Renae Cinanni | Clinical Nutritionist | Perth WA & Online Australia wide
What the GI Map Stool Test Measures — and What It Can Reveal About Your Gut
FREE GI MAP TEST GUIDE
If your gut symptoms have not improved despite trying probiotics, dietary changes, or general gut health advice, the GI Map stool test may give you the answers you have been missing.
Most standard blood tests and colonoscopies are not designed to detect the infections, imbalances, and digestive dysfunction that commonly drive symptoms like bloating, constipation, loose stools, and fatigue. The GI Map is a different kind of test entirely. This guide explains exactly what it measures and why that information changes everything about treatment.
THE BASICS
What is the GI Map Test?
The GI Map (Gastrointestinal Microbial Assay Plus) is a DNA-based stool test that uses quantitative PCR (polymerase chain reaction) technology to accurately detect and measure what is living in your gut.
A single stool sample is collected at home in a small vial, posted to the lab, and results are typically returned within four weeks.
What makes it different from other stool tests is that it does not just report a yes or no result. It quantifies results as exact numbers of organisms per gram of stool. This means we can see how much of something is present and whether those levels are clinically significant, rather than simply whether something is detectable at all.
KEY DIFFERENCE
"Other stool tests report positive or negative. The GI Map reports exact quantities. That distinction determines whether what we find is actually causing your symptoms, or simply present at a harmless background level."
Every result is interpreted in context of your full clinical picture, including your symptoms, history, and what else the test reveals. No single marker is assessed in isolation.
THE FULL PICTURE
What does the GI Map test for?
WHAT IT MEASURES
WHY THEY MATTER
Campylobacter, C. difficile (Toxin A and B), pathogenic E. coli strains, Salmonella, Vibrio cholerae, Yersinia enterocolitica
Often missed on standard testing. Can cause ongoing gut inflammation and altered bowel habits even at low levels.
UNDERSTANDING GI MAP RESULTS
Bacterial pathogens and H. pylori
The GI Map tests for bacterial pathogens that commonly cause gut illness, many of which can persist at low levels without causing acute illness but still drive chronic gut symptoms. These include Campylobacter, Clostridium difficile (C. diff), several strains of pathogenic E. coli, Salmonella, Vibrio cholerae, and Yersinia enterocolitica.
C. diff in particular is commonly associated with antibiotic history. It can be present asymptomatically but warrants attention, especially when toxin genes are actively expressed. Yersinia enterocolitica is notable because it can trigger autoimmune thyroiditis and inflammatory arthritis in susceptible individuals, a connection that is rarely made in conventional settings.
H. PYLORI - WHY IT NEEDS ITS OWN SECTION
H. pylori is a bacterial infection estimated to be present in around half the global population. Many people carry it without knowing. When symptomatic, it is a significant driver of reflux, heartburn, nausea, burping, poor appetite, and upper abdominal discomfort.
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What makes the GI Map particularly useful for H. pylori is that it tests not just for its presence, but for virulence factor genes. These include CagA, VacA, BabA, DupA, IceA, and OipA. These genes indicate whether the specific strain has higher potential to cause serious complications including gastric ulcers and elevated gastric cancer risk. Two people can both test positive for H. pylori, but one may carry a high-risk virulent strain and the other a low-risk one. The treatment approach is different in each case.
Clinical note: H. pylori impairs stomach acid production and digestive enzyme function. This creates a cascade of downstream effects including bacterial overgrowth, poor protein digestion, and nutrient deficiencies that often persist even after the infection is cleared, if those effects are not also addressed.
UNDERSTANDING GI MAP RESULTS
Parasites: commonly missed on standard testing
Parasitic infections are regularly missed on standard testing because conventional stool cultures rely on methods that are far less sensitive than the DNA-based quantification the GI Map uses. The GI Map tests for Giardia, Cryptosporidium, Entamoeba histolytica, Blastocystis hominis, Dientamoeba fragilis, Cyclospora, and several worm species including hookworm, roundworm, whipworm, and tapeworm.
One of the most commonly missed infections in people with IBS-type symptoms.
Symptoms include chronic loose stools, urgency, bloating, fatigue, weight loss, and B12 deficiency. Often acquired through water exposure but can be contracted locally. Can persist for years undetected on standard testing.
UNDERSTANDING GI MAP RESULTS
Gut Microbiome balance
OPPORTUNISTIC BACTERIA AND WHAT HAPPENS WHEN THEY OVERGROW (DYSBIOSIS)
Opportunistic bacteria are microbes that are normally present at low levels but cause significant problems when they overgrow. Overgrowth is driven by poor diet, antibiotic use, parasitic infection, low stomach acid, and a weakened immune system.
Klebsiella
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A histamine producing bacteria linked to gut inflammation, bloating, food sensitivities, diarrhoea, and gas. Also associated with Crohn's disease, ulcerative colitis, and ankylosing spondylitis in research. Common after long-term antibiotic use.
HISTAMINE PRODUCER
Morganella
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Another significant histamine producer. Elevated levels contribute to histamine intolerance symptoms including diarrhoea, skin reactions, headaches, and systemic inflammation. Often found elevated in patients with food sensitivities that do not have a clear dietary explanation.
HISTAMINE PRODUCER
Methanobacteriaceae
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A methane producing organism strongly associated with chronic constipation and certain types of small intestinal bacterial overgrowth (SIBO). High methane slows gut transit, leading to hard, infrequent stools and bloating that is often worse at the end of the day.
