Interpretation Of My GI-Map
December 2025
I recently had a GI-Map performed. Below are my results followed by my interpretation and action plan. Be sure to read Smarter Gut Repair for more context, better understanding, and applications.
GI MAP – December 2025
Bacteroides fragilis:
Low levels signal IBD, weak gut barrier, weakened immune function, higher inflammation, reduced short chain fatty acids (butyrate). Often low levels result from a low fiber diet.
Use the following probiotic supplements:
- Bacteroides fragilis SNBF-1: Shows promise as an NGP with cholesterol-lowering, antioxidant, and carbohydrate-regulating effects, suggesting broad gut benefits.
- Bacteroides fragilis BF839: Used adjunctively to improve gut microbiota and potentially enhance responses to cancer therapies, demonstrating immune modulation.
- Bacteroides fragilis ZY312: Shown to protect against pathogens like C. difficile and C. sakazakii, supporting gut barrier function.
- NTBF Strains (Non-Toxigenic): These are key for health, producing Polysaccharide A (PSA) to regulate immunity and improve gut integrity, making them ideal next-gen probiotics.
Escherichia spp:
A low Escherichia spp. result on a GI-MAP test suggests a reduced presence of beneficial E. coli, which can mean compromised gut barrier health, less protection against harmful pathogens, lower production of beneficial compounds (like short-chain fatty acids), and potential dysbiosis (microbial imbalance). Essentially, it points to a weaker "mucosal firewall," making the gut lining more vulnerable and impacting overall immune support.
To increase beneficial Escherichia spp. (like E. coli Nissle 1917, or EcN) in the gut, focus on specific probiotic strains like Lactobacillus spp. (e.g., L. plantarum, L. rhamnosus, L. reuteri).
- E. coli Nissle 1917 (EcN): The most well-known probiotic E. coli, used for over a century to treat diarrhea, constipation, and Inflammatory Bowel Disease (IBD), especially ulcerative colitis.
- E. coli MG1655 (K-12): A human commensal strain that effectively competes for nutrients, helping to prevent pathogenic colonization.
- E. coli HS: Another true human commensal, known for strong gut colonization and found in healthy individuals.
Resistant Starches: Found in cooked/cooled potatoes, bananas, oats.
Prebiotic Fibers: Inulin (chicory root), FOS (fructooligosaccharides) found in onions, garlic, leeks.
Glucose & Lactose: Standard favorites, E. coli prefers glucose first (catabolite repression).
Arabinose, Galactose, Fucose, Ribose, Maltose: These are also good carbon sources that E. coli can utilize for energy
Faecalibacterium prausnitzii:
This bacterium is a primary producer of butyrate, a short-chain fatty acid that provides energy to the cells lining your colon (colonocytes) and maintains the intestinal barrier. Low levels are associated with increased intestinal inflammation and a higher risk of inflammatory conditions. Significantly low levels of F. prausnitzii are frequently observed in patients with IBD and IBS.
Faecalibacterium prausnitzii is an obligate anaerobe, which means it cannot live in the presence of oxygen making it impossible to put in a probiotic supplement, but Bifidobacterium catenulatum can support its growth.
Consuming foods rich in inulin (found in chicory root, leeks, and garlic) or resistant starch (green bananas, cooked and cooled potatoes/rice). The specific 2'-Fucosyllactose (2'-FL) form of HMO is particularly good (which is in my HMO from Amazon.
Bacteroidetes:
A low Bacteroidetes level on a GI-MAP test signals an imbalanced gut microbiome, potentially linked to digestive issues like IBD, metabolic problems (obesity), compromised immunity, and poor nutrient absorption, as these beneficial bacteria help break down fiber and support the gut lining. It indicates a need to boost fiber, prebiotics, fermented foods, and consider lifestyle changes to promote gut health and restore balance with Firmicutes.
To boost low Bacteroidetes shown on a GI-MAP, focus on probiotics like Lactobacillus rhamnosus GG (LGG) and Bacteroides fragilis.
Fiber-rich prebiotics (garlic, onions, asparagus) and varied plant foods to support these fiber-fermenting bacteria, as research shows specific strains and fiber intake directly influence this phylum.
Firmicutes:
A low level of Firmicutes on a GI-MAP indicates dysbiosis (imbalance) potentially linked to reduced butyrate (gut fuel), leaky gut, weakened gut barrier, inflammation, poor nutrient absorption, and potential links to autoimmune issues, depression, or metabolic changes, as Firmicutes are crucial for gut lining health, fiber digestion, and anti-inflammatory signals.
