienced in reading the GI-MAP. Many general practitioners are unfamiliar with functional stool testing and how to build a treatment protocol from the results.

It is typically functional medicine practitioners and integrative health practitioners who use these tests, and knowing how to interpret the pattern of results as a whole, rather than treating individual markers in isolation, is what drives good clinical outcomes.

Even if you have ordered the GI-MAP through another provider, a consultation is available to help you understand your results and implement a treatment plan.

Is the GI-MAP Test Worth It?

Yes. It is an expensive test, but it consistently saves time and money by replacing guesswork with clarity. For anyone dealing with a complex or chronic digestive disorder, IBS, IBD, unexplained symptoms, or persistent gut infections, the GI-MAP provides the specific information needed to direct treatment effectively rather than cycling through generic approaches.

It can be a valuable test to do if you have an autoimmune condition, skin issues, brain fog or other chronic health problems.

If you are weighing up the GI-MAP against the Vibrant Wellness Gut Zoomer, a consultation can help you determine the best option based on your clinical picture and goals.

GI-MAP Test Preparation

There are no special preparation requirements for the GI-MAP. Continue eating your normal diet and do not stop any prescribed medications. The purpose of the test is to assess how your current lifestyle is affecting your gut, and changing your routine before testing would undermine that.

For specific guidance on probiotics and herbal medicines prior to testing, more detailed instructions are provided once the test kit is ordered from Planet Naturopath. In general I recommend stopping antibiotics for at least two weeks before testing, also stop herbal anti-microbials and probiotics at least one week before testing.

What is Included in the GI-MAP Test Kit?

The kit contains everything needed to collect the stool sample, including a specimen vial and a prepaid FedEx clinical pak for returning the sample to the lab. The video below walks through the kit contents in detail.

[VIDEO EMBED: TPVJmcQHyZE]

How to Perform the GI-MAP Test

Collection is straightforward and non-invasive, done entirely at home. A small stool sample is collected into the specimen vial using the spoon attached to the cap, then sealed and shipped back to Diagnostic Solutions Laboratory for analysis. Detailed instructions are included in the kit, and the official step-by-step collection guide from DSL is available here: GI-MAP Collection Instructions.

If adding the StoolOMX panel, the same single sample and collection process applies, with no additional collection needed.

How Long Will It Take to Get Results?

Results are typically available within 8 to 10 business days after the lab receives the sample. Once your sample arrives at the lab you will receive a notification to let you know testing has begun.

How Much Does the GI-MAP Test Cost?

The base price is $420, which includes shipping within the US. Add-on panels (StoolOMX, antibiotic resistance genes, zonulin, gluten peptide) carry additional costs. Contact us for current pricing on specific add-on combinations.

How Do I Order the Test?

You can order directly from Planet Naturopath without a prior consultation. The test kit is delivered to your home within 2 to 4 business days. Once results are ready, a follow-up consultation is available to review findings and develop a treatment plan via Zoom.

Who Can Order the GI-MAP Test?

A registered healthcare practitioner must order the GI-MAP, as patients cannot order directly from Diagnostic Solutions Laboratory. You can ask your physician to order it, or order through Planet Naturopath where I will place the order on your behalf and the kit will be delivered directly to you. You can learn more about DSL’s ordering policies here.

Still Not Sure What Is Driving Your Symptoms?

If you have been trying to address your gut health independently without clear results, a one-on-one consultation can help identify the root cause and create a plan tailored to your situation.

What Alternatives Are There for the GI-MAP Stool Test?

The Gut Zoomer Test by Vibrant Wellness and the GI-MAP are the two leading microbiome tests for comprehensive gut health assessment, and both have genuine strengths.

The Gut Zoomer tests a significantly larger number of bacterial species, over 170, which makes it particularly valuable for patients focused on microbiome diversity and optimization. It provides detailed analysis of beneficial bacteria alongside pathogen identification, and the breadth of microbiome data is exceptional, especially given the growing research on the gut microbiota’s role in overall health.

The GI-MAP, by contrast, is the stronger choice where pathogen identification is the primary clinical concern. Its qPCR technology is particularly precise for detecting low-level organisms, and its H. pylori analysis is unmatched, providing not just a quantitative load but virulence factors that help determine how aggressive the strain is and whether it carries elevated risk for ulcers or gastric cancer. The antibiotic resistance gene data for H. pylori, included in the standard panel, is also clinically distinctive.

When comparing the two, the right choice depends on the individual’s goals. A patient primarily focused on optimizing their microbiome and beneficial bacteria may do better starting with the Gut Zoomer. A patient with suspected infection, persistent gut pathology, or where H. pylori is a concern will generally get more targeted information from the GI-MAP.

Related article: GI-MAP and Viome Tests — What Is the Difference?

Frequently Asked Questions

To order the GI-MAP test, visit the GI-MAP order page, or contact us here to discuss which test and add-ons are right for your situation.