Why Does SIBO Relapse? And How to Prevent It
Ever wonder why your SIBO keeps coming back, even after you’ve followed all the right interventions and eradicated the bacterial or archaea overgrowth? Maybe you’ve done the diet, taken the antimicrobials, and followed every step of the protocol... only to have your SIBO relapse a few months later.
The truth is, SIBO isn't just an overgrowth you can clear and forget about. It’s the result of deeper gut imbalances that, if left unaddressed, allow it to keep recurring. Studies and clinical experience suggest that SIBO relapse rates can be as high as 40-60% within a year with conventional approaches that only target the overgrowth.
But the good news is with the right strategy, you can stop the cycle of recurring SIBO and eliminate SIBO for good. In this blog, we’ll cover how SIBO develops and break down the seven most important root causes of SIBO, why they matter, and what you can do to prevent SIBO relapse.
Here is what we are going to cover in this guide:
TL;DR (Summary): Why SIBO relapse is so common
- SIBO is rarely just a one-time overgrowth. It stems from deeper imbalances like poor gut motility or structural blockages.
- The two main root causes of SIBO are a sluggish migrating motor complex (MMC) and structural issues such as adhesions or ICV dysfunction.
- Even if you clear the overgrowth, SIBO is likely to return if those root causes aren't addressed.
- Relapse prevention includes supporting digestive function, rebuilding the microbiome, improving motility and addressing nervous system dysregulation.
- A proactive approach, started during or just after the eradication phase, is essential to long-term success.
- With the right testing, support, and personalized protocol recommendations, long-term healing is absolutely possible.
- Skip to our 7-step strategy to stop SIBO coming back
Three Routes of Bacteria and Archaea Overgrowth
Before we dive into root causes, it’s helpful to understand how bacteria and archaea overgrow in the small intestine in the first place. There are three primary ways this can happen:
Ingested bacteria: Bacteria can enter the digestive system through contaminated food, water, or even from your own mouth’s oral microbiome. When stomach acid, enzymes or bile are low, these microbes can survive the journey and overgrow in the small intestine. Archaea, such as Methanobrevibacter smithii, don’t usually enter the body with food or water, but they can take hold in the small intestine when conditions are good for their survival. Conditions like slowed small intestine motility, excessive carbohydrate fermentation, or imbalances in the gut microbiome.
Retrograde migration: The ileocecal valve (ICV) acts as a one-way door between your large and small intestines, preventing bacteria and archaea from moving backwards. When it’s dysfunctional, or stuck open, microbes from the large intestine (which contains a million times more bacteria than the small intestine) can migrate backward into the small intestine and set the stage for a bloom or overgrowth, which is SIBO.
In situ bloom: Even in a healthy gut, small numbers of bacteria and archaea live in the small intestine. Under normal conditions, they're kept in check by the body's clearing mechanisms. One is the migrating motor complex (MMC) which sweeps through the intestine between meals, and another is a healthy gut microbiome of beneficial bacteria competing with opportunists and keeping each other in check. If these clearing and balancing processes aren't working properly, certain bacteria and archaea can multiply excessively, leading to an overgrowth.
So, whether bacteria or archaea are coming in from the outside, moving backward from the large intestine, or simply overgrowing in place, each of these routes can contribute to the overgrowth in the small intestine that we call SIBO.
Now that we’ve covered how bacteria and archaea can overgrow in the small intestine, let’s dive into SIBO root causes - the underlying factors that, when working properly, should actually prevent SIBO. We’re going to look at two key areas agreed upon by most SIBO experts as our current framework for SIBO root causes.
SIBO Root Cause Category #1: Impaired Gut Motility
The number one reason why SIBO develops and relapses is a slow or dysfunctional migrating motor complex (MMC). The MMC is this cleansing wave-like motion that sweeps bacteria, archaea and food out of the small intestine between meals. When the MMC doesn't function properly bacteria and archaea can stay in the small intestine and multiply.
