#117: So, you think you have SIBO?
Underlying Causes, Symptoms, Diagnosis, Herbal vs. Antibiotic Treatment
From my vantage point, it seems like everyone either has or thinks they have SIBO lately—and many are on some kind of protocol to eliminate this overgrowth of microbes in the small intestine.
But like many gut-related disorders, SIBO’s symptoms, diagnosis, and treatment aren’t always straightforward.
Let’s clear up some confusion…
What is SIBO?
Simply put, SIBO (Small Intestinal Bacterial Overgrowth) is just that—too much bacteria in the small intestine.
Most of our gut bacteria (aka the microbiome) reside in the large intestine. Stomach acid and pancreatic enzymes help keep the small intestine relatively low in bacteria. When these barriers are weakened, overgrowth can occur.
What Causes SIBO?
There’s no one root cause. It’s usually due to disrupted motility, structure, or secretions. Common causes include:
Post-infectious — food poisoning or gastroenteritis
Structural abnormalities — removal of the ileocecal valve, diverticula, adhesions from surgery, weight-loss surgery
Low stomach acid — gastritis, chronic PPI use, H. pylori
Slow motility — due to narcotics, anticholinergic meds, hypothyroidism, Sjögren’s, connective tissue disease, Crohn’s strictures
Small intestinal inflammation — NSAID overuse, Crohn’s, unmanaged celiac disease
Low pancreatic enzymes — exocrine pancreatic insufficiency
Chronic alcohol overuse
End-stage kidney disease
What Does SIBO Feel Like?
While symptoms vary, some classic SIBO red flags include:
Gas and bloating shortly after meals (30–60 minutes post-eating)
Mornings are often better
Triggered by FODMAPs, sugar, carbs, fat
Abdominal discomfort or pain
Nausea
Acid reflux
Brain fog
Fat malabsorption in some cases (leading to oily/floating stools, weight loss, fat-soluble vitamin deficiencies)
And while many associate SIBO with diarrhea, certain bacteria (especially methane-producing) can cause constipation instead.
Bottom line: SIBO symptoms mimic many other conditions. You can’t diagnose it by symptoms alone.
How Is SIBO Diagnosed?
Breath testing is the current gold standard—although not perfect. Stool testing is not a valid method.
How the breath test works:
Arrive fasted
Provide a baseline breath sample
Drink a sugar solution (usually lactulose or glucose)
Breathe into a bag every 15–20 minutes for 3 hours
Machine measures hydrogen/methane gas levels
How to Reduce Testing Errors:
No colonoscopy or endoscopy within 4 weeks
Avoid the following before testing:
Antibiotics: stop 4 weeks prior
Probiotics: stop 2–4 weeks prior
Motility agents (e.g., Linzess, magnesium): stop 3–5 days prior
Follow a low-fermentation diet the day before (e.g., plain chicken, white rice, hard cheese, clear broth)
Fast 12 hours before (only water)
Avoid exercise, gum, smoking 1 hour before and during the test
Coming soon: At-home diagnostic capsules are in development and may eventually offer more accurate insights into intestinal bacterial load.
What’s the Best Way to Treat SIBO?
Right now, the only evidence-backed treatment is antibiotics—usually rifaximin, sometimes paired with neomycin or metronidazole, depending on gas type.
Some small studies suggest herbal protocols can be just as effective as rifaximin. But these studies are limited, lack large randomized control, and don’t offer clear guidance on strains or dosages.
That said, some clinicians use herbals when patients prefer a more natural approach.
Why Not Try Herbal Treatment First?
Herbal protocols (like Candibactin AR/BR or Biocidin) are not risk-free. They can have side effects, and unlike pharmaceuticals, are not regulated for potency or purity, meaning dosing and efficacy can vary widely.
Common herbs and their side effects:
Berberine – GI upset, headache, constipation, drug interactions (CYP450)
Oregano oil – Nausea, burping, burning, allergic reactions
“Wait… don’t antibiotics have side effects too?”
Yes—antibiotics can cause:
GI symptoms: nausea, cramping, gas, diarrhea
Yeast infections
Headaches
Altered taste
Antibiotic-associated diarrhea (including C. difficile)
But there are caveats:
Rifaximin, the most commonly prescribed antibiotic for SIBO, is poorly absorbed—so it acts locally in the gut with fewer systemic side effects…
And a short course of rifaximin won’t wipe out your entire microbiome. Bacterial populations typically rebound within weeks of stopping treatment.
Here’s a silly analogy to sum up my recommendations:
Using rifaximin is like following a GPS—you know the route, even if there’s some traffic. Herbal protocols are more like using a hand-drawn map—might get you there, but not without a few wrong turns.
Can Diet Treat SIBO?
Diet can help manage symptoms—but it won’t eliminate SIBO.
A low FODMAP diet reduces fermentable carbohydrates that fuel gas production in the small intestine. While not curative, it can significantly reduce bloating, gas, and pain.
In my practice, I often pair a short-term low FODMAP plan with antibiotic (or herbal) treatment to maximize relief.
Final Thoughts on SIBO Treatment
I get the appeal of going natural. If a client prefers the herbal route, I provide the guidance and resources to do it safely.
My job is to present the evidence and the unknowns—their job is to choose what feels right for them.
Still have questions? Leave them below or send a DM on Instagram.
Until the next edit,
Lydia