GI Map test (comprehensive stool analysis) - results and interpretation

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What is a GI Map test

The GI Map test is a comprehensive stool analysis that can be done from the comfort of your home.

The GI Map test kit comes with prepaid shipping materials and everything needed to ensure proper delivery to the lab. This test screens for commensal and pathogenic bacteria, H-Pylori, parasites, fungi, opportunistic pathogens, and viruses – all of which have a negative impact on your body and overall health if imbalanced. It also assesses pancreatic and immune function, occult blood, fat absorption, Secretory IgA, Anti-gliadin IgA and B-glucoronidase.

The GI Microbial Assay Plus, also known as the GI Map, uses DNA analysis to assess health benefits or disease risks from microorganisms that inhabit the body. The GI Map goes beyond techniques of culturing or microscopy that can miss up to 50% of bacterial species. This occurs in traditional stool testing because a small stool sample is sent to the lab, the lab then takes a small section of the sample and cultures it or views the sample specimen under a microscope. Some microorganisms, especially yeast, bacteria and parasites may not be present or viable for viewing or culturing in that one little sample and as a result, many pathogens are missed.

Since implementing DNA techniques, many previously unknown organisms have been identified. This allows for greater identification of infection and specificity of pathogens that might be present.

Who can benefit from testing with GI Map

The information this test provides can benefit pretty much everyone. More specifically, it can be valuable for anyone with digestive issues such as chronic constipation, bloating, IBS, IBD, acid reflux, SIBO, etc. It’s also a great tool when dealing with food allergies and sensitivities.

It is also a valuable test for those who are dealing with hormonal imbalances as this test measures the amount of beta-glucuronidase, which can affect the detoxification of estrogen. High levels of beta-glucuronidase will lead to your body reabsorbing the estrogen that has gone through phase one of liver detoxification, causing estrogen dominance.

The GI Map test can also be very helpful for those who have an autoimmune disorder and other chronic conditions as it gets an extensive collection of microbial targets and digestive and immune markers.

If you’re experiencing anxiety, depression, brain fog and/or mood disorders, this can be strongly influenced by your gut bacteria. There is more research coming out to confirming the gut brain connection.

Quantifying results

The GI Map uses quantitative qPCR, which stands for quantitative real-time polymerase chain reaction. This technique combines amplification and detection into one step. It’s considered one of the most powerful and sensitive gene analysis techniques available and is capable of quantifying gene expression, analyzing single nucleotide polymorphisms, or SNPs. It determines genotypes, detects pathogens, and provides prescriptive drug direction for certain positive markers. The GI Map gives quantitative information about many pathogens. It is important to note that not all pathogens cause disease if they are present. Knowing how much DNA is present gives us critical information for making better decisions about the protocols.

The GI-MAP reports quantitative findings in magnitude levels. <dl indicates under detectable limits/levels which means it is not measurable and virtually nonexistent. Markers are quantified by an e, which indicates the quantitative presence of the pathogen. For example, if a normal value is <1.00e4, that means a result of less than 1.00 to the fourth power is normal and there is no pathogenic infection. On the other hand, if the result indicates a quantity such as 4.5e5, that can be read as 4.5 to the fifth power and indicates the pathogenic presence is over 10 times higher than normal, because e5 is ten times higher than e4. Conversely, if normal is given as 1.00e3 and the result of a given pathogen is 9.0e0, that means the DNA was measurable, but less than what is considered an infection. In addition to microbial quantification, H. Pylori virulence factors are reported as either positive or negative. This is the same for fecal occult blood, and the presence of various worms is reported as detected or not detected.

Advantages of the GI Map test

The first advantage is that only one stool sample is required instead of two or three. This is a huge benefit to clients who have to stop supplements in order to test and for those constipated clients for whom collecting three stool specimens within a week is virtually impossible. Since this testing method is fully automated, it also minimizes the chance for human error, making your results much more reliable. Because the GI Map uses DNA sequencing, it is by far the most sensitive stool test on the market today.

Test results report and interpretation

I want to share my GI Map test results so that you can see what the report looks like and what exactly is being tested. I am interpreting my results only and will not be describing every single pathogen as that would be a very long blog post.

My presentation: chronic constipation, abdominal bloating, many food sensitivities and chronic hives, fatigue and low energy, insomnia mostly due to itching at night, hormonal imbalances such as debilitating PMS symptoms, irritability and low mood. History of long term antibiotics use for severe cystic acne.

Page 1 - Pathogens


The GI Map measures bacterial pathogens as seen above. The presence of a pathogen does not, by itself, indicate disease. Results must be interpreted together with clinical symptoms and history by a qualified health practitioner.

