If you have been dealing with chronic bloating, unpredictable digestion, fatigue that does not improve with rest, skin flares, mood instability, or a long list of food reactions — the answer is often not in your blood work. It is in your gut.
The GI-MAP (Gastrointestinal Microbial Assay Plus), offered by Diagnostic Solutions Laboratory, is the most comprehensive DNA-based stool test available. It does not just look for obvious infections — it maps the entire microbial ecosystem of your gut, assesses your digestive function, measures gut inflammation, and evaluates your immune response at the intestinal lining.
This guide covers everything: what the GI-MAP tests, who benefits from it, what each section of the report means, and how we use the results to build a targeted, sequenced healing protocol.
What Is the GI-MAP?
The GI-MAP uses quantitative PCR (qPCR) technology — the same DNA-sequencing method used in clinical research — to identify and quantify over 40 different microorganisms in a single stool sample. Unlike older culture-based stool tests that can only detect organisms that grow in a lab environment, qPCR detects the actual DNA of bacteria, viruses, parasites, and fungi directly from the sample. This makes it significantly more sensitive and accurate.
The test is collected at home using a simple kit, shipped to the lab, and results are typically available within 10–14 business days. No dietary restrictions or medication changes are required before collection.
What makes the GI-MAP uniquely valuable is not just the breadth of what it tests — it is the clinical context it provides. Each finding is reported with a quantitative value, allowing us to see not just whether something is present, but how much of it is there and whether it is within a healthy range.
"The gut houses approximately 70% of the immune system and produces the majority of the body's serotonin. When the gut microbiome is disrupted, the effects ripple outward — immune dysregulation, hormonal imbalances, mood instability, skin conditions, and fatigue are all common downstream consequences."
Who Benefits from a GI-MAP?
The GI-MAP is one of the most versatile functional tests available because gut health is foundational to virtually every system in the body. It is valuable both for people with obvious digestive symptoms and for those whose primary complaints appear entirely unrelated to digestion.
Chronic Digestive Dysfunction
IBS, IBD, SIBO, chronic bloating, gas, constipation, diarrhea, heartburn, or indigestion that has not responded to standard approaches.
Autoimmune Conditions
Gut dysbiosis is a documented contributor to autoimmune disease. Identifying and addressing microbial imbalances can provide crucial support in managing these conditions.
Skin Conditions
Acne, eczema, psoriasis, and rosacea are frequently connected to gut dysbiosis. The gut-skin axis means that what is happening in the microbiome often shows up on the skin.
Mood & Cognitive Symptoms
Brain fog, anxiety, depression, and poor concentration are often downstream of gut imbalances via the gut-brain axis and the vagus nerve.
Metabolic & Weight Issues
The Firmicutes:Bacteroidetes ratio directly influences caloric extraction from food, insulin sensitivity, and inflammation — all of which affect weight regulation.
Unexplained Fatigue
Chronic fatigue that does not improve with rest is frequently rooted in gut-driven inflammation, nutrient malabsorption, or a high pathogen or toxin burden.
Food Sensitivities
Multiple or worsening food reactions are often a sign of intestinal permeability, dysbiosis, or an overactivated immune system — all visible on the GI-MAP.
Preventative Health Optimization
Even in the absence of symptoms, the GI-MAP provides a detailed baseline of microbiome health and identifies imbalances before they become symptomatic.
What Is Included in the GI-MAP Report?
The GI-MAP report is organized into six major sections. Understanding what each section measures — and why it matters — is the key to interpreting results in a clinically meaningful way.
Section 1: Pathogens
The GI-MAP screens for bacterial, parasitic, and viral pathogens that are known causes of gastrointestinal illness. It is important to understand that a positive result does not always mean active disease — some pathogens can be present in the digestive tract without producing virulence factors that cause symptoms. Clinical context, symptom history, and the quantity of the pathogen all inform how a positive finding is interpreted.
