Most people I work with are pretty well read on SIBO, you may even know more than your GP about it. But one thing that people find confusing is why it comes back?

In this article, we’ll look at the reasons for SIBO relapsing, how to support long-term relief by addressing underlying issues.

What is SIBO?

Small intestine bacterial overgrowth (SIBO) is where microbes overgrow in your small intestine. These microbes can interfere with normal digestion and lead to symptoms such as bloating, abdominal cramps, diarrhoea, excessive gas and hypersensitivity.

Treatments like antibiotics or herbal antimicrobials can be effective — but for many people, symptoms come back within months.

What’s the relapse rate for SIBO?

In fact, a 2008 study found relapse rates of 43% within 9 months. 

That sounds really bad, right? But it’s really important to look at how the people in that study were treated. They only took Rifaximin for seven days (1,200 mg per day for 1 week).

Many other studies recommend taking antibiotics for much longer than one week to eradicate SIBO, so the duration of treatment may have affected the rate of relapse. 

Here are six reasons SIBO can relapse.

1. Not treating your SIBO root cause

SIBO is usually a symptom of a deeper issue, not the problem itself. Excessive microbes can only overgrow when there is an issue with motility, or reduced natural defences.

The possible root causes can include poor gut motility, low stomach acid, slow bile flow, structural changes after surgery, adhesions, and more. Read more about finding your SIBO root cause in this blog post.

If the causes of SIBO aren’t addressed, it’s very possible you can get a return of the overgrowth.

2. Ongoing issues with your Migrating Motor Complex (MMC)

The MMC is like the gut’s housekeeping. When we haven’t eaten for a while it kicks into action sweeping up bacteria, dead cells and any other debris left behind. 

If your MMC isn’t working well, bacteria can linger and multiply. We know motility is one of the main issues in SIBO. 

MMC dysfunction may be caused by previous food poisoning. This can lead to an autoimmune effect that damages nerve cells controlling the migrating motor complex. 

If you felt better after a SIBO treatment, but if the MMC is still impaired, the microbes can return in time. 

For people who have this post-infectious SIBO as a root cause it may be necessary to stay on low levels of antimicrobials or prokinetics to keep the overgrowth at bay. It’s best to discuss this with a knowledgeable doctor to ensure you don’t get unnecessary side effects from the ongoing treatments. 

3. Not using a prokinetic after treatment

Prokinetics stimulate the MMC to keep things moving in between meals. You might find that taking a prokinetic after SIBO treatment reduces the chance of relapse. 

Examples include low-dose erythromycin (Rx) or natural options like ginger or artichoke extract. 

4. Incomplete treatment may cause a relapse

Feel like you’ve tried to treat SIBO, but nothing happened?

Breath tests aren’t perfect but they can indicate the amount of gas your small intestine microbes are making. And this can give you an idea of what kinds of treatments to use.

Sometimes treatment courses are too short or not strong enough. I typically find clients who use a mixed antimicrobial supplement will not have made enough progress.

Methane-dominant SIBO (IMO) is especially stubborn in my experience working with clients. This may be because you also need to work on getting the bowels moving properly which can take time with trial and error of foods to help constipation.

It is a relapse if it wasn’t really ever gone?

Relapse may not really be “relapse” — it may be that the original overgrowth wasn’t fully cleared

If your relapse is within a few months of the last treatment round, you might want to repeat that. But if the relapse occurs after 3-4 months it might be better to run another SIBO test to check that is the cause of your symptoms.

5. Not supporting your gut microbiome after treatment

Antibiotics and herbs kill bacteria, including the microbes in your large intestine. If you’ve had repeated rounds of antibiotics or strong antimicrobial herbs you may have affected the bacterial balance in the gut. 

If beneficial bacteria aren’t replenished, it’s easier for bad bacteria to take hold again. The best thing you can do for your large intestine, is to eat a wide variety of different fibres.

This helps to feed the beneficial gut bacteria which support a healthy digestion and motility.

But what if I can’t eat fibre??

Yes I know this means expanding your diet, which can feel very scary, but it is the best long term approach for avoiding SIBO relapse. 

6. Structural issues in the gut

Surgeries, scar tissue (adhesions), strictures, or small intestine diverticula can create pockets where bacteria get stuck. These physical barriers can’t be fixed with diet alone, but if you know you have these issues you can work on keeping the motility as good as it can be with diet and supplements. 

I sometimes see this with rectocele as well in women who have pelvic floor issues, or have had damage during childbirth. 

In some cases, surgical review or specific manual therapy (e.g. visceral manipulation) may be worth exploring. I often recommend clients see a pelvic health physiotherapist if there are potential structural issues. 

Conclusion: How to reduce your risk of SIBO relapse

When you find out you’ve got SIBO, it’s quite natural to gon on a mission to “kill the bacteria”. You want it gone. 

But for the best long term approach you also need to consider areas such as gut motility, digestion of nutrients, microbiome health, and structural issues. 

Working with a trained practitioner can help you create a personalised plan for recovery. You don’t have to keep going in circles with symptoms. 

SIBO is a complicated condition, with multiple root causes.   I recommend working with a nutritionist who has trained in SIBO for best results.

If you’d like me to help you with your digestion we can set up a free call to discuss what you’re looking for.