To boost low Firmicutes (a key gut phylum) shown on a GI-MAP, focus on Lactobacillus strains like L. acidophilus, L. rhamnosus, L. plantarum, L. reuteri, L. casei, and L. fermentum, often found in fermented foods (yogurt, kefir, kimchi) and specific supplements, as these help break down fibers, support immunity, and strengthen the gut lining, but also include prebiotic foods (garlic, onions, bananas) to fuel their growth.
To increase low Firmicutes on a GI-MAP, focus on a diverse, fiber-rich diet with prebiotic foods (onions, garlic, green bananas), fermented foods (yogurt, kimchi), and resistant starches (cooked & cooled potatoes) while limiting sugar and processed items, plus consider targeted probiotics, exercise, and stress management for overall gut balance.
Bacillus spp.:
For managing bacterial overgrowth, particularly of Bacillus spp. in the colon, the specific and well-researched strain you need is Saccharomyces boulardii CNCM I-745, found in products like Florastor, as it's proven to restore gut balance, prevent harmful microbe colonization, and modulate the microbiota, even against other pathogens, offering a robust solution for dysbiosis.
Staphylococcus aureus:
Bacillus subtilis probiotics have shown significant success in reducing S. aureus in the gut and nose by blocking colonization, not just killing bacteria.
Focus on Bacillus subtilis probiotics to outcompete it, and use specific prebiotics like Inulin, FOS (Fructooligosaccharides), or Beta-Glucans to feed beneficial bacteria, but avoid foods/supplements that promote S. aureus growth (like excess sugar/refined carbs) while working on S. aureus reduction with Bacillus. The goal is to create an environment where B. subtilis thrives, inhibiting S. aureus quorum sensing (communication) without killing it outright, often in synbiotic (probiotic + prebiotic) approaches.
Desulfovibrio spp.:
For reducing specific bacterial overgrowths like Desulfovibrio, the most researched and clinically supported strain of Saccharomyces boulardii is CNCM I-745, found in products like Florastor, known for modulating gut flora, counteracting harmful bacteria, and supporting gut health, though direct Desulfovibrio studies often use other S. boulardii strains in research, emphasizing strain-specific effects.
Methanobacteriaceae:
For reducing Methanobacteriaceae (methane-producing archaea) in the gut, Lactobacillus reuteri (especially strain DSM 17938) is a promising probiotic, as it competitively inhibits methanogens and can reduce methane production linked to constipation. Other helpful probiotics might include certain strains of Bifidobacterium, Lactobacillus acidophilus, and Saccharomyces boulardii, but it's crucial to work with a practitioner, as some probiotics can worsen methane-S(mall) I(ntestinal) B(acterial) O(vergrowth).
For combating Methanobacteriaceae overgrowth (SIBO/IMO), the primary, well-researched strain of Saccharomyces boulardii is CNCM I-745, often found in supplements like Florastor, as it helps restore microbial balance, reduces inflammation, and interacts with pathogens, creating a less favorable environment for archaea like Methanobrevibacter smithii by influencing fermentation byproducts and gut motility, though it doesn't directly kill methanogens.
Secretory IgA:
On a GI-MAP test, low secretory IgA (sIgA) means your gut's immune defense is weak, suggesting it can't effectively block pathogens, toxins, and irritants, potentially leading to "leaky gut," inflammation, food sensitivities, IBS, autoimmune issues, and increased susceptibility to infections, often linked to chronic stress, poor nutrition, or adrenal fatigue. It signifies a depleted immune system in the gut, making you vulnerable to invaders.
To improve low secretory IgA (sIgA) on a GI-MAP, focus on healing the gut barrier, nurturing beneficial gut bacteria with specific probiotics (like Saccharomyces boulardii, Lactobacillus, Bifidobacterium). Specific Lactobacillus strains known to support secretory IgA (sIgA) include Lactobacillus plantarum AYA, Lactobacillus gasseri SBT2055, certain L. rhamnosus strains (like CCFM1228, 28L2, W6L1), Lactobacillus paracasei K71, and specific isolates like Lactiplantibacillus plantarum CJW55-10. Specific Bifidobacterium strains like Bifidobacterium bifidum OLB6378, B. longum subsp. infantis (e.g., I4MI, I10TI, B6MNI, FHNFQ4M11, CCFM1269), and Bifidobacterium lactis BB12 are shown to support secretory IgA (sIgA) production
To boost secretory IgA (sIgA), focus on prebiotics like inulin, oligofructose (FOS), and resistant starch, found in garlic, onions, bananas, oats, and chicory, as they feed beneficial gut bacteria that promote IgA.
