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Understanding SIBO: What It Is, What Causes It, and How to Treat It

August 18, 2025

Ever feel like your gut is working against you?

Instead of feeling content and nourished after a meal, you’re left with painful gas, unpredictable digestion, and bloating that makes your stomach feel like a balloon.

Maybe you’ve tried to “fix” it—filling your plate with veggies and whole grains—only to feel worse. Or maybe your doctor dismissed your concerns, chalking it up to IBS or stress, even though you know something isn’t right.

Trust your gut—literally. Those persistent symptoms might be pointing to small intestinal bacterial overgrowth (SIBO).

SIBO is often misunderstood, even by healthcare professionals. Its symptoms mimic other digestive disorders, leaving many people with vague diagnoses and ineffective treatments.

But SIBO is real, and it’s more than just an inconvenient nuisance. This gut imbalance can affect digestion, energy, mood, and overall health.

To make matters worse, the very foods you thought were helpful might be fueling the problem.

The good news? You don’t have to live like this.

In this article, you’ll learn what SIBO is, why it happens, and how to take back control of your gut health. Because you deserve real answers, real relief, and a gut that works with you.

First Things First: What’s SIBO?

SIBO occurs when bacteria that normally reside in other parts of your digestive tract migrate to and multiply in your small intestine, where they don’t belong.

These bacteria ferment carbohydrates and produce hydrogen gas (H₂). (Keep carbohydrate fermentation in mind—it’ll be important when you learn about dietary interventions.)

Your gut is also home to a different type of microbe called archaea, which aren’t bacteria at all. (If it’s been a while since your last high school science class, microbe is simply another name for microscopic organisms, like bacteria and fungi, that live all around you—including in your body.)

Archaea consume this hydrogen and go on to produce methane gas (CH₄).

Both hydrogen and methane gas in your small intestine can cause hallmark SIBO symptoms, like bloating and that uncomfortable feeling that you’re suddenly carrying triplets.

There are three primary categories of SIBO based on dominant symptoms:

SIBO-D (diarrhea-dominant) comes with frequent loose stools, bloating, cramping, and urgency. It’s typically caused by hydrogen- or hydrogen sulfide-producing bacteria.
SIBO-C (constipation-dominant) comes with abdominal bloating and hard, infrequent stools. It’s often linked to methane-producing archaea.
Mixed Type alternates between diarrhea and constipation.

These aren’t the only symptoms to keep an eye out for, though. SIBO can affect your entire body.

What Are the Common SIBO Symptoms?

If you have SIBO, you might struggle with:

Digestive symptoms: Gas, bloating, constipation, diarrhea, and abdominal discomfort are the most common signs of SIBO.
Nutrient deficiencies and fatigue: Bacteria in the small intestine consume essential nutrients like B12, magnesium, and iron before your body can absorb them. This can lead to fatigue, weakness, and even neurological symptoms.
Mood disruptions: The gut-brain connection means SIBO often contributes to anxiety, depression, and brain fog. Inflammation and imbalances in your gut bacteria can interfere with serotonin production and cortisol balance, leading to heightened mental health struggles. (Importantly, these symptoms aren’t “just in your head”—they’re a reflection of your gut’s health.)
Systemic inflammation: Toxins released by bacteria can trigger widespread inflammation, affecting your energy, memory, and immune function.
Skin irritation: Issues like rosacea, psoriasis, and even systemic sclerosis can be linked to SIBO.

What Causes SIBO?

Your body is equipped with several defenses to keep bacteria from overgrowing in your small intestine:

Stomach acid creates an acidic environment that kills harmful bacteria.
Bile secreted by your liver prevents bacterial growth while aiding digestion.
Immunoglobulins live in your small intestine and serve as a frontline defense to fight off bacteria and other pathogens.
The ileocecal valve is a one-way valve that allows digested material to flow from your small intestine into your large intestine—keeping bacteria in your large intestine.
The migrating motor complex (MMC) is a cyclical wave of muscular contractions in the walls of your stomach and small intestine that clears waste and bacteria from your small intestine during fasting periods.

When these defenses weaken or fail—due to factors like low stomach acid, bile deficiencies, motility issues, or immune dysfunction—bacteria can set up camp in your small intestine.

For example, a bad bout of food poisoning could damage your MMC enough to set you up for SIBO. Research shows that after an episode of infectious gastroenteritis, your risk of developing irritable bowel syndrome (IBS)—which is closely linked to SIBO—increases by up to six times.

Another risk factor? Certain medications. Proton pump inhibitors (PPIs), for instance, may suppress your stomach acid—opening the door for SIBO.

How Is SIBO Diagnosed?

Because SIBO can overlap with so many other conditions (like leaky gut and small intestinal fungal overgrowth), an accurate diagnosis is the first step to relief.

A simple breath test measures hydrogen, methane, and hydrogen sulfide gas levels to confirm SIBO and identify its type. Your doctor can order a breath test for you, or you can get a breath test kit online.