Bacterial Pathogens
- · Campylobacter
- · C. difficile Toxin A & B
- · Enterohemorrhagic E. coli
- · E. coli O157
- · Enteroinvasive E. coli/Shigella
- · Enterotoxigenic E. coli LT/ST
- · Shiga-like Toxin E. coli stx1 & stx2
- · Salmonella
- · Vibrio cholerae
- · Yersinia enterocolitica
Parasitic Pathogens
- · Cryptosporidium
- · Entamoeba histolytica
- · Giardia
Viral Pathogens
- · Adenovirus 40/41
- · Norovirus GI/II
H. Pylori (Special)
H. pylori is reported separately because of its unique clinical significance. It is linked to ulcers, chronic gastritis, stomach cancer, GERD, and dyspepsia. The GI-MAP uses DNA analysis to identify H. pylori virulence factors — the genetic markers that indicate whether a particular strain has the potential to cause pathology. This distinction guides treatment decisions more precisely than a simple positive/negative result.
Section 2: Commensal / Keystone Bacteria (Beneficial Flora)
These are the beneficial bacteria that form the foundation of a healthy microbiome. High levels are generally a positive sign. These organisms promote nutrient absorption, produce vitamins (including biotin and vitamin K), maintain the mucosal lining of the gut, support detoxification, regulate immune function, and protect against pathogen colonization. Low levels suggest a need for dietary changes, targeted probiotics, or prebiotic support.
The Firmicutes:Bacteroidetes Ratio
The GI-MAP also reports the two major bacterial phyla — Firmicutes and Bacteroidetes — and their ratio. These two groups constitute the dominant bacterial populations in the human microbiome. An elevated Firmicutes:Bacteroidetes ratio has been linked to increased caloric extraction from food (contributing to weight gain and obesity), decreased insulin sensitivity, and increased systemic inflammation. This ratio is one of the most clinically actionable findings on the entire report for clients dealing with metabolic dysfunction or difficulty losing weight.
Section 3: Opportunistic Bacteria
Opportunistic bacteria are organisms that exist in small amounts in a healthy gut without causing harm — but when they overgrow, particularly in the context of a compromised gut lining or a weakened immune system, they can drive significant symptoms including diarrhea, loose stool, abdominal pain, and constipation. Several strains in this category have also been linked to autoimmune conditions.
Dysbiotic & Overgrowth Bacteria
- · Bacillus spp.
- · Enterococcus faecalis
- · Enterococcus faecium
- · Morganella spp.
- · Pseudomonas spp. / aeruginosa
- · Staphylococcus spp. / aureus
- · Streptococcus spp.
- · Desulfovibrio spp.
- · Methanobacteriaceae (family)
Inflammatory & Autoimmune-Related
- · Citrobacter spp. / freundii
- · Klebsiella spp. / pneumoniae
- · M. avium subsp. paratuberculosis
- · Proteus spp. / mirabilis
- · Enterobacter spp.
- · Escherichia spp.
- · Fusobacterium spp.
- · Prevotella spp.
Section 4: Fungi / Yeast, Viruses, and Parasites
Fungi / Yeast
Fungal organisms are a normal part of the microbiome in small amounts, but overgrowth — particularly of Candida — can cause significant symptoms including fatigue, brain fog, sugar cravings, recurrent infections, and digestive disturbance. Overgrowth is especially problematic in the context of intestinal permeability. The GI-MAP tests for Candida spp., Candida albicans, Geotrichum spp., Microsporidium spp., and Rhodotorula spp. Positive findings may warrant additional testing such as urinary D-arabinitol or Candida antibodies.
Viruses
The GI-MAP tests for Cytomegalovirus (CMV) and Epstein-Barr Virus (EBV) in stool. The presence of these viruses has been correlated with inflammatory bowel disease (IBD), and IBD patients with these viruses may be more susceptible to flare-ups during viral reactivation. A positive finding indicates current active infection.
Parasites
Parasitic infections are far more common than most people realize, and they are frequently missed by conventional stool testing. The GI-MAP tests for both pathogenic and non-pathogenic parasites, including protozoa (such as Blastocystis hominis, Dientamoeba fragilis, Giardia, and Entamoeba histolytica) and worms (including Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Trichuris trichiura, and Taenia spp.). Even "non-pathogenic" parasites can contribute to symptoms in individuals with a compromised gut lining or immune system.
Section 5: Digestive Markers
These markers assess how well the digestive system is actually functioning — not just what is living in it. Digestive dysfunction is frequently the underlying driver of dysbiosis: when food is not properly broken down, it becomes fuel for pathogenic organisms and fermentation in the wrong part of the gut.
