SIBO Treatment in Toronto
A root-cause approach to resolving bloating, gas, and IBS symptoms
If you’ve been diagnosed with SIBO – or suspect it based on ongoing digestive symptoms – effective treatment requires more than a simple protocol.
SIBO (Small Intestinal Bacterial Overgrowth) is a complex condition that often involves multiple underlying factors, including gut motility, digestion, and nervous system function.
With over 20 years of clinical experience, Dr. Makoto Trotter, ND provides personalized SIBO treatment for patients in North York, Toronto, and the GTA, focusing on long-term resolution – not temporary symptom relief.
Book a free 15-minute consultation to discuss your symptoms and next steps
What is SIBO?
Small Intestinal Bacterial Overgrowth (SIBO) occurs when bacteria accumulate in the small intestine in higher-than-normal amounts.
This can interfere with digestion, nutrient absorption, and gut motility leading to symptoms such as bloating, gas, and IBS-like discomfort.
SIBO is often more complex than it appears, and effective treatment requires addressing the underlying factors contributing to the imbalance.
Symptoms of SIBO
SIBO may contribute to:
- Persistent bloating (often worse after eating)
- Excess gas or belching
- Abdominal discomfort or cramping
- Diarrhea, constipation, or alternating IBS symptoms
- Brain fog or fatigue
- Symptoms of IBS
- Food sensitivities, especially to carbohydrates
If these symptoms feel familiar, addressing the underlying cause is key.
👉 Not sure if it’s SIBO? Learn more about SIBO testing in Toronto
What causes SIBO?
SIBO typically develops due to underlying disruptions in digestion, gut motility, or microbial balance:
- Overuse of antibiotics
- Yeast overgrowth (e.g. Candida)
- Use of acid blockers
- Presence of H. pylori
- Constipation/Low motility in the small intestine
- Gallbladder disease/Liver dysfunction, leading to decreased bile secretion
- Poor digestive enzyme production
- Excessive carbohydrates/sugar/fructose in diet
- Ileocecal valve dysfunction
- Parasitic infections
Why SIBO Treatment Often Fails
Many patients try restrictive diets or short-term protocols but don’t see lasting improvement.
This is because SIBO is rarely just a bacterial overgrowth problem.
Common underlying contributors include:
- Impaired gut motility
- Low stomach acid or digestive enzyme function
- Nervous system dysregulation (stress response)
- Previous infections or antibiotic use
Without addressing these factors, symptoms often return.
How SIBO is Treated
SIBO treatment is tailored to your specific symptoms, test results, and underlying causes.
Your treatment plan may include:
Targeted Antimicrobial Therapy
Herbal or natural antimicrobial support to reduce bacterial overgrowth
Dietary Strategies
Short-term dietary adjustments to reduce fermentation and symptoms
Gut Motility Support
Improving movement through the digestive tract to prevent recurrence
Digestive Support
Support for stomach acid, enzymes, and nutrient absorption
Nervous System Regulation
Addressing stress and its impact on digestion and gut function
A Personalized, Multi-Step Approach
SIBO treatment is not linear.
It often involves phases:
- Reducing bacterial overgrowth
- Supporting digestion and absorption
- Restoring gut motility
- Preventing recurrence
This approach is designed to create sustainable, long-term improvement, not temporary relief.
Why Patients Choose Dr. Makoto Trotter for SIBO Treatment
- 20+ years of clinical experience
- Focus on root-cause digestive health
- Experience with complex and chronic cases
- Individualized treatment plans
- Integrated, evidence-informed approach
- Published author of a book on Leaky Gut Syndrome (intestinal permeability)
- Experienced treating patients with an IBS diagnosis
Do You Need Testing Before Treatment?
In most cases, testing helps guide more precise and effective treatment.
👉 Learn more about SIBO testing in Toronto
In some situations, treatment may begin based on symptoms and clinical history.
Additional testing, such as comprehensive stool analysis or GI-MAP stool microbiome test, may also be used to assess gut health, inflammation, and microbial balance.
FAQs About SIBO Treatment
What is SIBO and how do I know if I have it?
SIBO (Small Intestinal Bacterial Overgrowth) occurs when bacteria that normally live in the large intestine migrate and overgrow in the small intestine, disrupting digestion and nutrient absorption. It is confirmed through a SIBO breath test which measures hydrogen and methane gas levels. Many patients with a long-standing IBS diagnosis are later found to have SIBO as the underlying cause.
What causes SIBO?
Common causes include impaired gut motility, low stomach acid, prior gut infections, overuse of antibiotics, structural issues, and chronic stress. Identifying the root cause is essential – without addressing it, recurrence is common even after successful treatment.
How long does SIBO treatment take?
Treatment timelines vary, but most protocols range from several weeks to a few months depending on complexity and whether underlying causes are also being addressed.
Can SIBO come back after treatment?
Yes, if underlying causes are not addressed. Preventing recurrence is a central part of Dr. Trotter’s approach – treatment doesn’t stop at clearing the overgrowth, it continues with restoring healthy gut motility and microbiome balance.
Is SIBO connected to leaky gut?
Yes. SIBO and leaky gut frequently co-exist. Bacterial overgrowth in the small intestine can damage the intestinal lining and increase permeability, allowing unwanted particles into the bloodstream and driving systemic inflammation. Addressing both simultaneously is often necessary for lasting improvement.
Do I need a strict diet long-term?
No. Dietary strategies such as low-FODMAP are typically used short-term and are always individualized. The goal is to restore a gut environment where a varied, healthy diet is tolerable – not to restrict indefinitely.
Can SIBO cause symptoms beyond the gut?
Yes – and this surprises many patients. Because SIBO affects nutrient absorption and drives systemic inflammation, it can contribute to fatigue, brain fog, skin conditions like acne and eczema, joint pain, and mood changes. Treating SIBO sometimes resolves symptoms patients never connected to their gut.
SIBO frequently overlaps with IBS and other digestive concerns. View our full list of digestive conditions treated to explore related issues.
Ready to Start Treatment?
If you’re dealing with ongoing bloating, gas, or IBS symptoms, a personalized approach can help identify and address the root cause.
Book your consultation today to start your personalized SIBO treatment plan