Healing the Digestive Tract: Herbal Antimicrobials, Probiotics, and Dietary Changes for SIBO

For over 25 years, I have worked with people struggling with digestive diseases. I’ve lived through my own healing journey and shared what works in my books and on Listen To Your Gut.

Today, I want to talk about small intestinal bacterial overgrowth (SIBO), a condition that is becoming more common, especially in young women.

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In this blog, I’ll share insights from my recent podcast with Natasha Trenev, founder of Natren probiotics and a true pioneer in gut health. Natasha has over 60 years of experience in this field.

Together, we’ve seen what works and what doesn’t when it comes to treatment of SIBO.

This isn’t just about bacteria in the small intestine. It’s about the digestive tract as a whole—how it functions, what causes disruption, and how we can bring it back into balance using natural treatments.

Watch the full episode of my conversation with Natasha Trenev below. You can watch the video:

Or listen to the podcast:

Listen To Your Gut

Holistic Treatment of SIBO: Natural Remedies, Diet, and Probiotics

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Topics Covered in This Episode:

What SIBO really is (beyond bacterial overgrowth)
Problems with conventional antibiotic treatment
Why many probiotics don’t work for SIBO
The role of the elemental diet and healing foods
Dietary changes that soothe the digestive tract
How wild oregano oil and herbal supplements support healing
The link between thyroid, motility, and SIBO recurrence
Gut-brain connection, stress, and emotional healing tools

What SIBO Really Is

When most people hear SIBO, they think only of bacterial overgrowth in the small intestine. But SIBO is more complex.

It can mimic irritable bowel syndrome (IBS), with overlapping symptoms like abdominal pain, bloating, and digestive discomfort.
It often appears alongside low stomach acid, poor gut motility, and hormonal imbalances like low thyroid.
Many patients chase only the “bad bacteria” problem, using antibiotic therapy or restrictive diets, without looking at the bigger picture.

In reality, the root cause of SIBO involves motility issues, immune dysfunction, food sensitivities, and stress. This is why so many people relapse after standard treatment.

The Problems With Standard Treatment

Doctors often prescribe antibiotic treatment like rifaximin for SIBO. Yes, antibiotics can reduce symptoms. But here’s what I’ve seen:

They don’t restore the gut microbiome.
They may cause antibiotic resistance.
They allow candida yeast and fungal organisms to overgrow.
The relief is usually temporary—symptoms return within weeks or months.

In fact, Natasha and I both agree: relying on antibiotics alone is like putting a band-aid on a deep wound. It does not address dietary changes, lifestyle changes, or the need to replenish good bacteria.

Why Probiotics Matter

In the treatment of SIBO, one of the most powerful steps is to restore the balance of good bacteria in the gut. But not all probiotics are created equal.

I’ve tested products around the world. From Germany to Japan, I looked for alternatives. But only Natren probiotics consistently meet the strict criteria needed to survive stomach acid, reach the small intestine, and stay alive through the expiration date.

Without potent probiotics, you risk wasting time and money. When you’re healing, every step matters.

Diet as a Healing Tool

Healing the digestive tract requires food that is easy to digest. Many SIBO patients turn to the low-FODMAP diet, or even the specific carbohydrate diet. While these can help reduce digestive symptoms, they are not long-term solutions.

From my own experience, and hundreds of thousands of my readers, I recommend:

Cooked vegetables: zucchini, squash, carrots, peeled cucumber.
Cooked fruits: apples, pears, peaches, papaya.
Simple carbohydrates: organic white rice or Japanese Haiga rice.
Bone broth: rich in gelatin; healing for the gut lining.
Healthy fats: butter, ghee, olive oil, avocado oil, coconut oil, or pasture-raised lard or tallow.

Avoid raw foods during the healing phase. Raw produce carries bacteria and is harder to digest when gut motility is impaired.

This approach may feel restrictive at first. But remember, it’s a short-term elimination diet designed to calm your system while you repair the gut microbiome.

