Basic SIBO Protocol: A protocol for naturally treating SIBO effectively.

Small Intestinal Bacterial Overgrowth (SIBO) affects thousands of people worldwide, causing uncomfortable symptoms like bloating, gas, diarrhea, and abdominal pain. Many struggle to find lasting relief because SIBO requires a targeted approach that addresses its root causes. This post offers a clear, natural protocol to support your body’s healing process and restore gut balance effectively.

What Is SIBO and Why It Is Often Missed

If you’re constantly bloated, reacting to foods, dealing with constipation or diarrhea, and feel like nothing is working… there’s a high chance you’re not dealing with “just IBS.”

You may be dealing with SIBO (Small Intestinal Bacterial Overgrowth).

SIBO happens when bacteria that are supposed to stay in your large intestine start growing in your small intestine, where they don’t belong. Most treatments only address the bacteria, and almost none address why it happened. That’s why so many people go through rounds of antibiotics, diets, and supplements… and it keeps coming back.

Common Signs You May Have SIBO

SIBO doesn’t always show up the same way, but these are the most common patterns I see in patients:

• Bloating (especially after eating...even “healthy” foods)

• Gas and abdominal pressure

• Constipation, diarrhea, or alternating both

• Food sensitivities that keep increasing

• Brain fog and fatigue after meals

• Nutrient deficiencies (iron, B12, vitamin D)

• Feeling full quickly or uncomfortable after eating small amounts

If you’ve been told “your labs are normal” but you feel like this daily, something deeper is being missed.

What Actually Causes SIBO: The Root Issues Most People Miss

SIBO develops when your gut environment breaks down.

There are three major systems I look at with every patient:

1. Low Stomach Acid & Weak Digestion

Your stomach acid is your first defense against bacteria.

When it’s low:

• Bacteria survive when they shouldn’t

• Food sits longer and ferments

• Gas and bloating increase

This is extremely common in people with:

• Thyroid dysfunction (especially Hashimoto’s)

• Chronic stress

• Long-term use of acid blockers

• H. pylori history

  
  

2. Slow Gut Motility (This Is HUGE)

Your gut has a built-in “cleansing wave” called the migrating motor complex (MMC).

It sweeps bacteria out between meals. If this slows down it causes bacteria to build up and SIBO develops.This is one of the biggest reasons people relapse.

Common causes:

• Eating too frequently (no gaps between meals)

• Nervous system dysregulation

• Low thyroid function

• Blood sugar instability

• Post-viral or post-infectious gut damage

  
  

3. Structural or Functional Disruptions

Sometimes the issue is physical or mechanical:

• Prior abdominal surgery

• Adhesions

• Gallbladder removal

• Ileocecal valve dysfunction

If flow through the gut is disrupted, bacteria accumulate.

How SIBO Affects Your Labs

SIBO doesn’t just affect digestion, it affects your entire body.

Because nutrients aren’t absorbed properly, I commonly see:

• Low ferritin (iron stores) fatigue, hair loss

• Low B12 brain fog, nervous system symptoms

• Low vitamin D immune + hormone issues

• Imbalanced folate

If you’re trying to “fix deficiencies” without fixing your gut, you’ll stay stuck.

How to Test for SIBO

The most common test is a breath test using lactulose or glucose.

It measures:

• Hydrogen (often diarrhea type)

• Methane (often constipation type)

• Hydrogen sulfide (less commonly tested, but important)

But testing alone isn’t enough. You also need to ask: Why did this happen in the first place?

That’s where functional labs come in to look at the whole picture:

• Full thyroid panel (NOT just TSH and T4)

• Iron panel + ferritin

• B12 and folate

• Gut testing (when needed)

  
  

The Functional Medicine SIBO Protocol:

Depending on type of SIBO and how aggressive the approach needs to be the Elemental Diet may or may not be part of the recommended protocol.

Phase 1: Reduce the Bacterial Overgrowth

Herbal Antimicrobials

• Oregano oil

• Berberine

• Neem

• Allicin (especially for methane types)

  
  

Elemental Diet (Most Aggressive + Most Effective)

This is a short-term liquid nutrition protocol that:

• Starves bacteria

• Feeds your body

• Reduces symptoms quickly

For severe or stubborn cases, this can be a game-changer. Not all cases. of SIBO will require the Elemental Diet. Do not attempt this portion of the protocol unless being monitored by a physician or practitioner.

Phase 2: Reduce Symptoms with Diet

Common approaches:

• Low FODMAP

• SIBO Bi-Phasic Diet

• Specific Carbohydrate Diet

These reduce fermentation and give your gut a break. But if diet is all you do, SIBO will come back.

Phase 3: Rebuild Digestion

If digestion is weak, bacteria will always return.

This is where we support:

• Stomach acid

• Digestive enzymes

• Bile flow

This step is often skipped and it’s a major reason protocols fail.

Phase 4: Restore Motility (Prevents Relapse)

Without proper motility, SIBO WILL come back.

We focus on:

• Meal spacing (4–5 hours between meals)

• Prokinetic support (natural or targeted)

• Nervous system regulation

  
  

Phase 5: Fix the Root Cause

This is what makes results stick. We identify and correct:

• Thyroid dysfunction

• Chronic stress/nervous system imbalance

• Hormonal issues

• Blood sugar instability

• Post-infectious damage

If this step is skipped, you stay in a cycle.

Why Most SIBO Treatments Fail

Because they only do one of these:

• Kill bacteria

• Change diet

But they ignore:

• Motility

• Digestion

• Root cause

SIBO is more than a gut issue, it’s a system regulation issue.

Our Approach

When I work with clients, we don’t guess. We:

1. Identify your type of SIBO

2. Map your root causeBuild a step-by-step protocol

3. Support your body through each phase

4. Prevent relapse (this is the most important part)

   
   

We can help!

If you’ve been stuck in cycles of:

• Bloating

• Food reactions

• “Trying everything”

• Temporary relief with no lasting results

We hope the basic information provided helps to point you in the right direction. If you need help reach out and let us know! We’ll build a plan specific to your body, your labs, and your symptoms, so you can finally move forward.