So, what actually disrupts the MMC and causes it to malfunction? Let’s break down the most common causes of MMC dysfunction that we currently understand.
Post-infectious IBS and food poisoning
One of the most well-documented causes of SIBO is a condition called post-infectious IBS, which often develops after a bout of food poisoning, gastroenteritis or traveler’s diarrhea.
It’s important to understand how SIBO develops from food poisoning, so please stick with us as we explain. Specific pathogenic bacteria, such as Campylobacter, Escherichia coli, Salmonella and Shigella, produce a toxin called Cytolethal Distending Toxin B (CdtB). Your immune system creates antibodies against the CdtB toxin, which it should do to stop it making us sick. But then, a process called molecular mimicry occurs and the immune system gets a little confused. Your immune system mistakenly cross-reacts with a protein in your gut nerves called vinculin, thinking vinculin is the CdtB toxin which needs to be eliminated, leading to autoimmune nerve damage in the small intestine. In trying to attack these harmful CdtB toxins, our own immune system actually attacks the motor proteins in our MMC.
Since vinculin plays a key role in regulating gut motility, damage to it can cause a permanently weakened MMC, reducing the gut’s ability to clear bacteria and archaea and setting the stage for chronic, relapsing SIBO.
The good news here is that we can now test for anti-vinculin and anti-CdtB antibodies using the IBS Smart test by Gemelli Labs. This blood test can confirm if food poisoning is one of the root causes of your SIBO. A positive test indicates nerve damage and MMC dysfunction, which makes relapse prevention strategies even more important. Unfortunately this lab is only available in some countries so for our clients who can’t access this lab we will use their healthy history information, like ‘did you have a bout of food poisoning prior to the onset of SIBO symptoms’ as well as their response to prokinetics as clues. If prokinetics like ginger improve symptoms, it suggests MMC dysfunction is potentially a part of the clients SIBO root cause list.
Example extract from example IBS-Smart Test
Neurological disorders
The second biggest impact on MMC functioning is neurological disorders. Because the MMC is regulated by the enteric nervous system, the gut’s built-in ‘second brain’, any condition that affects the brain, spinal cord or vagus nerve can impair gut motility.
The most common neurological conditions we see that are linked to SIBO are Parkinson’s disease, diabetes, traumatic brain injury, autonomic nervous system dysfunction like postural orthostatic tachycardia syndrome (PoTS) and dysautonomia, and very importantly, vagus nerve dysfunction. The vagus nerve controls gut motility. When it’s weak, it reduces MMC activation, meaning that the regular cleansing waves are not really happening, allowing bacteria and archaea to accumulate, leading to SIBO.
Addressing neurological conditions is an area that I strongly recommend seeking thorough support for. It’s multi-faceted and requires a personalized approach.
Chronic infections
Chronic infections are an overlooked cause of impaired gut motility and SIBO relapse. Conditions like Lyme disease, Epstein-Barr virus, parasites and mold exposure can disrupt the nervous system, vagus nerve function and the MMC, making it difficult for the small intestine to clear bacteria and archaea effectively.
Parasites, Lyme, EBV and co-infections have been shown to damage gut nerves, trigger autoimmune attacks on nerve cells, suppress vagus nerve functioning and cause chronic inflammation. Mold exposure from water-damaged buildings suppresses immune function, triggers widespread inflammation and disrupts autonomic nervous system signaling, including vagus nerve function.
That’s a long way of saying, if SIBO keeps coming back despite many rounds of intervention, chronic infections and/or mold exposure could be the missing link. Testing for parasites, mycotoxins, Lyme and co-infections or viral reactivations may be helpful for you to figure out next steps. If you've tried everything for SIBO without success, then you may need to focus here.
Chronic stress and HPA axis dysregulation
Your gut is highly sensitive to stress, and chronic activation of the stress response can significantly reduce MMC function.
