IS YOUR IBS ACTUALLY SIBO? 5 Signs You May Be Misdiagnosed

A Toronto naturopath’s perspective on getting to the root of chronic bloating, gas, and bowel changes

If you’ve been told you have IBS, you’re not alone — and you’re not imagining your symptoms.

IBS can take over your day-to-day life: persistent bloating, uncomfortable gas, unpredictable bowel movements, and food reactions that never seem consistent. Many of my patients come to me feeling dismissed after being told “everything looks normal” or that they’ll just have to manage symptoms long-term.

But here’s the question I ask almost every new patient with chronic digestive symptoms:

What if your IBS isn’t actually IBS at all?

In clinical practice, I see this over and over again — people diagnosed with IBS who are actually dealing with Small Intestinal Bacterial Overgrowth (SIBO). Identifying this distinction can be the turning point between endless symptom management and real, lasting improvement.

Let’s walk through how IBS and SIBO overlap, the signs you may be misdiagnosed, and how we approach natural SIBO treatment in Toronto using root-cause medicine.

IBS vs SIBO: Why These Conditions Are So Often Confused

Common IBS Symptoms

IBS is a symptom-based diagnosis, meaning it’s diagnosed by what you feel — not by a definitive test. Symptoms commonly include:

• Bloating and abdominal discomfort

• Constipation, diarrhea, or alternating between the two

• Gas, cramping, and urgency

• Fatigue and food sensitivities

• Normal findings on imaging and routine labs

Because there’s no clear biomarker, IBS is often diagnosed after more serious conditions are ruled out.

How SIBO Hides Behind the IBS Label

SIBO occurs when bacteria that belong in the large intestine migrate and overgrow in the small intestine, where they interfere with digestion and nutrient absorption.

Research shows that 33–78% of patients diagnosed with IBS test positive for SIBO — a staggering overlap.

Different types of SIBO often mimic specific IBS patterns:

• Hydrogen-dominant SIBO → diarrhea (IBS-D)

• Methane-dominant SIBO (IMO) → constipation (IBS-C)

• Hydrogen sulphide SIBO → bloating, gas, urgency, loose stools

The key difference? SIBO explains why symptoms are happening. IBS often doesn’t.

5 Signs Your IBS May Actually Be SIBO

In my Toronto clinic, these are the patterns that raise immediate red flags:

1. Severe bloating shortly after eating (often within 30–90 minutes)

2. Symptoms that worsen with probiotics or high-fibre foods

3. Constipation that doesn’t respond to magnesium or fibre

4. Diarrhea triggered by carbs, fruit, or FODMAP foods

5. IBS that started after food poisoning, travel illness, or antibiotics

If this sounds familiar, deeper testing is often warranted.

What Causes SIBO in the First Place?

SIBO isn’t about “bad bacteria.” It’s about gut defences breaking down.

Your digestive system relies on several mechanisms to keep bacteria where they belong:

• Adequate stomach acid

• Digestive enzymes and bile flow

• A healthy ileocecal valve

• Strong gut motility via the Migrating Motor Complex (MMC)

When one or more of these systems falter, bacteria can accumulate in the small intestine.

Common Root Causes I See Clinically

• Low stomach acid (often with stress, aging, or PPI use)

• Slowed gut motility

• Post-infectious IBS after food poisoning (what appears to be the most common root cause)

• Scar tissue or adhesions from surgery

• Chronic stress and nervous system dysregulation

• Immune imbalances, including early-life factors

This is why SIBO treatment must go beyond antibiotics/antimicrobials alone.

How We Test for SIBO in Canada

Accurate testing matters — guessing leads to relapse.

SIBO Breath Testing

• Lactulose breath testing is the most accessible and validated option in Canada

• Measures hydrogen and methane gas production over time

• Can be done via clinic-based or mail-in testing in Toronto

While jejunal aspirate testing is considered the gold standard, it’s rarely used outside of research settings.

Additional testing (stool analysis, nutrient markers, and inflammatory markers) often helps uncover why SIBO developed in the first place.

Natural SIBO Treatment: A Root-Cause Approach

There is no one-size-fits-all SIBO protocol — and that’s where many people go wrong.

In my practice, treatment is individualized, phased, and strategic.

Step 1: Reduce the Overgrowth

Depending on the type of SIBO:

• Prescription options like rifaximin

• Or herbal antimicrobials (oregano, berberine, neem, allicin)

Step 2: Address Biofilms

Targeted supplements can help disrupt bacterial biofilms, improving naturopathic treatment success.

Step 3: Restore Gut Motility

Supporting the MMC is essential to prevent relapse:

• Natural or prescription prokinetics

• Nervous system regulation

• Meal spacing and circadian rhythm support

Step 4: Strategic Dietary Support

• Short-term low-FODMAP or elemental approaches

• Avoiding long-term restriction to protect the microbiome

Step 5: Fix the Root Causes

This may include:

• Digestive enzyme or stomach acid support

• Stress and vagal tone regulation

• Gut lining repair

Step 6: Thoughtful Reintroduction of Probiotics

Timing matters — probiotics are not always helpful early in SIBO treatment, and the type of probiotics use will matter!

Is Your IBS Actually SIBO? Here’s What to Do Next

If you’ve been living with chronic IBS symptoms and nothing seems to work, here are your next steps:

• Work with a practitioner trained in SIBO and functional gut health

• Ask about SIBO breath testing in Toronto

• Rule out other conditions such as celiac disease or IBD

• Address digestion, motility, and nervous system health — not just bacteria

Uncovering SIBO often shifts patients from symptom management to true healing.

You Don’t Have to Live With “Just IBS”

For many patients, asking “Is my IBS actually SIBO?” is the moment everything changes.

With the right testing, targeted treatment, and a root-cause approach, digestive health can improve — even after years of frustration.

If you’re looking for natural SIBO treatment in Toronto, support is available. I work closely with patients to uncover what’s driving their symptoms and build a plan that’s realistic, evidence-based, and sustainable.

Your gut isn’t broken — it just needs the right approach. Book a consultation with Dr. Courtney Holmberg to discuss more today at 647 351 7282.