Elastase-1 (Pancreatic Function)
Elastase-1 is a digestive enzyme produced exclusively by the pancreas, making it the most reliable indirect marker of pancreatic exocrine function. Critically, elastase levels are not affected by supplemental digestive enzymes — so this marker reflects the pancreas's own output regardless of what the patient is taking. Low elastase indicates pancreatic insufficiency, which means proteins, fats, and carbohydrates are not being adequately broken down. This leads to malabsorption, nutrient deficiencies, and a downstream environment that promotes dysbiosis.
Steatocrit (Fat Malabsorption)
Steatocrit measures fecal fat. Under normal circumstances, dietary fat is emulsified by bile acids in the small intestine and absorbed efficiently. Elevated steatocrit indicates fat maldigestion or malabsorption — which can be caused by bile insufficiency, pancreatic dysfunction, small intestinal damage, or dysbiosis. Fat malabsorption means fat-soluble vitamins (A, D, E, K) are also not being absorbed adequately, which has broad implications for immune function, bone health, hormone production, and inflammation.
Section 6: Inflammatory, Immune, and Additional Markers
Calprotectin
Calprotectin is considered the gold standard marker of intestinal inflammation. Elevated levels indicate active inflammation in the GI tract and are used clinically to distinguish IBD (Crohn's disease, ulcerative colitis) from IBS — a critical distinction because IBD involves a pathological inflammatory process while IBS is a functional diagnosis. Calprotectin is also used to monitor treatment response in IBD and to assess the degree of intestinal inflammation in dysbiosis.
Secretory IgA (sIgA)
Secretory IgA is the primary immunoglobulin at the mucosal border of the digestive system and the first line of immune defense in the gut. Elevated sIgA indicates the immune system is actively responding to an acute infection, chronic dysbiosis, food sensitivities, or stress. Low sIgA — often caused by chronic stress, immune compromise, or prolonged dysbiosis — means the gut's immune defense is depleted, leaving the intestinal lining more vulnerable to pathogens and inflammatory triggers.
Anti-Gliadin sIgA
Gliadin is a component of gluten. Anti-gliadin sIgA measures the immune response to gluten specifically at the gut lining. A positive result indicates an immune reaction to gluten in the digestive tract — which does not necessarily correlate with blood-based celiac markers, making this a valuable additional data point for clients with suspected gluten sensitivity who have had negative conventional testing.
Eosinophil Activation Protein (EDN/EPX)
Eosinophils are white blood cells that support immunity and maintain the protective mucosal barrier of the gut lining. The Eosinophil Activation Protein is secreted in response to infections (particularly viral), allergic reactions, and inflammatory processes. Elevated levels suggest active immune activation at the gut wall and can help identify the nature of the inflammatory process driving a client's symptoms.
Occult Blood
The presence of blood in the stool that is not visible to the eye can indicate bleeding anywhere in the GI tract. This marker adds an important safety screen to the overall assessment.
Beta-Glucuronidase
Elevated beta-glucuronidase indicates dysbiosis and may also point to impaired liver detoxification — specifically the glucuronidation step of Phase II liver detoxification. This is clinically significant because rising beta-glucuronidase has been correlated with impaired estrogen metabolism and an increased risk of estrogen-driven conditions including certain hormone-sensitive cancers. For clients with hormonal imbalances, this marker adds an important gut-liver-hormone connection to the clinical picture.
Antibiotic Resistance Genes
Detection of antibiotic resistance genes helps guide treatment decisions — specifically whether antibiotic therapy is appropriate in a given case, and which antibiotics may not be effective against the organisms present. This is particularly valuable for cases involving H. pylori or other bacterial pathogens where treatment selection matters.
How We Use GI-MAP Results at Innovative Nutrition NC
Rather than applying a generic gut protocol, we use GI-MAP findings to build a sequenced, personalized healing plan. The order of interventions matters enormously — and this is where my approach diverges significantly from the conventional functional medicine model.
Support Motility First
Before anything else, we assess and support gut motility — the rhythmic muscular contractions that move food and waste through the digestive tract. Poor motility creates the stagnant environment that allows pathogens and opportunistic bacteria to overgrow in the first place. Attempting to address dysbiosis without restoring motility is like bailing water from a boat without fixing the leak.
