If you’ve been diagnosed with SIBO (Small Intestinal Bacterial Overgrowth), you’re not alone. It’s one of the most common and frustrating digestive conditions I see in clinic. Many people go through treatment, experience relief, then find their symptoms creeping back weeks or months later. The cycle repeats, and hope begins to fade. But here’s what I want you to know: SIBO relapse isn’t inevitable. Understanding why it happens is the first step toward lasting healing.
What is SIBO?
SIBO occurs when bacteria that normally live in the large intestine migrate upward and overgrow in the small intestine. The small intestine is meant to be relatively low in bacterial count – it’s where we absorb most of our nutrients. When bacteria proliferate here, they ferment the food we eat before we can properly digest it, producing gas and other byproducts that cause uncomfortable symptoms.
Common signs of SIBO include:
- Bloating (especially after meals)
- Abdominal pain or cramping
- Diarrhoea, constipation, or alternating between both
- Excessive gas, smelly gas and belching
- Food intolerances that seem to multiply
- Fatigue and brain fog
- Joint pain
- Nutrient deficiencies despite eating well
SIBO can feel all-consuming. It affects not just your digestion, but your energy, your mood, your social life, and your relationship with food.
Common Naturopathic Approaches to SIBO Treatment
Treatment for SIBO typically involves a multi-pronged approach. Here are just some of the examples.
Antimicrobial Therapy
Herbal antimicrobials like oregano oil, berberine, neem, and allicin can reduce bacterial overgrowth without the harsh side effects of antibiotics. These natural compounds are selective, targeting problematic bacteria while being gentler on beneficial microbes.
Dietary Modifications
Low FODMAP diets, the Bi-Phasic Diet, or Specific Carbohydrate Diet can help reduce fermentation and starve the overgrown bacteria. The goal is to ease symptoms while treatment works, not to restrict forever.
Gut Healing Support
L-glutamine, zinc carnosine, slippery elm, and aloe vera can help repair the intestinal lining that may have been damaged by the overgrowth and inflammation.
Prokinetic Support
Herbal prokinetics like ginger and gentian help restore the migrating motor complex (MMC) which is the wave-like contractions that sweep the small intestine clean between meals.
Prebiotic and Probiotic Therapy
Carefully selected strains can help restore microbial balance once the overgrowth is addressed. Timing matters here, introducing these too early can sometimes worsen symptoms.
These approaches work. I’ve seen many clients experience significant relief within weeks of starting treatment. But then for some…. the symptoms return.
Why Do People Relapse After SIBO Treatment?
Here’s the truth that’s often missed: SIBO is not the disease. It’s the end result!
Think of SIBO as smoke billowing from a fire. You can clear the smoke (treat the bacterial overgrowth), but if the fire is still burning (the root cause remains), the smoke will return.
Most standard SIBO protocols focus on reducing the bacterial overgrowth. And while that’s essential, it’s only half the picture. If we don’t address why the bacteria overgrew in the first place, the conditions that allowed SIBO to develop remain and relapse becomes almost inevitable.
Common Root Causes of SIBO
Insufficient Stomach Acid
This is the most common issue I see. Stomach acid is your first line of defence against unwanted bacteria. It sterilises food, signals digestive processes downstream, and keeps bacteria from traveling upward. When stomach acid is low (often from stress, age, or prolonged antacid use), bacteria can survive the journey into the small intestine.
Impaired Gut Motility
The migrating motor complex (MMC) is like a housekeeper for your small intestine, it sweeps through between meals, clearing out debris and bacteria. When motility is sluggish (due to food poisoning, hypothyroidism, nerve damage, or certain medications), bacteria linger and multiply.
Bile Flow Issues
Bile doesn’t just digest fats- it also has antimicrobial properties. When bile production or flow is compromised (often related to liver congestion, gallbladder dysfunction, or stress), bacteria can flourish unchecked.
Insufficient Digestive Enzymes
Without adequate enzymes, food sits partially digested in the small intestine, becoming a feast for bacteria. Enzyme insufficiency can stem from pancreatic dysfunction, chronic stress, or nutrient deficiencies.
Chronic Stress
This is the big one. Stress shuts down “rest and digest” mode, reducing stomach acid, enzyme production, bile flow, and motility all at once. It also alters the gut-brain axis and changes the microbial environment. You simply cannot heal your gut without addressing stress.
Prolonged Antibiotic or Antacid Use
Antibiotics disrupt the entire gut ecosystem, often leading to dysbiosis that sets the stage for SIBO. Antacids suppress stomach acid, removing a crucial protective barrier.
