SIBO & Low-FODMAP Diet: A Clinical Guide to Gut Healing in Woodbury, MN

TL;DR:- SIBO (small intestinal bacterial overgrowth) is estimated to cause 60–80% of IBS diagnoses — and most people with IBS have never been tested for it.- Low-FODMAP foods for SIBO help starve bacterial overgrowth and reduce symptoms during treatment, but diet alone won't resolve SIBO.- Paula Fortin, FNP at Secoya Health uses a 4-phase clinical protocol: Eradicate → Restore → Repair → Reinforce.- Functional testing (hydrogen/methane breath test + GI-MAP stool analysis) reveals what's actually driving your symptoms.- Untreated SIBO can cascade into leaky gut, brain fog, autoimmune activation, and nutrient deficiencies — making early identification critical.

If you've been told you have IBS, you may actually have SIBO — and the difference matters more than your doctor may realize. IBS is a label. SIBO is a mechanism. One describes symptoms; the other explains why they're happening. When you treat the mechanism, the symptoms resolve. That's the root-cause difference Paula Fortin, FNP brings to every gut health evaluation at Secoya Health in Woodbury, MN.

What Is SIBO (Small Intestinal Bacterial Overgrowth)?

SIBO — small intestinal bacterial overgrowth — is a condition where bacteria colonize the small intestine in numbers they were never supposed to reach. Your gut is not a sterile environment. Bacteria belong there. But location matters enormously. The vast majority of your gut bacteria are designed to live in the large intestine (colon), far downstream. The small intestine, where most of your nutrient absorption happens, is supposed to remain relatively bacteria-free.

When bacteria migrate upstream into the small intestine, they begin fermenting the carbohydrates you eat before your body can absorb them. That fermentation produces hydrogen and methane gas, causes bloating and pain, and disrupts the nutrient absorption your cells depend on.

Research estimates that SIBO accounts for 60–80% of all IBS diagnoses. That means the majority of people managing "IBS" have never had the actual problem identified or addressed. They've been handed symptom management — when what they needed was a test and a targeted protocol.

What Are the Symptoms of SIBO?

The hallmark symptom of SIBO is bloating that begins 60–90 minutes after eating. That timing reflects the fermentation cycle — bacteria processing the food you just ate before your body could. But the symptom picture goes much further than a bloated belly.

Common SIBO symptoms include:

• Bloating within 60–90 minutes of eating
• Alternating constipation and diarrhea
• Excessive gas, especially after carbohydrates or high-fiber foods
• Nutrient deficiencies — particularly B12, iron, and fat-soluble vitamins A, D, E, and K (the bacteria steal them before absorption)
• Brain fog — bacteria in the small intestine produce lipopolysaccharides (LPS), which can cross the blood-brain barrier and trigger neurological inflammation
• Fatigue, skin problems, and joint pain driven by systemic inflammation
• Worsening symptoms after taking probiotics or eating fiber (both can feed SIBO bacteria)

That last point surprises most people. If your gut symptoms get worse after starting a probiotic, it's a meaningful clinical signal. You may be feeding the wrong bacteria. This is exactly why Paula evaluates the full picture before recommending any supplement protocol. You can read more about the gut-brain connection in our post on the gut-brain axis and mood.

How Is SIBO Diagnosed? Testing at Secoya Health

SIBO is diagnosed through a combination of clinical assessment and targeted functional testing. The gold standard is the hydrogen/methane breath test. Here's how it works: you drink a lactulose or glucose solution, and breath samples are collected every 20 minutes over two to three hours. Elevated hydrogen or methane readings at specific intervals indicate bacterial fermentation in the small intestine — confirming SIBO.

But Paula doesn't stop there. At Secoya, the diagnostic picture can also include:

• GI-MAP stool analysis: A comprehensive DNA-based stool test that reveals microbial imbalances, pathogens, opportunistic bacteria, and markers of gut permeability (leaky gut).
• Organic acids testing: Identifies metabolic byproducts of bacterial and yeast fermentation, giving a systemic view of what's happening downstream.

This three-layer approach — symptom pattern, breath test, and stool analysis — gives a clear, actionable picture that most conventional workups never provide. Conventional medicine often prescribes rifaximin (an antibiotic) and moves on. But rifaximin has a high recurrence rate because it doesn't address why the bacteria overgrew in the first place. Paula's functional medicine approach at Secoya is built to find and fix that root cause.

As Emily R. shared: "Paula Fortin is amazing. She takes the time to listen and her functional medicine approach helped me fix my gut health when nothing else worked."

What Are the Best Low-FODMAP Foods for SIBO?

Low-FODMAP foods for SIBO are foods that minimize fermentable carbohydrates, which starve bacterial overgrowth and reduce the gas and inflammation it causes. FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols — a mouthful, but the concept is simple. These are the types of carbohydrates that ferment quickly in the gut. For someone with SIBO, high-FODMAP foods are rocket fuel for the wrong bacteria.