When cortisol is elevated, the body can enter ‘fight, flight or freeze’ mode, shutting down non-essential functions like digestion. This inhibits MMC contractions, and we get slowed motility and bacteria and/or archaea overgrowth. Chronic stress also lowers vagus nerve tone, weakening your guts ability to clear bacteria and archaea. It’s a nasty cycle and why emotional stress from anxiety, trauma and burnout, poor sleep and chronic inflammation all need to be a priority when you’re working on gut healing.
We ask our clients who have identified chronic stress or Hypothalamic-Pituitary-Adrenal (HPA) axis dysregulation as a root cause to focus on supporting their MMC functioning through implementing lifestyle changes. We typically start with vagus nerve exercises like deep breathing, gargling, humming and singing, mindfulness & relaxation techniques like meditation, yoga and HRV training and optimizing sleep & circadian rhythms by having a consistent bedtime, focussing on morning sunlight exposure and more. For clients who suspect trauma history is relevant for them, we strongly encourage them to find a trauma-informed coach for support.
Hypothyroidism
Hypothyroidism reduces gut motility because thyroid hormones T3 and T4 stimulate the MMC. When thyroid function is low, these signals weaken, and we are more likely to have slower gut clearance. Constipation is also common in hypothyroid clients, increasing fermentation and slowed motility in the small intestine. A full thyroid blood panel that tests for TSH, free and total T4 and T3, reverseT3 and antibodies are helpful to see what’s going on with thyroid function.
Medications
Certain medications have the unfortunate side-effect of significantly suppressing gut motility and MMC function, which can lead to bacteria and archaea hanging around in the small intestine.
Common MMC-suppressing medications include opioids like Oxycodone, Morphine and Codeine, Proton Pump Inhibitors and H2 Blockers, antibiotics and anticholinergic medications such as some antidepressants, antihistamines and bladder medications. If these medications are necessary for you, working with a practitioner to support motility through diet, movement and prokinetics will be helpful.
When motility is impaired in the small intestine, bacteria and archaea aren’t cleared properly, making relapse almost inevitable unless this is addressed. This is why repeating rounds of antimicrobials to kill off the bacteria and archaea may not be the best approach for everyone.
SIBO Root Cause Category #2: Structural Issues
Even with a fully functional MMC, bacteria and archaea can still overgrow if they get stuck in the small intestine or if they migrate backward from the large intestine. These structural issues create physical roadblocks that prevent bacteria and archaea from being cleared out properly, making SIBO more likely to develop and harder to resolve. Let’s break down the most common structural causes of SIBO that we know of.
Adhesions
Adhesions are bands of scar tissue that form between organs and tissues after surgery and abdominal infections. The most common surgeries our clients have had prior to testing positive for SIBO are c-sections, endometriosis surgeries and appendix removal surgery. Adhesions from these can create kinks or narrow areas in the intestines, restricting normal flow of food and waste and trap bacteria and archaea in the small intestine.
Blind loops
A blind loop is a section of the intestine where bacteria and archaea can accumulate and multiply instead of being cleared out. This can happen because of past surgeries that changed the intestinal shape like gastric bypass and bowel resections, diverticula or small pouches in the intestine and intestinal kinking or narrowing from chronic inflammation or scar tissue.
Ileocecal valve (ICV) dysfunction
We touched on this earlier when talking about retrograde migration. The ileocecal valve or ICV is a one-way ‘door’ between the small and large intestine that prevents bacteria and archaea from moving backward. When this valve isn’t working properly the door remains open, so large intestine bacteria and archaea can backflow into the small intestine, increasing the risk of SIBO.
Ehlers-Danlos Syndrome (EDS) and other connective tissue disorders
EDS affects the strength and flexibility of connective tissue throughout the body, including in the gut. This can lead to loose and uncoordinated movement of the intestines, which slows digestion. It may also weaken the ICV, allowing bacteria and archaea to move backward from the large intestine into the small intestine. In some cases, the intestines may become stretched or prolapsed, creating pockets where bacteria can get trapped and overgrow.