As per my results, C. difficile, toxin B and Shiga-like toxin E. coli stx2 are marked as high. As for the Clostridium difficile (C. difficile or C. diff), the GI map tests only for the genes for toxin A and toxin B. It does not measure toxins directly for the microbes. We need to check for clinical symptoms like inflammation, abdominal pain, cramping, fever and diarrhea. GI infection can cause reactive arthritis. C. diff releases toxins that cause inflammation and damage to the GI lining. Toxins A and B are the major virulence factors believed to be responsible for C. diff infection symptoms. They are proinflammatory and cytotoxic. They damage the cytoskeleton of intestinal epithelial cells, permitting fluid influx, they open tight junctions in the GI lining, and thereby damage the GI lining.

In my case, it seems that the C. diff infection is not acute as I don’t have diarrhea. However, the bacteria is present in high quantities and may be causing inflammation and damage to the GI lining (leaky gut) which could be behind the food sensitivities and the chronic hives I’m experiencing.

Shiga-like toxin E. coli has been involved in foodborne illness outbreaks, especially from undercooked meat, unpasteurized milk, juice and water. It causes various GI illnesses, including bloody and non-bloody diarrhea.

In my case, again it does not seem that it is an acute infection as I don’t have diarrhea. However, interestingly, this bacteria was also found in my urine culture causing a UTI (75% to 95% of urinary tract infections are caused by E. coli).

In this section, the GI Map also tests for parasitic pathogens. Some parasites cause infectious disease in humans, while others do no. Parasites can live inside the gut, removing vital nutrients and damaging the gut lining. Symptoms of parasitic infection range from mild discomfort to severe illness, including death. These pathogens can cause diarrhea, constipation, abdominal cramping, bloating, nausea, and vomiting. If present in someone who is severely immunocompromised, symptoms can progress to involve the central nervous system.

In my case, there is a number next to Giardia but it is not marked as high. This can indicate a past infection with some DNA still present.

In this section, there are also viral pathogens listed. If they were marked high, it would mean that an acute infection is present. Adenovirus and norovirus are viral causes of gastroenteritis that are normally self-limiting in healthy individuals. These viruses can cause diarrhea, abdominal pain, and vomiting.

Page 2 - H. pylori and normal bacterial flora (beneficial flora)


Numerous papers suggest the clinical utility of PCR testing for H. pylori. Everyone has some H. pylori bacteria in the stomach but it is rarely found elevated in normal gastric mucosa. When H. pylori proliferates, it is predominantly associated with inflamed mucosa, or gastritis. The role of H. pylori in GERD remains controversial, yet recent studies showed that when levels are normalized, the symptoms improved at the six month follow up. There is a correlation between H. pylori infection and ulcers and gastric cancer. Acute H. pylori infections result in hypochlorhydria, while chronic infection results in either hypo- or hyperchlorhydria, depending upon the anatomic site of infection.

The GI Map also tests for virulence factors. Virulence factors give us additional information about the pathogenicity of the H. pylori strain. A positive virulence gene for some factors can represent the potential for an H. pylori strain to be pathogenic.

For example, virulence factor cagA is cytotoxin associated protein A and its presence has been associated with gastric cancer and peptic ulcers. Once inside the host’s gastric epithelial cells, cagA can disrupt cell signaling, leading to abnormal proliferation, motility and changes in the cytoskeleton. This can initiate cancer in the affected areas.

The Gi Map includes a list of commensal flora as a general screening to assess normal, protective flora and to monitor the success of probiotic supplementation. We coexist with our commensal bacteria. They play a role in the extraction of nutrients and energy from the food we eat, they help maintain gut barrier function, they produce vitamins like biotin and vitamin K, and protect against the colonization of potential pathogens. Our microbiota interacts with our immune system and it has anti-inflammatory and antioxidant activity. The goal is to keep commensal bacteria diverse and balanced as disruption leads to dysbiosis, which is associated with obesity, malnutrition, inflammatory bowel and autoimmune disease, neurological disorders, and cancer. Dysbiosis can be described as an undesirable shift in the microbiota composition, where potentially harmful microbes proliferate and protective bacteria diminish.

In my case, there is some imbalance in the commensal flora detected by the GI Map. The most important one is the low Lactobacillus. It constitutes a large component of the microbiota in specific sites like the gastrointestinal tract, renal system, and genitals. Lactobacillus protects the host against invasions by pathogens and the host provides nutrients that feed it.