False negatives can occur, so it’s essential to work with an experienced practitioner who can guide you through proper test preparation and substrate selection. Retest after treatment to ensure the overgrowth is resolved.

Now that you’ve learned your SIBO foundations, let’s explore what you can do about it.

Diet: The First Line of Defense Against SIBO

As you’ve probably noticed by now, some foods move through your digestive system without much trouble, while others cause chaos.

That’s where FODMAPs come in.

FODMAPs—fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (yep, it’s a mouthful)—are a specific group of carbohydrates found in a wide variety of foods.

They can be incredibly nutritious for folks with healthy guts. Veggies, whole grains, beans… this is the stuff many “healthy diets” are made of.

But with SIBO, bacteria start munching on these carbs too early—up in your small intestine where they’ve camped out—meaning gas starts building up where it shouldn’t.

By the time FODMAPs reach your large intestine, the fermentation can be like a runaway train, exacerbating symptoms like flatulence, bloating, abdominal pain, and reflux.

Basically, FODMAPs can be serious troublemakers for folks with SIBO.

A low-FODMAP diet can starve bacteria of their primary fuel source—reducing unpleasant symptoms and improving your overall gut health.

Here’s a quick overview of how to do it:

1. Start with an elimination diet.

Limit high-FODMAP foods, like onions, garlic, legumes, milk, honey, high-fructose corn syrup, and certain fruits. You may also want to temporarily minimize high-fiber foods, which can also exacerbate SIBO symptoms.

Stick with this low-FODMAP plan for 6–12 weeks to starve the bacterial overgrowth. (Heads up: This diet can be challenging, but tools like the Monash University FODMAP app can help you identify problematic foods and track your symptoms. And remember, it’s temporary!)

2. Reintroduce FODMAPs gradually.

After all your symptoms subside, you can slowly start reintroducing foods. Try one FODMAP at a time so you can identify which ones your body can (or can’t) tolerate. Don’t reintroduce alcohol or sugar into your diet until you have gone at least three months with no SIBO symptoms.

3. Restore balance.

Include prebiotic foods (like mushroom, onions, and apples) and probiotic foods (like yogurt, kefir, and sauerkraut) once your symptoms are under control to rebuild your gut microbiome.

Importantly, the low-FODMAP diet is not a long-term, standalone solution. It’s simply an elimination phase to provide some quick relief.

Long-term restriction can deplete the beneficial gut bacteria in your large intestine, so it’s important to balance food restrictions with strategies to restore gut flora.

Since this diet can be tricky, it helps to work with a functional medicine doctor, nutritionist, or health coach for extra guidance.

Going Beyond Diet: Holistic Treatment Strategies

Recovering from SIBO requires a multi-pronged approach.

While you’re symptomatic:

Starve the bacteria: Go low-FODMAP to cut bacteria off from their food source. (That said, listen to your body here. You may have to experiment with different dietary approaches to see what works best for you. For example, many patients also see strong results with my 10-Day Detox , which can be a game-changer for GI discomfort. Or, you might do better with a ketogenic diet or a fasting protocol.)
Eradicate overgrowth: Use herbal antimicrobials or antibiotics tailored to your SIBO type to knock out pesky bugs.
Support digestion: Add digestive enzymes and hydrochloric acid (HCl) supplements to boost your digestive health.
Detoxify: Incorporate activated charcoal or bentonite clay. As bacteria die off, they release toxins—these binders help flush them out.

(My SIBO Recovery Protocol and its corresponding Phase 1 Recovery Stack include all the tools you need here.)

Once your symptoms have resolved:

Rebuild gut flora: Restore balance in your gut microbiome with prebiotics and probiotics.
Prevent relapse: Address underlying causes, like MMC dysfunction, with prokinetics and lifestyle changes. A functional medicine doctor can help if you need more advanced support.

Preventing Relapse: Long-Term Strategies

SIBO has a high recurrence rate, making relapse prevention a critical part of treatment.

Here’s how to maintain your progress:

Eat a balanced diet: Emphasize a diverse, whole-food diet to support gut health. Avoid extreme dietary restrictions that could harm your microbiome. Continue minimizing sugar, alcohol, and gluten, which are SIBO’s preferred snack foods.
Continue supporting digestion: Keep taking digestive enzymes, hydrochloric acid (as tolerated), and probiotics for ongoing digestive support.
Incorporate prokinetics: Support your MMC and prevent bacterial buildup with natural or prescription prokinetics, if you have SIBO-C. A functional medicine doctor can provide guidance here.
Get regular testing: Catch overgrowth early with periodic breath tests.
Manage your stress: Practice mindfulness, meditation, and other self-care strategies to reduce chronic stress, which can impair motility and weaken your immune system.
Live a healthy lifestyle: Prioritize adequate sleep and regular physical activity to support digestion and immunity.