Since EDS-related motility issues impact both structure and functioning of the MMC, SIBO for these clients often requires long-term management with prokinetics, dietary strategies, and periods of reducing the bacteria and archaea that may continuously overgrow.
Unlike motility-based SIBO, which we discussed first, structural SIBO often requires longer-term management. Physical therapies like visceral manipulation and osteopathic interventions can help mobilize stuck areas of the gut. In some cases, if adhesions or strictures are severe, surgical intervention may be needed to restore normal flow through the small intestine.
Risk Factors That Weaken Gut Defenses
Beyond our two categories of SIBO root causes, impaired motility and structural issues, there are other risk factors that weaken your gut’s ability to prevent bacteria and archaea overgrowth.
Low stomach acid, bile and enzymes: These digestive secretions are your gut’s natural defense mechanisms. When they’re low, microbes aren’t kept in check and can overgrow.
Microbiome depletion: Antibiotics, poor diet or stress can wipe out beneficial gut flora, which are protective against dysbiosis and overgrowth, and support normal gut functioning.
Immune suppression: Age, illness and medications can all contribute to lowered immune function and set the scene for SIBO.
These factors don’t directly cause SIBO, but they make it more likely to develop or return when combined with motility or structural issues.
Why SIBO Keeps Coming Back
Even after successfully killing off the overgrowth, many people find SIBO comes right back. So why does this happen? Let’s take a moment to revisit our SIBO Framework, because this is where most conventional approaches miss the mark.
In Phase 1, the focus is on clearing the overgrowth using antimicrobials, restrictive diets and digestive supports to reduce symptoms and lower gas levels. And for many people, this phase works… temporarily. Their bloating goes down. Their constipation or diarrhea improves. They start to feel like themselves again. But here’s the problem - most protocols stop here.
What gets left out is Phase 2, the part where we rebuild your gut’s natural defense systems and address what allowed the overgrowth to develop in the first place. This is relapse prevention.
If your stomach acid is still low, if your MMC is still sluggish, or if adhesions or ICV issues are still causing bacteria and archaea to get stuck in the small intestine, the conditions that caused SIBO in the first place are still there. And that means it's only a matter of time before the bacteria or archaea come back.
That’s why relapse prevention isn’t optional, it’s an essential piece of the SIBO healing puzzle. And it needs to be baked into protocol recommendations from the start, not saved for later once the ‘kill phase’ is over.
In our clinic, we don’t wait until Phase 1 is finished to start Phase 2. We begin laying the foundation for long-term healing early on. This typically looks like supporting digestion, supporting motility, reducing stress and beginning microbiome restoration while we’re still tackling the overgrowth.
Because that’s the real key to lasting SIBO eradication success. A proactive, layered approach that works with your body to eliminate the overgrowth and address all of the factors that may allow it to come back.
What We Do to Prevent SIBO Relapse:
7 Step Strategy
Here’s an actionable list of strategies from Phase 2 of our framework that demonstrate how we help break the SIBO relapse cycle and keep symptoms from returning for our clients. To understand why each of these steps is necessary, make sure you read the first part of the blog about why SIBO relapse is so common.
1. Diet Diversity and Food Reintroduction
After clients have followed some level of dietary restriction during Phase 1, one of the most important goals in Phase 2 is to reintroduce fermentable fibers to support microbiome diversity. We encourage clients to take a ‘low and slow’ approach:
Start by reintroducing one new food every few days, ideally something you’ve missed or eliminated most recently.
Begin with small portions of fermentable foods like garlic, onion, lentils, or green banana flour.
Monitor symptoms, and if something isn’t tolerated, set it aside and try again later. We can likely get this food back in, the microbiome just needs more time to repopulate and diversify before trying it again.
This process isn’t linear, and it requires patience. But rebuilding diet diversity is essential for developing a resilient gut microbiome, one that can naturally resist overgrowth.