A low-FODMAP diet is a powerful therapeutic tool during SIBO treatment. It is not a permanent lifestyle, and it is not the treatment itself. Think of it as starving the fire while you put it out.

Phase 1 — Elimination (2–6 Weeks)

Remove all high-FODMAP foods. The biggest offenders:

• Garlic and onion (the two highest-FODMAP foods)
• Wheat, rye, and barley
• Most legumes (chickpeas, lentils, kidney beans)
• Lactose-containing dairy
• High-fructose fruits (apples, pears, mangoes, watermelon)
• Stone fruits (peaches, plums, cherries)
• Artificial sweeteners ending in "-ol" (sorbitol, xylitol, mannitol)

What You Can Eat: Key Low-FODMAP Foods

This is where most resources fall short — they tell you what to avoid without giving you a workable food list. Here's what works well during SIBO treatment:

Grains & Starches: White rice, potatoes, rice cakes, gluten-free oats (in moderation)

Vegetables: Carrots, zucchini, cucumber, green beans, kale, spinach, bok choy, bell peppers, eggplant

Fruits: Blueberries, strawberries, kiwi, oranges, grapes, cantaloupe

Proteins: Chicken, turkey, fish, eggs, firm tofu

Dairy: Lactose-free milk, hard cheeses (cheddar, parmesan), lactose-free yogurt

Fats & Flavoring: Olive oil, coconut oil, fresh ginger, fresh herbs, green onion tops (the green part only — not the white bulb)

Phase 2 — Reintroduction

After the elimination phase, food groups are reintroduced one at a time, systematically, to identify individual triggers. Everyone's tolerances differ — not all high-FODMAP foods will be problems for every person.

Phase 3 — Personalization

Long-term, the goal is the least restrictive diet that keeps you feeling well. Low-FODMAP is a reset and diagnostic tool, not a forever plan. Paula builds a personalized post-treatment nutrition strategy for every participant.

Herbal Antimicrobials: The Functional Medicine Approach to SIBO Eradication

When it comes to eradicating SIBO, Paula Fortin frequently uses herbal antimicrobials instead of — or alongside — rifaximin. The reason is clinical: herbal protocols offer a broader antimicrobial spectrum, carry no antibiotic resistance risk, cause less disruption to the beneficial bacteria in your colon, and work against both hydrogen-dominant and methane-dominant SIBO.

Key herbal antimicrobials used in SIBO treatment:

• Berberine: A potent broad-spectrum antimicrobial compound found in plants like goldenseal and barberry. It also improves insulin sensitivity, which matters because blood sugar instability can contribute to gut motility problems.
• Oil of Oregano: The active compound carvacrol has strong antimicrobial and antifungal properties, directly disrupting bacterial cell membranes.
• Allicin (garlic extract): Here's the clinical paradox — fresh garlic is extremely high-FODMAP and will worsen SIBO symptoms. But allicin extract (a concentrated, isolated compound from garlic) is one of the most effective SIBO-killing agents available, especially for methane-dominant SIBO. You avoid garlic as a food while using it as medicine.
• Neem: An intestinal antiseptic herb with a long history of use in Ayurvedic medicine. Effective against a broad range of gut pathogens.
• Biofilm disruptors (NAC, systemic enzymes): SIBO bacteria don't just float freely — they form protective biofilms, like microscopic shields, that antibiotics and herbs have difficulty penetrating. NAC (N-acetyl cysteine) and specific enzymes break down these biofilms, dramatically improving eradication outcomes.

A typical herbal antimicrobial protocol runs 4–6 weeks, with clinical monitoring through symptom tracking and repeat breath testing at the end of treatment to confirm clearance.

What Is the Full SIBO Protocol at Secoya Health?

The full SIBO protocol at Secoya Health follows four sequential phases: Eradicate, Restore, Repair, and Reinforce. Most SIBO treatments stop after phase one — and that's why most people relapse.

Phase 1 — Eradicate

Herbal antimicrobials (or rifaximin when clinically indicated) combined with a low-FODMAP diet. The diet starves the bacteria; the antimicrobials kill them. Both are happening simultaneously for 4–6 weeks.

Phase 2 — Restore

This is the phase most treatments miss entirely — and it's arguably the most important for preventing recurrence. The goal is to restore the migrating motor complex (MMC), the wave-like muscular contraction that sweeps bacteria out of the small intestine between meals. MMC dysfunction is the most common reason SIBO comes back.

Prokinetic agents used to restore MMC function include ginger extract, 5-HTP (a serotonin precursor — most serotonin is made in the gut), and in some cases low-dose naltrexone under medical supervision. Without restoring the MMC, the small intestine becomes a welcoming environment for bacterial re-colonization.

Phase 3 — Repair

After eradication, the gut lining needs to be rebuilt. Bacteria and their endotoxins damage the intestinal tight junctions — the cellular "glue" that keeps the gut wall intact. Repair nutrients include L-glutamine (the primary fuel for intestinal cells), zinc carnosine (supports tight junction integrity), and slippery elm (a demulcent herb that soothes and coats the gut lining).

