Food Intolerance · IBS · SIBO · Leaky Gut
IBS, SIBO, leaky gut — they look the same. They aren’t.
Bloating, IBS, food sensitivities, and intolerances usually point to one of three things: a microbial imbalance, an intestinal barrier problem, or both. Functional stool, breath, and permeability testing tell us which.
Open to the public · No referral required · Functional medicine evaluation
Why elimination diets only get you halfway
If you don’t test, you guess.
THE OVERLAP PROBLEM
IBS, SIBO, and leaky gut look identical.
The same symptom set — bloating, irregular stools, sensitivity to multiple foods — can come from three completely different physiological problems requiring three different protocols.
THE TRIGGER PROBLEM
Food sensitivity tests are noisy.
IgG food panels show what you’ve been exposed to, not what’s actually causing inflammation. They’re a starting point — not a diagnosis.
THE UPSTREAM PROBLEM
Gut problems often come from elsewhere.
Low stomach acid, slow motility, undertreated thyroid, chronic stress, and old antibiotic exposure all create gut dysfunction. Treating the gut without addressing the upstream rarely lasts.
The three tests that find the answer
Stool, breath, and barrier.
Each test catches a different layer of the gut dysfunction. Together they tell us not just what’s wrong, but where in the GI tract it’s happening and which mechanism is driving it.
MICROBIOME + PATHOGENS
GI-MAP Stool Analysis
Quantitative PCR mapping of beneficial bacteria, opportunistic overgrowth, candida, parasites, H. pylori, pancreatic enzymes, calprotectin (inflammation), beta-glucuronidase (estrogen recirculation), and secretory IgA. The single most informative gut test we run.
SMALL INTESTINE
SIBO Breath Testing
Three-hour lactulose or glucose breath test measuring hydrogen and methane gas production. Distinguishes small intestinal bacterial overgrowth (hydrogen-dominant) from intestinal methanogen overgrowth (methane-dominant) — they require very different treatment.
BARRIER INTEGRITY
Genova Intestinal Permeability
Lactulose/mannitol urine challenge that quantifies intestinal barrier function — the “leaky gut” problem. Identifies whether the tight junctions are letting through what they shouldn’t, which drives food sensitivities and systemic inflammation.
The cascade view
How gut dysfunction actually develops.
Most patients with food intolerance, IBS, or chronic bloating have an upstream story — often years long — that ends in the symptoms they arrive with.
Low stomach acid
From age, stress, PPI use, or H. pylori — the first defense fails, bacteria survive into the small intestine.
Antibiotic + stress history
Repeated antibiotic courses and chronic stress wipe out beneficial bacteria; opportunists fill the niche.
Slow motility (MMC)
Often thyroid- or stress-driven; the migrating motor complex stalls, letting bacteria colonize the small intestine.
Thyroid + insulin drift
Both directly affect gut motility, mucus layer, and barrier function. Untreated, the gut can’t fully heal.
Dysbiosis or SIBO
Microbial balance tips; bacteria ferment carbohydrates in the wrong place, producing gas, bloating, and inflammation.
Barrier breakdown
Tight junctions open; partially digested food particles cross the barrier, triggering immune reactions throughout the body.
Systemic inflammation rises
Inflammatory cytokines circulate; skin, joints, mood, and metabolic function all start to suffer downstream.
Bloating + gas
IBS-D / IBS-C
Growing food list
Skin issues (eczema, acne)
Joint pain + brain fog
Fatigue + mood
Nutrient deficiencies
Autoimmune flags
Eliminating foods reduces symptoms but doesn’t restore the barrier or correct the microbiome. The protocols that actually resolve gut dysfunction work in phases: remove, replace, reinoculate, repair, rebalance.
How we treat it
5R protocol — sequenced, not stacked.
Functional gut restoration follows the classic 5R framework, but the order — and what gets emphasized — depends on what the testing actually shows.
1. Remove. Identified pathogens, opportunists, or overgrowth (per GI-MAP and SIBO breath). Reduce inflammatory food triggers identified in history and testing.
2. Replace. Where stomach acid, digestive enzymes, or bile flow is insufficient, replace clinically — usually the most underestimated step.
3. Reinoculate. Targeted probiotic and prebiotic strategy based on what’s missing in your microbiome, not a generic strain.
4. Repair. Mucosal healing nutrients (L-glutamine, zinc carnosine, polyphenols, mucin support) for the barrier itself.
5. Rebalance. Address the upstream drivers — thyroid, HPA axis, motility, stress — so the gut doesn’t slide back into dysfunction.
Where to go from here
Get the actual picture before the protocol. HSA/FSA eligible · Telehealth nationwide · No referral required
TALK FIRST
Free 30-min consultation
Free · 30 min · no pressure
Talk through your gut history and figure out which testing makes sense for your case — full Blueprint, targeted gut workup, or something simpler.
FULL GUT WORKUP
Metabolic Blueprint
~$1,250 · GI-MAP + permeability + full workup · written report
GI-MAP stool analysis + Genova intestinal permeability + full chemistry + DUTCH hormones. The complete picture of your gut + upstream drivers.
Open to the public. No referral required. HSA/FSA typically accepted for clinical components. Located at 1700 Hwy 36 W, Suite 400, Roseville, MN 55113 · (651) 636-0055.
Medical disclaimer. The content on this page is for educational purposes only and does not constitute medical advice, diagnosis, or treatment. Twin Cities Metabolism delivers functional medicine evaluation and clinical protocols; results vary by individual and depend on adherence and underlying physiology. Always consult a licensed clinician about your specific situation. Reviewed by Dr. Jared Larsen, LN, CNS, DC, MS. Last reviewed: May 2026.
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