Oxalates:
Research indicates that oxalates do not directly increase secretory IgA (sIgA) in the gut. Instead, conditions associated with high oxalate absorption, such as gut inflammation or a lack of oxalate-degrading bacteria, may correlate with dysfunctional or altered sIgA levels as part of a general inflammatory response or altered gut environment.
Here is a breakdown of the actual relationship:
Normal Oxalate Metabolism and the Gut
- Microbial Degradation: Specific gut bacteria, most notably Oxalobacter formigenes, use oxalate as their sole energy source, effectively breaking it down in the gut lumen before it can be absorbed into the bloodstream.
- Oxalate Secretion: The presence of these bacteria or their derived bioactive factors can also induce the gut lining to actively secrete endogenous oxalate (oxalate produced by the body) into the intestine, where it can be further degraded and eliminated in the feces. This helps maintain systemic oxalate homeostasis.
- sIgA is a primary immune defense in the gut mucosa, helping to maintain a healthy balance of commensal bacteria and protecting against pathogens.
- sIgA binds to gut microbiota, which helps lessen inflammatory reactions and promotes a balanced immune response.
- The production of sIgA can be influenced by microbial metabolites, such as short-chain fatty acids (SCFAs), which generally promote a healthy gut environment and immune function.
The user's premise, that "oxalates increase secretory IgA," is not directly supported by the provided information. Rather, the following dynamics are observed:
- Gut Dysbiosis/Inflammation: Conditions like inflammatory bowel disease (IBD) or a "leaky gut," which are sometimes associated with high oxalate absorption, are linked to an altered or potentially dysfunctional IgA response and general inflammation markers.
- Healthy Gut: A healthy gut microbiome with ample oxalate-degrading bacteria is associated with efficient oxalate processing and general immune balance, which includes functional sIgA levels. Probiotics (like certain Lactobacillus and Bifidobacterium strains) have been shown to increase fecal sIgA, suggesting a healthy, balanced microbiome is key to a robust and functional immune response.
For removing oxalates, the most effective probiotic strains are often from the Lactobacillus and Bifidobacterium genera, especially Lactobacillus acidophilus, L. gasseri, L. plantarum, and Bifidobacterium breve, as they contain enzymes to break down oxalate into less harmful substances like formate and CO2, preventing absorption and kidney stone formation, with Oxalobacter formigenes being a key native gut bacterium for this job.
Key Oxalate-Degrading Strains:
- Lactobacillus acidophilus: Highly efficient at degrading oxalate and reducing urinary excretion.
- Lactobacillus gasseri: Also very effective in oxalate breakdown.
- Lactobacillus plantarum: Shows strong oxalate-metabolizing capabilities.
- Bifidobacterium breve: A promising strain for oxalate reduction.
- Bifidobacterium longum: Another beneficial Bifidobacterium species.
- Oxalobacter formigenes: A natural gut bacterium that uses oxalate as its sole energy source, making it crucial for oxalate regulation.
- Oxalobacter formigenes: This is a specialist bacterium that uses oxalate as its sole source of carbon and energy. It transports oxalate into the bacterial cell where two specific enzymes, oxalyl coenzyme A decarboxylase (oxc) and formyl coenzyme A transferase (frc), break it down into formate and carbon dioxide. This process is highly efficient at reducing the amount of oxalate available for absorption into the bloodstream and subsequent excretion by the kidneys.
- Lactobacillus and Bifidobacterium species: Certain strains of these generalist bacteria, such as Lactobacillus acidophilus and Lactobacillus gasseri, can also degrade oxalate, though they use other carbon sources as well. They possess similar oxc and frc genes and the ability is an adaptive response to the presence of oxalate, which can be toxic to them in high concentrations.
Action Plan for GI MAP December 2025
Probiotics Needed:
Lactobacillus plantarum ZLP001 (support Faecalibacterium prausnitzil)
Lactobacillus plantarum (support Eschericia spp.)
Lactobacillus plantarum AR342 (degrade oxalates)
Lactobacillus plantarum AR1089 (degrade oxalates)
Lactobacillus plantarum J-15 (degrade oxalates)
Lactobacillus plantarum N-1 (degrade oxalates)
Lactobacillus plantarum AN1 (support Firmicutes)
Lactobacillus plantarum ZDY2013 (support Firmicutes)
Lactobacillus plantarum NCIMB8826 (support Firmicutes)
Lactobacillus plantarum BW2013 (support Firmicutes)
Lactobacillus plantarum MH-301 (support Firmicutes)
Lactobacillus plantarum 299v (support Firmicutes)
Lactobacillus plantarum AYA (increase secretory IgA)
Lactobacillus rhamnosus (support Eschericia spp.)