We also focus on structured meal spacing to activate the MMC, the wave-like motion that clears food, waste, bacteria and archaea from the small intestine. We aim for:
3-4 hours between meals
12 hour overnight fast
These simple meal timing changes can significantly improve motility and reduce the risk of relapse.
2. Microbiome Support
With the overgrowth reduced, Phase 2 is the time to repopulate your gut with beneficial microbes, and that starts with feeding them the right food. We typically begin with well-tolerated prebiotic fibers like:
Partially Hydrolyzed Guar Gum (PHGG)
Galactooligosaccharides (GOS)
Acacia fiber
We also use prebiotic-rich whole foods, such as:
Artichokes, leeks, garlic and onions
Polyphenol-rich berries
Resistant starches from green banana flour, cooked-and-cooled potatoes and rice or well-prepared legumes (as tolerated)
We’ll often titrate these slowly. For example, starting with 1/4 tsp of PHGG and building up over weeks to 5-7 grams daily while watching for bloating and gas.
When appropriate, we also add targeted probiotic supplements to support motility, gut lining repair and immune function. Our go-to options include:
Lactobacillus reuteri for motility and gut-brain axis found in Biogaia, Protectis.
Bifidobacterium infantis for inflammation and IBS symptoms, found in many products.
Multi-strain blends like Seeking Health, ProBiota Sensitive or Megasporebiotic for clients who need gentle microbiome support without triggering bloating or immune responses.
Probiotic-rich foods can also be introduced, such as coconut kefir or sauerkraut brine, especially if histamine intolerance has improved.
3. Digestive Supports
Weak digestion is one of the most overlooked contributors to relapse. If you’re not breaking down food properly, undigested particles ferment in the small intestine and feed opportunistic microbes who aren’t being cleared properly. We support digestion for our clients by using:
Betaine HCl to improve stomach acid levels, especially if burping, bloating or reflux are reported.
Digestive bitters or bile-supporting herbs like dandelion and gentian to improve fat digestion and bile flow.
Digestive enzymes with meals to ensure full breakdown of proteins, carbs and fats.
These are typically recommended for 2–3 months post-eradication, especially during food reintroduction.
4. Motility Support
Supporting the MMC is one of the most powerful ways to prevent SIBO from returning, and it’s a core part of Phase 2. We use natural prokinetics with our clients to gently stimulate the MMC:
Ginger root: around 1000 mg at bedtime
Iberogast: 30-60 drops at bedtime, helpful for our clients who don’t tolerate ginger
MotilPro, Motility Activator, SIBO-MMC or other blends: at bedtime
We typically introduce prokinetics toward the end of Phase 1, then continue for at least 3 months, especially during that critical relapse window.
For some clients, especially those with a history of severe food poisoning, neurological conditions or EDS, higher doses of natural prokinetics can be used or prescription options via their medical doctor like Prucalopride or low-dose Naltrexone may be worth considering.
Finding trustworthy supplements can be tricky. That’s why we’ve set up a Supplement Dispensary for our clients in the US, with 20% off all recommended products. It’s an easy way to access professional-grade antimicrobials. Access our dispensary here: https://us.fullscript.com/welcome/blindemann
We also layer in vagus nerve support, which is essential for activating motility naturally:
Gargling, singing and humming
Deep breathing or heart rate variability training
Meditation
Yoga and yogic breathing
Cold exposure
The nervous system plays a huge role in digestive function, so regulating it is part of every relapse prevention plan.
5. Structural Interventions
If adhesions, blind loops, or ICV dysfunction were part of the root cause list, they’ll need targeted support in Phase 1 and 2 to prevent relapse. Some strategies we recommend include:
Visceral manipulation: with a trained therapist to gently break up adhesions and restore gut mobility.
Osteopathy or craniosacral therapy: to address restrictions in the abdominal area.
Pelvic floor physical therapy: for clients with constipation, bloating, or post-surgical scar tissue.
If these interventions aren’t enough, we may recommend clients consider a surgical consultation, especially if imaging or history suggests significant structural blockages.
