Written by Emma M Stevens (intern) of Viterbo University and Orli Rabin of ThrivingBiome
Feb 5th, 2025
Gut health is at the center of overall well-being, influencing everything from nutrient absorption to immune system regulation to brain function and mood. Imbalance, illness, or infection in the gut is like throwing a pebble into a smooth, glassy pond. A single disturbance sends ripples out into the surrounding water, affecting the entire system.
Some of the ways this can show up in your body include:
As you can see, many common ailments can be linked back to gut health. This makes sense, given that 70% of the immune system is in the gut. The GI-MAP test is an invaluable tool for identifying and understanding the root causes of gut-related and systemic health issues. This test delves below the surface of symptoms to help pinpoint why you may not be feeling or functioning at your best.
What is the GI-MAP?
GI-MAP, which stands for Gastrointestinal Microbial Assay Plus, is an extensive stool test that uses cutting edge qPCR (or quantitative polymerase chain reaction) technology to detect and measure microorganism DNA. It also analyzes biomarkers related to intestinal integrity, organ function, and detoxification processes. Sounds super complicated, right?
Let’s break it down: The GI-MAP is essentially a detailed picture of your gut’s ecosystem and overall health. It provides valuable data on the types and amounts of organisms living in the gut, the balance of “good” and “bad” gut bacteria, and the presence of potentially illness-causing microorganisms, like parasites and viruses. Several markers on the GI-MAP reveal crucial information about a variety of gut functions, including how well your body is digesting and absorbing food, whether the gut lining is weakened, and if detoxification processes are working efficiently. Additional markers tell us about the immune defense in the gut. Think of the gut immune system as a team of soldiers defending against invaders. When the immune response is underactive, the soldiers are overwhelmed, leaving us susceptible to pathogenic invasion. When the response is overactive, the soldiers charge into battle with extreme force, only to realize the threat was smaller than expected. Because there is such an excessive response, these immune system soldiers may mistakenly attack the body’s own cells, leading to autoimmune conditions. Over time, this constant battle can leave the immune system exhausted and underactive.
Widely used in functional and integrative health practices, the GI-MAP test helps you and your provider drill down to the root cause of symptoms like digestive discomfort, fatigue, skin flares, and even mental health concerns. Unlike the simplified positive or negative results from traditional tests, the GI-MAP offers a comprehensive look into your gut microbiome and its essential functions. Ultimately, these results provide actionable insights to guide personalized interventions like dietary changes, supplements, and treatments.
What does the test analyze? A detailed report of your GI-MAP test results is broken down into key areas, including:
To see a full set of GI-MAP results, check out this sample report.
Who can benefit from a GI-MAP test? Simply put, anyone can benefit from learning about their gut health through the GI-MAP. Most often, testing is recommended for those struggling with:
The Next Steps: How can GI-MAP test results guide your gut health journey?
Your provider will design a personalized, targeted treatment protocol based on the specific organisms detected by the GI-MAP. While protocols will vary from person to person (and provider to provider), the overarching treatment approach tends to follow a similar path: eliminating potential pathogens from the gut, supporting digestive health, recolonizing the gut with beneficial bacteria, strengthening and repairing the intestinal barrier, and ultimately achieving sustainable whole body balance.So, what does this look like in practice? Let’s dive into a patient case study.
Case Study: Jane’s Story
Jane came to our practice several months ago for help with troublesome GI symptoms. For years, she struggled with chronic constipation and severe bloating and gas. After a full day of eating, her stomach would be so distended that she felt about five months pregnant. Jane also suffered from frequent migraine headaches, fatigue, and a recent infection that required two rounds of aggressive antibiotics.
To uncover the root of Jane’s symptoms, we ran a GI-MAP test, as well as some comprehensive blood labs and HTMA.
While waiting for the test results, we worked with Jane to establish a strong foundation for treatment by focusing on the five pillars of health (nutrition, exercise, environment, stress, and sleep), and introducing helpful practices and supplements for symptom relief. This included encouraging mindful eating habits and incorporating bitters to boost stomach acid, improve digestion, and lessen the severity of her bloating; we also recommended castor oil packs and motility enhancing supplements to combat her chronic constipation and support efficient elimination.
Based on Jane’s symptoms, and lots of experience, we anticipated that her GI-MAP would show an underactive immune response related to her recent antibiotic use. When we received Jane’s results a few days later, we saw very low levels of Secretory Immunoglobulin A (SIgA), one of the first-line defenses of the intestinal immune system.
Establishing a strong, robust immune response is an essential piece of combatting dysbiosis (or an imbalance of “good” and “bad” gut bacteria). Before introducing any additional treatments for pathogens, we prioritized immune support for Jane with herbal teas, and targeted nutrients like zinc, vitamin A, and essential fatty acids.
After supporting Jane’s immune response, we turned our focus to clearing pathogens and tapering the overgrowth of opportunistic organisms. As expected, her GI-MAP detected that both major groups of beneficial bacteria were practically bottomed out, and individual types of these “good” bacteria were also on the low end of normal. Coupled with her previously lowered immune response, this environment created the perfect storm in Jane’s gut that allowed pathogenic organisms to take root.