Page 3 - Opportunistic bacteria: additional dysbiotic/overgrowth bacteria and potential autoimmune triggers; fungi/yeast; viruses


Dysbiotic/overgrowth bacteria - these bacteria are opportunistic. Overgrowth and excessive colonization of opportunistic bacteria can occur when the commensal bacteria are suppressed through poor diet, use of antibiotics, a parasitic infection, or a weakened immune system. Certain opportunistic pathogens have be recognized in the integrative and functional medical field as creating imbalance in the gut microbiota or otherwise preventing proper healing of the GI mucosal barrier. Some of these organisms have been implicated in contributing to extra-intestinal disease.

In my case, there are four strains of overgrowth bacteria, one of them is in the potential autoimmune triggers category. This could be due to the antibiotics I was taking for cystic acne and also due to low numbers of the beneficial bacteria.

Potential autoimmune triggers, which, as the name implies, are bacteria that are associated with certain autoimmune conditions. It’s important to note that elevated levels of these bacteria do not predict or indicate an autoimmune disease per se, but simply have been found in elevated numbers in those with certain autoimmune diseases.

In my case, Prevotella copri is marked as high. Several studies correlate the overgrowth of Prevotella copri with enhanced susceptibility to rheumatoid arthritis. Although a definitive link cannot yet be made that increased Prevotella copri causes rheumatoid arthritis, research shows that it is more prevalent in individuals with RA.

Fungi/yeast - the GI map tests for an overgrowth of Candida and other fungi. High levels have been associated with diarrhea, fatigue, muscle or joint pain, constipation, skin problems, etc.

There are also two viruses tested: Cytomegalovirus (CMV) and Epstein Barr virus (EBV).

Cytomegalovirus (CMV) is a common virus that can infect anyone. Once infected, the body retains the virus for life. Most people aren’t aware that they have CMV because it rarely causes problems in healthy people. However, it is cause for concern in pregnancy and with a weakened immune system. In otherwise healthy adults, initial symptoms are similar to infectious mononucleosis and include fatigue, fever, sore throat, and muscle aches. CMV can cycle through periods when it lies dormant and then reactivates. CMV has been implicated in autoimmune disease: lupus, systemic sclerosis, type 1 deabetes, and rheumatoid arthritis.

Epstain Barr Virus (EBV) in one of the most common viruses in humans. It is best known as the cause of infectious mononucleosis and is also associated with specific forms of cancer, namely Hodgkin’s lymphoma, gastric cancer, nasopharyngeal carcinoma and conditions associated with HIV. Some evidence shows that infection with EBV is associated with a higher risk of certain autoimmune diseases, like systemic lupus, rheumatoid arthritis, Sjogren’s syndrome, type 1 diabetes and multiple sclerosis. After the primary infection, EBV remains in the body in an inactive state. It can reactivate, as with other latent viruses and produce symptoms, especially when the immune system is compromised.

It is important to understand that the GI Map test detects active EBV and CMV infections, not past infections.

Page 4 - parasites, intestinal health, antibiotic resistance genes, phenotypes



Non-pathogenic parasites are generally self-limiting and do not cause disease. They can, however, be associated with gastrointestinal symptoms like gas, bloating, constipation, and diarrhea.

In my case, there was Blastocystic hominis detected on the GI Map but was not marked as high.

Blastocystis hominis is a genus of single-celled parasites that include algae, diatoms, and water molds. It lives in the GI tracts of several species, including humans, and it is one of the most common parasites in the world and has global distribution. The role of Blastocystis hominis in human disease is controversial and the need to address it when present is up for debate. However, most published studies show that up to 80% of infected individuals will show symptoms. They include diarrhea, constipation, nausea, abdominal cramps, bloating excessive gas, anal itching, as well as issues with the skin.


The GI-MAP reports the findings in this category as Not Detected, Detected, or Detected high. A negative result indicates no intact adult worms or egg DNA was detected in the fecal sample.If the test reports “detected”, this means there was DNA present consistent with the detection of an egg in the sample. This does not necessarily indicate that an adult worm is present in the gastrointestinal tract. If the report indicates “detected high”, it signifies that a multicellular adult worm or a large volume of eggs, which were likely produced by an adult worm, is present in the stool.

Intestinal health

Elastase-1 is a fecal marker for assessing exocrine pancreatic function with a high degree of sensitivity and specificity in suspected cases of pancreatic insufficiency. The sensitivity of this marker is lower in cases of mild pancreatic insufficiency. Pancreatic elastase is an enzyme produced by the pancreas to assist in the breakdown of protein. Pancreatic insufficiency may be indicated with symptoms of bloating, pain, nausea, loose or watery stools, heartburn orGERD, and food sensitivities.

