It is a scenario we see in our clinic every single day.

A patient walks in, frustrated and exhausted. They tell us, “I wake up with a flat stomach, but by 4 PM, I look six months pregnant. I eat healthy, I exercise, but everything triggers me. My previous doctor told me it’s just IBS, told me to eat more fiber, and sent me home. But the fiber made it worse.”

Does this sound like you?

For years, Irritable Bowel Syndrome (IBS) has been a “wastebasket diagnosis”—a label given to patients when doctors can’t find a visible cause for their stomach pain, bloating, and irregular bowel movements.

But medical science has advanced. We now know that for a large percentage of people diagnosed with IBS (some studies suggest up to 60-70%), the root cause isn’t just a “sensitive gut.” It is a treatable condition called SIBO (Small Intestinal Bacterial Overgrowth).

If you feel like you are fighting a losing battle with bloating, you might not have IBS. You might have SIBO. Here is everything you need to know about the difference, the diagnosis, and the cure.

What is SIBO?

To understand SIBO, you have to understand the geography of your gut.

Your digestive tract has two main sections for processing food:

1. The Small Intestine: This is where food is digested and nutrients are absorbed. It is meant to be relatively clean, with low levels of bacteria.
2. The Large Intestine (Colon): This is where waste goes. It is teeming with trillions of bacteria (the microbiome) that help ferment fiber and produce vitamins.

SIBO happens when the bacteria from the colon migrate upwards and set up camp in the small intestine.

When these bacteria overgrow in the small intestine, they interfere with digestion. Instead of your body absorbing your food, these bacteria get to it first. They feast on the carbohydrates you eat and ferment them rapidly.

This fermentation releases gas (hydrogen, methane, or hydrogen sulfide) trapped in the narrow tube of your small intestine. The result? profound, painful bloating that feels like trapped air.

 

 

The “Tell-Tale” Signs: SIBO vs. IBS

Because SIBO is often a cause of IBS symptoms, the two look very similar. However, there are specific clues that point toward SIBO specifically.

1. The Timing of the Bloat

This is the biggest clue.

• Typical IBS: You might feel generally uncomfortable or have cramping, but bloating varies.
• SIBO: The bloating is directly tied to eating. You typically wake up with a flat stomach (because the bacteria have “fasted” overnight). However, within 60 to 90 minutes of eating breakfast or lunch, the bloating begins and progressively worsens throughout the day.

2. Fiber Intolerance

Doctors often tell IBS patients to “eat more fiber” or take Metamucil.

• The SIBO Reaction: Fiber is the favorite food of gut bacteria. If you have SIBO, eating a big salad, an apple, or taking fiber supplements often feels like pouring gasoline on a fire. You get more bloated, not less.

3. Probiotics Make You Worse

• The SIBO Reaction: Many people take probiotics to help their gut. But if you already have too many bacteria in your small intestine, adding more bacteria (even the “good” kind) can exacerbate the overcrowding and make symptoms worse.

4. Low Iron or B12 (Malabsorption)

• The SIBO Reaction: Because the bacteria are sitting in your small intestine (where nutrient absorption happens), they can steal your nutrients. We often see SIBO patients with low Vitamin B12 or Iron levels despite a healthy diet.

The 3 Types of SIBO (Gas Types Matter)

Not all SIBO is the same. The symptoms you experience depend on the type of gas the bacteria are producing. This distinction is critical for treatment.

1. Hydrogen SIBO:
   • Associated with: Diarrhea (IBS-D).
   • Mechanism: Hydrogen gas can speed up gut transit, causing urgency and loose stools.

1. Methane SIBO (IMO – Intestinal Methanogen Overgrowth):
   • Associated with: Severe Constipation (IBS-C).
   • Mechanism: Methane gas acts as a paralytic to the gut. It slows down peristalsis (muscle contractions), causing severe constipation that is resistant to laxatives.

1. Hydrogen Sulfide SIBO:
   • Associated with: “Rotten egg” smelling gas, bladder pain, and body aches.

Why Did I Get SIBO? (The Root Cause)

You cannot cure SIBO permanently unless you address why the bacteria are there in the first place. The small intestine has a self-cleaning mechanism called the Migrating Motor Complex (MMC). It’s a wave of muscle contractions that sweeps bacteria down into the colon between meals.

If your MMC is broken or slow, bacteria build up. Common causes include:

• Food Poisoning: A past bout of severe food poisoning (Salmonella, E. coli) can damage the nerves of the gut, slowing the MMC. This is called “Post-Infectious IBS.”
• Chronic PPI Use: Proton Pump Inhibitors (acid reflux meds) lower stomach acid. Acid is your body’s natural disinfectant; without it, bacteria can survive and multiply where they shouldn’t.
• Abdominal Surgery: Previous surgeries (C-sections, appendectomies, gastric bypass) can create scar tissue (adhesions) that interferes with the flow of the intestine.
• Hypothyroidism: Low thyroid function slows down every system in the body, including gut motility.

The Diagnosis: The Breath Test

The good news is that you don’t need invasive surgery to diagnose SIBO. We use a simple, non-invasive Lactulose Breath Test.

How it works:

1. You drink a solution containing a sugar called lactulose. Humans cannot digest lactulose, but bacteria love it.
2. You breathe into a tube every 15-20 minutes for 3 hours.
3. The Logic: If bacteria are present high up in the small intestine, they will eat the sugar and produce gas early in the test (within the first 90 minutes).
4. The machine measures the levels of Hydrogen and Methane in your breath to confirm the diagnosis and the type of SIBO.

 

 

How We Treat It: The “Kill and Restore” Protocol

Treating SIBO is a process, not a quick fix. It usually involves three phases.

Phase 1: Reduce the Bacteria (The “Kill” Phase)

We need to lower the bacterial load in the small intestine. We typically use:

• Antibiotics: The most common is Rifaximin (Xifaxan). Unlike other antibiotics, Rifaximin stays in the gut and isn’t absorbed into the blood, making it very safe with few systemic side effects.
• Herbal Antimicrobials: For patients who prefer a natural route, specific herbs like Oregano Oil, Berberine, and Neem can be effective, though the course of treatment is longer (4-6 weeks vs. 2 weeks).

Phase 2: Starve the Bacteria (Diet)

During and immediately after treatment, we often prescribe a Low FODMAP Diet or a Specific Carbohydrate Diet (SCD). These diets temporarily remove the fermentable carbohydrates that feed the bacteria. This reduces bloating and prevents the bacteria from rebounding quickly.

Phase 3: Restore Motility (Prevention)

This is the step most people miss, leading to relapse. Once the bacteria are gone, we must ensure the “cleaning wave” (MMC) is working again.

• We prescribe Prokinetics (motility agents). These can be low-dose prescription medications or natural supplements like Ginger and Artichoke extract taken before bed to stimulate the gut to “sweep” itself while you sleep.

Conclusion: You Are Not “Just” Anxious

For many of our patients, a SIBO diagnosis is a relief. It validates that the pain is real, physiological, and not “all in your head.”

If you have been managing “IBS” for years with little success, or if your bloating is affecting your quality of life, it is time to dig deeper. SIBO is treatable. You do not have to live with the bloat forever.