Dietary Patterns
Overconsumption of refined sugars and processed foods feeds problematic bacteria. A diet lacking in diversity also weakens the microbiome’s resilience.
Structural or Nerve Issues
Conditions like IBS, IBD, endometriosis, adhesions from surgery, or vagus nerve dysfunction can physically impair gut function and create an environment where SIBO thrives.
Food Poisoning
A bout of gastroenteritis can damage the nerves in the gut, affecting motility. This is why some people develop SIBO seemingly “out of nowhere” after a bad travel bug.
How to Prevent SIBO Relapse
Support Stomach Acid Production
If low stomach acid is suspected, we can support it naturally with:
- Bitter herbs before meals (dandelion, gentian, rocket)
- Apple cider vinegar or lemon water with meals
- Betaine HCl supplementation (under practitioner guidance)
- Reducing antacid use where possible
- Addressing the stress response (see below)
Restore Gut Motility
Motility is essential for keeping the small intestine clear. We support this with:
- Prokinetic herbs like ginger, gentian, barberry, artichoke.
- Vagus nerve stimulation practices (gargling, singing, humming, cold water exposure)
- Eating regular meals with 4-5 hours between (no constant grazing)
- Addressing thyroid function or other underlying conditions
- Incorporating gentle movement like walking after meals
Optimise Bile Flow and Liver Function
Supporting your liver and gallbladder helps maintain antimicrobial bile production:
- Bitter greens (rocket, dandelion, radicchio)
- Adequate healthy fats in the diet
- Herbal support like St Mary’s thistle, globe artichoke, or dandelion root.
- Staying well-hydrated
Enhance Digestive Enzyme Activity
Enzymes can be supported with:
- Chewing food thoroughly (digestion begins in the mouth)
- Eating mindfully, not rushed or distracted
- Supplemental digestive enzymes if needed
- Addressing zinc and B vitamin status
Address Chronic Stress. The Non-Negotiable
This is where the real, deep work happens. You cannot out-supplement stress. Your nervous system state directly impacts every aspect of digestion.
Stress management isn’t just about bubble baths (althought, theyre great!), it’s about creating sustainable practices that shift you out of fight-or-flight and into rest-and-digest mode:
Nervous System Regulation
- Breathwork (box breathing, 4-7-8 breathing)
- Vagus nerve exercises
- Yoga, tai chi, or gentle movement
- Spending time in nature
- Somatic practices or body-based therapy
- Identifying stressful circumstances and people in your life and addressing that
Sleep Hygiene
- Prioritise 7-9 hours of quality sleep
- Consistent bedtime routine
- Dark, cool sleeping environment
- Reduce screen time before bed
Mindfulness and Connection
- Meditation or prayer practices
- Journaling
- Time with loved ones
- Activities that bring you joy and presence
Professional Support
- Counselling or therapy when needed
- Bodywork (massage, acupuncture, osteopathy)
- Working with practitioners who see you as a whole person
Nourish Your Body Mindfully
Rather than restrictive eating long-term, we aim to rebuild food freedom:
- Gradually reintroduce a diversity of plant foods (aiming for 30+ types per week)
- Include fermented foods when tolerated (sauerkraut, kefir, kimchi)
- Balance blood sugar with regular, nourishing meals
- Stay hydrated
- Honour your hunger and fullness cues
Work with Your Unique Story
Every person’s SIBO picture is different. Your triggers, your history, your body’s needs. They’re uniquely yours. This is why cookie-cutter protocols often fall short. True healing requires understanding your root causes and building a plan that fits your life, your body, and your goals.
When It’s Time for Guided Support
If you’ve been stuck in the SIBO relapse cycle, feeling like you’ve tried everything, or struggling to navigate this alone – you don’t have to. Working with an experienced naturopath means you get:
- Comprehensive assessment of your unique root causes
- Functional testing if needed (breath tests, stool analysis)
- A personalised treatment plan that addresses the whole picture
- Support through every phase of healing
- Someone in your corner who believes your symptoms are real and valid
Healing from SIBO isn’t just about killing bacteria. It’s about restoring the conditions for gut health, and that means working with your nervous system, your lifestyle, your whole self.
If you’re ready to break the cycle and finally experience lasting relief, I’d love to support you. You can book a consultation with me, Ash, at BioSoul Naturopathy here in Kalamunda, Perth Hills. Together we’ll craft a plan that honours your body, your story, and your path to wellness.