The major pathogens discovered on Jane’s GI-MAP results included H. pylori, two types of parasites, high or detectable values of several opportunistic bacteria and autoimmune-related bacteria, and detectable levels of a potentially pathogenic yeast.
*By the way, these imbalances can show up in many different ways, both in the gut and throughout the body. If you’ve been struggling with troublesome symptoms, it’s not in your head. What you’re feeling is real, and it might be your body’s way of telling you what’s wrong. Here’s what to look for:
**Important Note: As much as we wanted to dive right into intensive pathogen treatments, we needed to make sure that detoxification and drainage pathways were functioning well first.
You can think of these pathways as packing up and moving to a new place. Detoxification is like packing up your belongings into moving boxes. Drainage is like the moving truck that takes these boxes away. If either pathway is not functioning well, toxins (including killed off pathogens) can build up in the system with nowhere to go.
After cultivating optimal detox and drainage pathways, we moved on to…
H. pylori is a very common intestinal bacterial infection. In fact, it is estimated that about 50% of the population carries it in some capacity. It can decrease stomach acid, which can disrupt digestion, and lead to symptoms like bloating, constipation, and early satiety (feeling full early). Long term infection has also been known to damage the intestinal barrier, and trigger inflammation, leaving you vulnerable to foodborne infections and digestive disturbances. Given its potential to wreak havoc on the system and her symptoms, we considered H. pylori a “heavy hitter” pathogen and treated it proactively, even though it’s levels were not flagged as not elevated. Herbal formulas (such as Mastic gum) and tinctures were our first-line approach to eradicate H. pylori. Jane’s digestive symptoms could be an indication of low stomach acid, so we also started supplemental hydrochloric acid (HCl) to support digestion and absorption.
*Note, HCL supplementation is not for everyone, especially those struggling with histamine related symptoms.
Parasites are another “heavy hitter” pathogen to address immediately. Depending on the type and quantity of parasites detected, we would aim to treat with anti-parasitic therapies like oregano oil and berberine. (If parasite levels are extremely elevated and are causing severe symptoms, a referral to a gastroenterologist for an antiparasitic medication may be helpful).
*Gentle Reminder*: Treating these “heavy hitters” can take time, but focusing on them first is vital for future strategies to be effective.In our next step, we worked to curb the overgrowth of opportunistic bacteria with antimicrobial herbs like berberine & oregano oil.
To simultaneously soothe inflammation and heal the gut lining, we introduced additional herbal supplements like marshmallow root, slippery elm and deglycyrrhizinated licorice (DGL). Another GI-MAP result that grabbed our attention was Jane’s detectable Candida levels. While Candida is a normal type of fungi in the digestive tract, overgrowth can contribute to many of Jane’s symptoms such as fatigue, constipation/diarrhea, and gas. We wanted to minimize her risk of continued growth, so we encouraged Jane to reduce her intake of sugar and refined carbohydrates (like white bread, juice, and many snack foods).
*Note*: “Killing off” the bad bacteria can take out some of the beneficial bacteria too. While we worked against the harmful organisms, we also wanted to begin nourishing the good organisms. Based on Jane’s GI-MAP results, we recommended a strain specific probiotic, prebiotics from foods like veggies, legumes, and oats, and small quantities of fermented foods (all as tolerated).
Next, we turned our attention to restoring overall microbiome balance. Here, the goal was to continue nourishing and boosting Jane’s beneficial gut bacteria, which was on the low end in her initial GI-MAP results. Following the strain-specific probiotic, we recommended a broad spectrum probiotic supplement for a short period along with fermented foods as tolerated to re-inoculate her communities of good bacteria. We also wanted to continue rebuilding her gut lining, because Jane’s GI-MAP test showed severely elevated levels of zonulin.
High zonulin, a marker of intestinal permeability (or “leaky gut”) is a striking red flag for intestinal health. Leaky gut can impact a vast array of body systems, from digestive discomfort like bloating, gas, and diarrhea or constipation, to skin flares like eczema, to brain fog, fatigue, and headaches, and everything in between. When Jane first came to us, she was experiencing many of these symptoms, so we were prepared for these results. To restore her gut integrity, we provided supplemental colostrum, and S. boulardii, a specialized probiotic, for immune support, as well as L-glutamine, zinc, vitamin A, B vitamins, and essential fatty acids to strengthen and repair the intestinal barrier.
With Jane’s gut in a renewed state of balance we set the foundation for long term, sustainable symptom relief and overall well-being. We empowered Jane with knowledge of how to soothe her gut and support a thriving gut microbiome. To support and nurture whole body balance we also recommended:
Treating imbalances found on the GI-MAP can be a complex, non-linear process, as we saw with Jane’s case. Through our experience working with patients navigating chronic imbalances–many of whom have been dismissed by traditional medicine for years–we have developed a seasoned and effective protocol, tailorable to each individual.