This is also when targeted probiotics are introduced — but only after eradication. The strains that work best at this stage are Saccharomyces boulardii (a beneficial yeast, not a bacteria) and spore-based probiotics, which don't colonize the small intestine and won't re-trigger SIBO.

Phase 4 — Reinforce

The final phase focuses on long-term maintenance and root-cause resolution. This includes sustainable dietary modifications, ongoing prokinetic support, and identifying the underlying drivers that allowed SIBO to develop in the first place. Common root causes include:

• Hypothyroidism: A sluggish thyroid slows gut motility, impairing MMC function and creating conditions for bacterial overgrowth.
• Chronic stress: Elevated cortisol disrupts gut motility at the neurological level. This is where Secoya's Quantum Neuro Reset Therapy (QNRT) becomes relevant — unresolved nervous system stress is a genuine physiological driver of gut dysfunction.
• Prior antibiotic use or food poisoning: Both can damage the MMC neurons, setting the stage for SIBO.
• Structural issues: Low stomach acid, slow gallbladder, or prior abdominal surgeries.

Erik J. described his experience: "My experience at Secoya literally changed my life. I had been on heartburn medication for 11 years, and my symptoms were steadily getting worse. I would feel full/bloated and very tired after every meal…" His symptoms — classic SIBO markers — resolved through a root-cause protocol, not another prescription.

Why SIBO Is Never Just a Gut Problem

SIBO doesn't stay contained to your small intestine. Left unaddressed, it triggers a downstream cascade that reaches your brain, your immune system, and your metabolism.

The SIBO cascade:

1. SIBO → Leaky Gut: Bacterial endotoxins (specifically lipopolysaccharides, or LPS) damage the tight junctions between intestinal cells. The gut wall becomes permeable — "leaky." Read more in our leaky gut and brain health post.
2. Leaky Gut → Systemic Inflammation: LPS enters the bloodstream, where the immune system mounts a response. The result is chronic low-grade inflammation — the upstream driver of brain fog, mood disorders, skin conditions, joint pain, and autoimmune activation. See our post on autoimmune disease and root-cause care.
3. SIBO → Nutrient Deficiency: Bacteria in the small intestine steal B12 and iron before absorption. Deficiencies in these two nutrients alone cause fatigue, cognitive decline, hair loss, and poor immune function.
4. SIBO → Fat Malabsorption → Vitamin D Deficiency: When fat-soluble vitamins can't be absorbed, immune regulation suffers. Vitamin D deficiency is deeply connected to immune dysregulation and autoimmune risk.
5. SIBO → Weight Loss Resistance: Malabsorption disrupts caloric signaling. Hormonal downstream effects — particularly leptin and insulin dysregulation — make it nearly impossible to lose weight through diet alone until the gut is addressed.

If you're experiencing brain fog alongside digestive symptoms, the gut is likely involved. Our post on brain fog and root-cause treatment covers that connection in depth.

For additional anti-inflammatory gut support during recovery, castor oil packs are a gentle, research-supported home therapy worth exploring. Our castor oil benefits post explains how they work.

Dana Masek shared this about her family's experience: "Dr. Schilling has put together a combination of natural protocols for real health — not just disease management. He has helped my son and I achieve health after a Crohn's and Lyme's diagnosis respectively."

What Should You Do If You Suspect SIBO?

Step 1: Stop guessing. Get tested. A hydrogen/methane breath test combined with a GI-MAP stool analysis gives you an objective clinical picture — not just a symptom diary.

Step 2: Don't self-treat with probiotics. If SIBO is the underlying problem, most standard probiotics will make symptoms worse. Wait for a confirmed diagnosis and clinical guidance.

Step 3: Start reducing high-FODMAP foods now. You don't need a confirmed diagnosis to benefit from reducing garlic, onion, wheat, and high-fructose foods. This is a low-risk, high-reward step while you pursue testing.

Step 4: Address the root causes. Stress management, thyroid optimization, and nervous system support are not optional add-ons — they're core to lasting resolution.

Your body was designed to heal. With the right testing, the right protocol, and a provider who takes the time to look at the full picture, SIBO is a solvable problem.

If you've been cycling through GI symptoms without answers — or managing "IBS" without ever being tested for SIBO — Paula Fortin can help. Book a gut health evaluation at Secoya Health to get properly tested and start a protocol that actually addresses the root cause.

Sources

• Dukowicz AC, et al. "Small Intestinal Bacterial Overgrowth: A Comprehensive Review." Gastroenterology & Hepatology, 2007.
• Pimentel M, et al. "ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth." American Journal of Gastroenterology, 2020.
• Gibson PR, Shepherd SJ. "Evidence-based dietary management of functional gastrointestinal symptoms: The FODMAP approach." Journal of Gastroenterology and Hepatology, 2010.
• Bures J, et al. "Small intestinal bacterial overgrowth syndrome." World Journal of Gastroenterology, 2010.