METHANE PRODUCER
Candida
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Yeast overgrowth driven by antibiotic use, high sugar and refined carbohydrate intake, low stomach acid, and compromised immunity. Symptoms include gas, bloating, sugar cravings, fatigue, brain fog, recurrent thrush, and skin issues.
FUNGAL OVERGROWTH
KEYSTONE AND BENEFICIAL BACTERIA: WHY THEY MATTER
When beneficial bacteria are depleted, the gut environment becomes unstable and reactive. This is a side of gut health that probiotics alone cannot fully restore if the conditions driving depletion are not addressed first.
Faecalibacterium prausnitzii
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One of the most researched anti-inflammatory bacteria in the human gut. Produces butyrate, a short-chain fatty acid that fuels gut lining cells and regulates immune responses. Low levels are consistently associated with IBS, Crohn's disease, ulcerative colitis, and other chronic inflammatory conditions.
KEYSTONE SPECIES
Akkermansia muciniphila
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The primary mucus-layer bacteria. Akkermansia supports gut barrier integrity and mucosal health.
Low levels are linked to increased intestinal permeability, metabolic dysfunction, obesity, and immune dysregulation. High levels are associated with multiple sclerosis.
KEYSTONE SPECIES
Roseburia
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Produces short-chain fatty acids including butyrate and propionate. Roseburia influences gut motility, supports immunity, and suppresses inflammation. Low levels are associated with IBS, obesity, type 2 diabetes, and nervous system conditions.
BUTYRATE PRODUCER
Bifidobacterium
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Present from birth and colonising the gut early in life. Bifidobacteria species thrive on diverse plant fibres. Low levels are linked to low fibre intake, reduced mucosal health, and compromised gut immunity. A common target for probiotic supplementation, though dose and strain matter significantly.
BENEFICIAL SPECIES
UNDERSTANDING GI MAP RESULTS
Intestinal health markers: digestion, immunity & inflammation
This section of the GI Map provides objective data on how well the gut is functioning beyond just what organisms are present. These markers are where some of the most clinically useful information sits.
GUT BARRIER/ LEAKY GUT
A biomarker for intestinal permeability (leaky gut). Zonulin regulates the tight junctions between gut lining cells. When elevated, these junctions are compromised, allowing partly digested food proteins and bacterial products to pass into circulation and trigger immune responses, food sensitivities, and systemic inflammation.
IS THE GI MAP RIGHT FOR YOU?
WHO CAN DO A GI MAP TEST?
The GI Map is most useful when gut symptoms have not resolved despite dietary changes, probiotics, or previous investigations. It is also valuable when symptoms suggest something more specific is driving the picture.
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The GI Map Test is not just for gut symptoms:
The GI Map test is also useful for unexplained health issues, imbalanced hormones, skin conditions such as eczema or other suspected gut imbalances or digestive conditions. It is ideal for those suffering from IBS/IBD, food sensitivities, skin issues, autoimmune conditions, or fatigue who are seeking to identify root causes like pathogens, bacteria, or parasite infections.
GI Map testing is most appropriate if you recognise any of the following:
Ongoing bloating, constipation, loose stools, reflux, or abdominal discomfort that has not responded to dietary changes or probiotics
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A diagnosis of IBS without further investigation into what is actually causing your symptoms
Gut symptoms that started or noticeably worsened after a gut infection, a course of antibiotics, a period of high stress, or overseas travel
Fatigue, brain fog, or low energy that is not explained by standard blood testing
Skin conditions including eczema, psoriasis, rosacea, or acne that have not resolved with topical treatments
Hormonal symptoms including PMS, heavy periods, or oestrogen-related concerns, since gut health directly influences hormone metabolism and clearance
Autoimmune conditions where gut involvement is suspected such as Hashimoto's thyroiditis
Food sensitivities that seem to be ongoing or shifting over time
Children with chronic constipation, loose stools, eczema, or behavioural changes linked to gut discomfort
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Suspected Gut Infections: People needing to check for pathogens, including bacteria, parasites, and fungi.
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Individuals suffering from unexplained fatigue, brain fog, mood disorders (anxiety/depression), or weight loss issues.
Anyone who wants objective data about their gut before starting a gut healing protocol
HOW TO DO A GI MAP STOOL TEST
The test kit is done in the comfort of your your home. The sample is collected and posted directly to the lab. Full instructions are included in your kit and will be discussed in your appointment.
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WHAT HAPPENS NEXT
Once results are returned, we sit down together and I walk through every marker in plain language. No jargon. No overwhelm. From there you receive a personalised treatment plan built entirely around your specific results.
GI MAP TEST PERTH
GUT HEALTH NUTRITIONIST PERTH
GUT MICROBIOME TESTING PERTH
GI MAP INTERPRETATIVE GUIDE AUSTRALIA
IS THE GI MAP TEST WORTH IT
HOW DO I GET A GI MAP TEST IN PERTH
READY TO GET REAL ANSWERS?
GI Map testing is available in Perth and online across Australia
Initial consultations and GI Map testing packages are available through Perth Nutrition & Natural Health Clinic.
The Gut Health Package includes the test kit, a full results interpretation appointment, follow up appointments and a personalised treatment plan based on your findings.