Steatocrit is a measurement of fat in the feces. It is an indication that fat digestion is impaired, either because of biliary stasis or insufficiency, or due to pancreatic lipase insufficiency.

Beta-Glucuronidase is an enzyme involved in one of the most important Phase II conjugation liver pathways for the excretion of carcinogens, lipid-soluble hormones, and steroid hormones. It is produced by cells in the liver, kidney, intestinal epithelium, endocrine, and reproductive organs and its purpose is to create a bond between a toxin or conjugated hormone targeted for excretion. Through a series of chemical reactions, the liver attaches glucuronic acid to the target chemical, then excretes this chemical complex into the bile to be carried into the intestine. Beta-Glucuronidase can also convert pro-carcinogens to carcinogenic compounds. When beta-glucuronidase is produced at high levels, it has to ability to break the bond between a targeted toxin or hormone and glucuronic acid, thus allowing them to be reabsorbed and recirculated. High levels of beta-glucuronidase can indicate unhealthy changes in the colon, with an increased risk of hormone-sensitive cancers or digestive tract cancer.

Fecal Occult Blood refers to blood in feces that is not visibly apparent. This test checks for hidden, which is what the word occult means, blood in the stool.

Immune and Inflammation

Secretory IgA is secreted by mucosal tissue and represents this tissue’s first line of defense to protect the intestinal epithelium against ingested toxins and pathogens. Adequate levels of sIgA are crucial for normal gut function and gut immunity. It has influence in the composition of the intestinal microbes, keeps inflammation processes under control, and strengthens the cellular tight junctions to maintain gut barrier integrity. Elevated levels indicate an upregulated immune response within the intestinal terrain and depressed sIgA is an indication of compromised mucosal immunity. Chronically low fecal sIgA indicates loss of normal tolerance and is often found in individuals who have chronic digestive conditions. Low sIgA can contribute to intestinal permeability and the development of food reactions. When this marker is elevated or depressed, we need to look for concomitant pathogenic involvement. In the absence of pathogens, food reactions are often the cause of the immune imbalance and inflammation.

In my case, the secretory IgA is low and I do have many pathogens present and suffer from chronic hives due to many food sensitivities.

Anti-gliadin IgA - Gliadin is a class of proteins present in wheat, rye, barley, kamut, and spelt. Gliadin is the water-soluble component of gluten. The presence of fecal anti-gliadin antibodies can indicate a response to gluten. Note that gluten must be in the diet and the individual must be sensitive to gliadin in order for this marker to be elevated. This is not a reliable test for celiac disease but can indicate gliadin or gluten sensitivity. Additionally, when sIgA is depressed, meaning gut immunity is low, the system may not be able to mount a response to gliadin. That means someone could have a sensitivity to gliadin but the immune system is so weak it can’t adequately react and we get a false negative with this marker.

Calprotectin is a protein released by the white blood cells, specifically neutrophils. The presence of neutrophils indicate inflammation and will cause calprotection to be released. This marker is considered the gold standard for the diagnosis and monitoring of inflammatory bowel disease (IBD). When elevated, calprotection indicates a high level of inflammation, diverticular disease, and even colorectal cancers. Calprotectin levels between

Antibiotic Resistance Genes, genotypes

The GI-MAP measures drug resistance genes in the bacterial genome of any pathogenic organism found positive in the fecal sample. These genes are carried by bacteria that confer a special resistance or protection from specific antibiotics. This is presented as information for clients wishing to use conventional antibiotics to address pathogens discovered on the GI Map.

* New bacterial strains have been added to the test since I have taken it. New commensal markers such as Akkermansia mucinophila (low levels are associated with obesity and metabolic dysfunction, while high levels are linked to multiple sclerosis). Clostridia (has many roles in promoting a healthy intestinal barrier, immune balance and protection against pathogens) and Faecalibacterium prausnitzii (major butyrate procuder; many chronic inflammatory and autoimmune diseases have been associated with low levels).

New opportunistic bacteria such as Methanobacteriaceae (high levels have been linked to chronic constipation and some types of SIBO and IBS) and Fusobacterium spp (may promote inflammatory processes and / or advanced disease states).

Source: The GI Microbial Assay Plus, GI Map, Quantitative PCR Stool Technology for the Integrative and Functional Medicine Practitioner by Diagnostic Solutions Laboratory

GI Map by Diagnostic Solutions Laboratory - General information about using the GI Map by Restorative Wellness Solutions, LLC