6. Address Hidden Infections and Mold
Sometimes the biggest driver of relapse is something deeper that hasn’t been uncovered yet, like chronic infections or environmental toxins. We commonly screen our clients who have relapsing SIBO for:
Parasites, opportunistic bacteria, yeast and gut pathogens using comprehensive stool testing, such as the GI-MAP.
SIFO, small intestine fungal overgrowth, can be screened for using an Organic Acids urine test, symptom history and clinical correlation.
Mycotoxins are common, especially for clients who live in a humid environment or have been exposed to a water damaged building. We are currently using urine-based mold toxin panels and Organic Acids testing.
Lyme and co-infections are something we are using screening questionnaires for since we have not completed the necessary training to support these clients. We are looking for symptoms like fatigue, neurological symptoms or flare-ups in pain symptoms that persist.
Most clients who are working with our practitioners are screened for these infections and environmental toxins before addressing SIBO, since we know relapse is likely. Our approach is to address most of these before SIBO, if it makes sense for the client, their symptoms and health history.
7. Regulate Stress and Sleep
Finally, we come to what is one of the most important, and most underestimated, factors in preventing SIBO relapse: stress and sleep.
Chronic stress suppresses digestion, shuts down motility, and weakens immune defenses. Poor sleep reduces vagus nerve tone, increases inflammation, and slows your healing capacity. In Phase 1 and 2, we help clients:
Build daily stress regulation routines, such as 5–10 minutes of breathwork, walking, or journaling.
Improve sleep hygiene through implementing a consistent bedtime, aiming to be asleep by 10pm, morning sunlight exposure, no screens before bed, and magnesium support if needed.
Address HPA axis dysregulation, especially if cortisol testing shows irregular patterns.
These recommendations aren’t optional extras, they are non-negotiables for sustainable gut healing and preventing relapse.
Chronic vs. Resolvable SIBO
One of the biggest questions we get from our clients is, “Can SIBO be fully resolved, or is it something you have to manage long-term?” And the answer really depends on the underlying causes.
If your SIBO was triggered by food poisoning, medications, adhesions, gut infections or short-term gut stress, addressing these root causes can often resolve it completely with the right interventions. However, if SIBO stems from chronic neurological disorders or EDS it may require longer-term management through prokinetics, dietary adjustments, and periodic intervention cycles to keep symptoms under control.
Understanding whether your SIBO is temporary or chronic is key to creating an intervention plan that actually works, and prevents relapse.
Final Thoughts and Next Steps: Healing Is Possible
SIBO relapse isn’t inevitable, but it does require more than just killing bacteria and archaea. By rebuilding the microbiome, supporting motility, addressing structural issues, and uncovering hidden infections, long-term gut health is absolutely possible.
If you’re feeling overwhelmed after SIBO has relapsed, don’t worry, you don’t need to solve everything at once. Start by identifying your key root causes. Was it food poisoning? Mold? Stress? Adhesions? Knowing what’s driving your SIBO is the first step and you can use the recommendations in this blog to start to address them systematically.
If you're ready to feel better, we’re here to help. You can:
Book an Initial Consultation with one of our experienced SIBO specialists and get started today.
Explore our recommended supplements through our Supplement Dispensary.
Or simply learn more about our process and how we work with clients via a Complimentary 15 Minute Pre-Consultation call with one of our practitioners.
Overcoming recurring SIBO starts with one step, and we’d love to walk it with you because you deserve to heal and feel vibrant and well.
About author: Bella Lindemann, FDN-P
Bella Lindemann is the founder and lead practitioner at The Functional Gut Health Clinic. With her science degree, functional nutrition certification and extensive experience, she is a recognized expert in gut health and the science of SIBO, parasites and other gut infections. With her own personal gut healing experience and having supported thousands of clients across the clinic, Bella is passionate about helping her clients address GI imbalances and take back control of their digestive symptoms.