Support Digestion — Stomach Acid, Bile Flow, and Pancreatic Enzymes
Next, we address the upstream drivers of digestive dysfunction: stomach acid production, bile flow from the liver and gallbladder, and pancreatic enzyme output. Low stomach acid is far more common than excess acid in most cases — yet it is routinely overlooked or, worse, treated with acid-suppressing medications that compound the problem. Without adequate stomach acid, proteins are not properly broken down, pathogens are not neutralized at the gastric level, and the downstream digestive cascade is compromised from the start. Bile flow supports fat digestion and acts as a natural antimicrobial in the small intestine. Pancreatic enzyme output is essential for breaking down all three macronutrients. Restoring this digestive infrastructure creates the conditions for everything that follows to actually work.
Repair the Gut Lining
This is where my approach differs most from the conventional functional medicine model. Most practitioners focus on eradicating pathogens before beginning the repair process. In my clinical experience, this sequencing causes more harm than good. When pathogens are killed before the gut lining is repaired, the die-off byproducts — endotoxins, cell wall fragments, and inflammatory compounds — are able to cross the compromised intestinal barrier and stimulate a systemic immune response. This is what drives the severe die-off reactions many clients experience: fatigue, brain fog, skin flares, and worsening symptoms. By repairing the gut lining first, we create a more contained environment where the subsequent pathogen removal is better tolerated and more effective.
Targeted Pathogen Removal
Only after motility is supported, digestion is restored, and the gut lining is reinforced do we address pathogen removal directly — using targeted antimicrobials, herbal protocols, and peptides when warranted. This sequencing makes the removal process more tolerable, more effective, and less likely to trigger the systemic inflammatory response that derails so many gut healing protocols.
Why We Pair the GI-MAP with the MRT and Organic Acids Test
The GI-MAP is a powerful tool, but no single test captures the full picture. We frequently pair it with two additional assessments:
MRT Food Sensitivity Testing — Identifying and removing reactive foods reduces the total inflammatory burden on the gut simultaneously with the microbial work. The two protocols reinforce each other: a less inflamed gut responds better to the healing protocol, and a less reactive diet reduces the immune activation that sustains dysbiosis.
Organic Acids Test (OAT) — Some pathogens and fungal overgrowth are present in the body but not detectable in the stool. The Organic Acids Test measures metabolic byproducts in the urine that are produced by bacteria and yeast — providing a window into what is happening systemically, not just in the gut lumen. Together, the GI-MAP and OAT give us a significantly more complete picture of the microbial environment and allow us to build a more targeted and comprehensive protocol.
Collection, Shipping, and What to Expect
| Step | Details |
|---|---|
| Preparation | No dietary restrictions or medication changes required before collection. Continue all medications unless your provider directs otherwise. |
| Collection | Collect stool at home using the provided kit. Fill the specimen vial to the indicated fill line using stool from multiple areas of the sample. Cap tightly, shake vigorously, and seal in the provided specimen bag. |
| Shipping | Ship via the provided FedEx Clinical Pak Mailer. Samples must reach the lab within 5 days of collection. If you cannot ship same day, refrigerate (do not freeze) and ship within 3 days. |
| Results | Results are typically released to your provider within 10–14 business days of the lab receiving the sample. Your provider will notify you when results are available and schedule a review appointment. |
| Review Appointment | Results are reviewed in the context of your full health history, symptoms, and any other testing you have completed. A personalized protocol is built from the findings. |
The Bottom Line
The gut is not just a digestive organ. It is the foundation of immune function, hormonal balance, mood regulation, metabolic health, and skin integrity. When the gut microbiome is disrupted — by pathogens, dysbiosis, inflammation, or digestive insufficiency — the effects ripple outward into virtually every system in the body.
The GI-MAP gives us the clinical precision to see exactly what is happening in the gut ecosystem — not just whether something is wrong, but what it is, how much of it is there, and how it is interacting with the rest of the picture. That precision is what allows us to build protocols that actually resolve the root cause rather than managing symptoms indefinitely.
If you have been told your digestion is "fine" or your symptoms are "just IBS" — or if you have been dealing with symptoms that seem entirely unrelated to your gut — the GI-MAP may be the most important test you have not yet done.