Lactobacillus rhamnosus GG (support Firmicutes)
Lactobacillus rhamnosus 185356 (support Firmicutes)
Lactobacillus rhamnosus CCFM1068 (support Firmicutes)
Lactobacillus rhamnosus GG (increase IgA)
Lactobacillus rhamnosus GG (support Bacteroidetes)
Lactobacillus rhamnosus HN001(support Bacteroidetes)
Lactobacillus rhamnosus hsryfm 1301 (support Bacteroidetes)
Lactobacillus rhamnosus CNCM I-3690 (support Faecalibacterium prausnitzil)
Lactobacillus paracasei CNCM I-3689 (support Faecalibacterium prausnitzil)
Lactobacillus reuteri (support Eschericia spp.)
Lactobacillus reuteri DSM 17938 (support Firmicutes)
Lactobacillus reuteri ATCC PTA 6475 (support Firmicutes)
Lactobacillus reuteri DSM 17938 (reducing Methanobacteriaceae overgrowth)
Lactobacillus acidophilus LA-5 (support Firmicutes)
Lactobacillus acidophilus NCFM (support Firmicutes)
Lactobacillus acidophilus CCFM137 (support Firmicutes)
Lactobacillus acidophilus FGSYC48L79 (support Firmicutes)
Lactobacillus acidophilus CICC 6075 (support Firmicutes)
Lactobacillus acidophilus LA-14 (degrade oxalates)
Lactobacillus casei BL23 (support Firmicutes)
Lactobacillus fermentum CECT5716 (support Firmicutes)
Lactobacillus fermentum NRAMJ5 (degrade oxalate)
Lactobacillus fermentum CCFM1225 (increase secretory IgA)
Lactobacillus fermentum CCFM1226 (increase secretory IgA)
Lactobacillus fermentum X6L1(increase secretory IgA)
Lactobacillus gasseri UBLG-36 (degrade oxalates)
Lactobacillus gasseri SBT2055 (increase IgA)
Lactobacillus paracase LPC09 (degrade oxalates)
Lactobacillus paracase UBLPC-87 (degrade oxalates)
Bifidobacterium bifidum OLB6378 (support secretory IgA)
Bifidobacterium lactis Bb12 (support secretory IgA)
Bifidobacterium breve MB 283 (degrade oxalates)
Bifidobacterium longum MB 282 (degrade oxalates)
Bifidobacterium longum ATCC 15707 (degrade oxalates)
Bifidobacterium longum MB 58 (degrade oxalates)
Bifidobacterium longum subsp. infantis I4MI (increase secretory IgA)
Bifidobacterium longum subsp. infantis I10TI (increase secretory IgA)
Bifidobacterium longum subsp. infantis B6MNI (increase secretory IgA)
Bifidobacterium animalis subsp. lactis DSM 10140 (degrade oxalates)
Bifidobacterium animalis subsp. lactis Bb12 (degrade oxalates)
Bifidobacterium animalis subsp. lactis Bi07 (degrade oxalates)
Bifidobacterium animalis ssp. lactis HY8002 (increase secretory IgA)
Bifidobacterium catenulatum KCTC 3221 (support Faecalibacterium prausnitzil)
Bifidobacterium catenulatum ATCC 27768 (support Faecalibacterium prausnitzil)
Bifidobacterium catenulatum A2-165 (support Faecalibacterium prausnitzil)
Bifidobacterium adolescentis L2-32 (support Faecalibacterium prausnitzil)
Saccharomyces boulardii lyo CNCM I-745 (increase secretory IgA) (Florastor)
Saccharomyces boulardii lyo CNCM I-745 (reduce Bacillus spp. overgrowth) (Florastor)
Saccharomyces boulardii lyo CNCM I-745 (reduce Desulfovibrio spp.) (Florastor)
Saccharomyces boulardii lyo CNCM I-745 (reduce Methanobacteriaceae) (Florastor)
Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) (increase secretory IgA)
Bacillus subtilis MB40 (Sporevia) (reduce Staphylococcus aureus)
Bacillus subtilis 6D1 (reduce Staphylococcus aureus)
Oxalobacter formigenes (brand Oxalo) (degrade oxalates)
Escherichia coli Nissle 1917 (EcN) (brand Mutaflor) (increase Eschericia coli Nissle 1917)
12/21/2025 – Start Florastor, 2 capsules once per day.
12/21/2025 – Start Bacillus subtillis HU58, 2 capsule once per day.
12/23/2025 - Start Life Space Triple Strength, 1 capsule per day.