I have also written a detailed blog about how to use an Elemental Diet to treat SIBO & IBS

Herbal Antimicrobials

When it comes to clearing harmful bacteria, herbal antimicrobials can be as effective as pharmaceuticals—with fewer side effects.

Wild oregano oil has strong antimicrobial properties. It kills bacteria, yeast, fungi, viruses, even certain parasites.
Other herbal remedies include olive leaf, garlic, neem and grapefruit seed extract.
Unlike antibiotics, these herbs work more gently, supporting long-term gut health. But you still have to take probiotics to replace the bacteria you are killing; this prevents secondary or opportunistic infection.

In clinical trials, herbal supplements performed just as well as rifaximin in SIBO patients. For many, this is encouraging news.

The Role of Gut Motility

A healthy migrating motor complex (MMC) keeps food moving through the digestive tract. When motility slows, food stagnates and bacteria multiply.

Common causes of slow motility include:

Low thyroid function
Chronic stress
Low stomach acid
Hormone imbalances

Supporting healthy motility means:

Chewing food thoroughly to stimulate digestive enzymes.
Eating slowly, giving your body time to produce stomach acid.
Using a mind/body therapy like Lazer Tapping, Somatic Experiencing or Craniosacral (Level 2 or higher) to resolve your stress and trauma.

Without normalizing motility, SIBO often comes back even after strict diets or herbal therapy.

Addressing Nutrient Deficiencies

Because of malabsorption, many SIBO patients suffer from nutrient deficiencies.

Vitamin B12 deficiency is common, leading to fatigue, mood changes, and neurological issues.
Vitamin D and fatty acids also play key roles in overall health and immunity.
If your body isn’t absorbing nutrients, your cells cannot rebuild properly.

Correcting these deficiencies, using a therapeutic nutrient blend like MultiAbsorb Daily Essential, along with crucial minerals like Bone Matrix, is part of restoring long-term balance.

Emotional Health and the Gut-Brain Connection

The gut is often called the “second brain.” Many with SIBO also report anxiety, depression, and stress.

That’s because the gut produces neurotransmitters like serotonin. When the microbiome is disrupted, your mood can spiral.

This is why I created free tools for you, like:

Guided meditation with wild horses for calming fear and loneliness.
Lazer tapping session to release trauma stored in the gut.

Stress management techniques are not optional. They are central to healing. Without addressing stress, the digestive system cannot recover fully.

Lab Testing: Helpful or Misleading?

While tests like the SIBO breath test or stool test can be useful, they are not the ultimate measure of healing.

In one study, 70% of patients reported major symptom relief, even though their breath tests remained abnormal.

That’s why I encourage you: don’t let a lab result override your body’s signals. Listen to your symptoms. Trust how your body feels.

My Recommended Healing Protocol for SIBO

Based on decades of experience, here’s a summary protocol for natural SIBO treatment:

Dietary reset: begin with cooked, soothing foods and possibly the elemental diet under supervision.
Herbal antimicrobials: wild oregano oil and other antimicrobial herbs to reduce overgrowth.
Probiotics: introduce good bacteria daily to restore the gut microbiome.
Digestive enzymes: support low stomach acid and improve absorption.
Nutrient supplementation: correct deficiencies like vitamin B12 and vitamin D.
Lifestyle changes: manage stress, avoid alcohol, reduce toxin exposure.
Long-term support: continue with probiotics, mind/body therapy, and balanced nutrition to prevent recurrence.

Final Thoughts

After decades of working in natural healing, one truth stands out: the body can heal itself when given the right tools.

SIBO is not a life sentence. By addressing the root cause, nourishing the digestive tract, using a good mind/body therapy, and restoring balance with herbal treatments, probiotics, and dietary changes, you can move from chronic symptoms to lasting health.

If you’d like more guidance, watch or listen to the full podcast episode with Natasha above.

And remember: listen to your gut. It always knows the way.