Does your SIBO keep coming back? Learn why recurrence happens, how to heal your gut motility and microbiome, and the functional medicine steps to stop SIBO for good.
When Chaya*, a 32-year-old mom of four, first came to me, she was exhausted — not only from the daily bloating, brain fog, and bathroom struggles, but from the endless cycle of doctor visits. After years of mysterious digestive symptoms, she was finally diagnosed with SIBO (Small Intestinal Bacterial Overgrowth) and prescribed two rounds of antibiotics.
Each time, her symptoms improved — only to return a few weeks later.
She had tried following a low FODMAP diet for months, which helped somewhat, but she wanted real, lasting healing. Her goal was to reintroduce the high-fiber, plant-based foods she loved without pain or fear.
She was caught in a frustrating loop I see all too often: treat, improve, relapse — repeat.
Here’s what I always tell my clients: when SIBO keeps coming back, it’s not just about clearing bacteria — it’s about understanding why the overgrowth happens in the first place.
SIBO 101: Why It Keeps Coming Back
SIBO occurs when bacteria — even healthy bacteria — migrate into the small intestine, where they ferment food too early and produce excess gas. This leads to hallmark SIBO symptoms like bloating, belching, constipation or diarrhea, abdominal pain, fatigue, and brain fog.
But why does SIBO return so often, even after treatment?
One of the most overlooked causes is damage to the Migrating Motor Complex (MMC) — the gut’s natural “cleaning wave” that sweeps bacteria out of the small intestine between meals.
The MMC functions like a broom, sweeping leftover food and bacteria downstream roughly every 90 minutes (starting about 1.5 hours after eating). When this process is impaired, bacteria linger and re-colonize in the wrong places.
How Infections Trigger SIBO
Research from Dr. Mark Pimentel and Dr. Allison Siebecker shows that SIBO often begins after a gut infection or food poisoning. These infections can damage the nerves that control the MMC, setting the stage for chronic bacterial overgrowth.
If you’ve ever had “a bad stomach bug” or food poisoning, that experience may have silently disrupted your gut’s natural cleansing mechanism. Months or years later, it can still be impacting your digestion.
With Chaya, I took a different approach. Instead of chasing symptoms or over-restricting foods, we focused on addressing the root cause with a comprehensive, science-based strategy for long-term relief.
Step 1: Re-Treat SIBO the Smart Way
We began by re-testing to confirm her SIBO gas type and levels. Based on her results, we used targeted herbal antimicrobials — but this time, we added a key ingredient: Partially Hydrolyzed Guar Gum (PHGG).
PHGG is a gentle prebiotic fiber that can make antimicrobial treatment more effective. It helps deliver the treatment deeper into areas where bacteria hide — and when introduced properly, it usually doesn’t worsen symptoms.
I often recommend Sunfiber, one teaspoon daily in water during the treatment phase.
We also used meal spacing (four hours between meals) to activate the MMC between meals — a small but powerful adjustment that can make a big difference.
Step 2: Support Gut Motility After Treatment
This is where most SIBO treatment plans fall short.
Chaya told me that after her antibiotics, she was simply told to “see how you feel.” No maintenance plan. No preventative strategy. That’s a recipe for relapse.
We now know that gut motility must be supported after treatment, especially when the MMC has been impaired.
I placed Chaya on a prokinetic for 12 weeks — a compound that gently stimulates the MMC and keeps the gut moving between meals.
There are both pharmaceutical options (like prucalopride) and herbal options (such as ginger, motility blends, or Iberogast). Chaya preferred a natural motility blend — and within two weeks, her bloating improved and bowel movements became more regular.
This step is non-negotiable in my practice. It’s one of the most effective ways to prevent SIBO from coming back.
Step 3: Use Probiotics Strategically — Not Randomly
Many people with SIBO are told to avoid probiotics for fear they’ll “feed the overgrowth.” But when chosen carefully, the right probiotic strains can help rebalance the gut and prevent relapse.
For Chaya, I recommended:
- Saccharomyces boulardii – A non-pathogenic yeast that supports immune balance, crowds out harmful bacteria, and protects the gut lining.
- Spore-based probiotics – These survive stomach acid and don’t ferment in the small intestine.
- BioGaia Protectis (L. reuteri) – Especially helpful for methane-dominant SIBO, this strain supports motility and helps reduce constipation.
The result? Chaya’s gut stabilized, and she was finally able to reintroduce a wide range of plant-based foods without discomfort.
Step 4: Address the Overlapping Issues That Mimic or Contribute to SIBO
Many clients with “SIBO” actually have co-existing gut issues that need to be addressed for full recovery. In Chaya’s case, two stood out:
- Chronic Constipation – When the bowels don’t move, neither do bacteria. We used magnesium oxide, meal timing, and motility support to restore healthy regularity.
- Low Digestive Enzyme or Bile Function – Often linked to stress or long-term SIBO, this can cause poor breakdown of fats and proteins. We added digestive bitters and enzymes to strengthen her digestion.
The Results: True Healing Beyond Symptom Control
Four months later, Chaya wasn’t just symptom-free — she was thriving.
Her bloating was gone, her energy was back, and her digestion was steady for the first time in years.
Most importantly, she was no longer afraid of food. She had the tools and confidence to maintain her progress — and to enjoy the nourishing, high-fiber foods she once avoided.
Reintroducing diverse, fiber-rich foods isn’t just about variety; it’s a crucial step toward long-term health. A balanced, plant-forward diet supports a resilient gut microbiome, reduces inflammation, and protects against chronic disease.
If you’re struggling with recurrent or stubborn SIBO, remember this:
It’s not because you’ve failed — it’s because the full picture hasn’t been addressed yet. Healing SIBO for good means healing the root cause, not just managing symptoms.