You’ve tried everything to relieve your symptoms of SIBO. First, you completed an elimination diet; then you tried the low-FODMAP diet. Symptoms may improve initially, but not long after you get off your protocol all your symptoms return. When this happens, you’re experiencing a SIBO relapse.

As a functional medicine doctor, I’ve helped many patients overcome SIBO. However, there were times when a patient would come back with a SIBO relapse… sometimes more than once! It can be so frustrating to feel like you have done everything to fix your SIBO, only to have your symptoms return.  

The good news is that you can reverse your symptoms and say goodbye to recurring SIBO infections. The key is to pinpoint the root cause of your SIBO relapse. I will discuss why SIBO relapses occur later on. First, let’s begin with a review of SIBO.

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What Is SIBO?

So, what is SIBO? SIBO occurs when the bacteria in your small intestine become unbalanced and overgrow. Ideally, the bacteria in your GI tract that make up your gut microbiome exist in a balanced state. I like to think of your microbiome as a rainforest. Inside this rainforest, several species live together in harmony. These species affect your immune system, thyroid function, and overall health. 

Most of your gut bacteria live in your large intestine and colon. This is where they help break down food, synthesize vitamins, and eliminate waste. However, external factors like medications or a poor diet can disrupt this balance.

Overgrown bacteria in your small intestine feed off undigested food that passes through. This undigested food begins to ferment, producing hydrogen. Hydrogen feeds archae, single-celled organisms in your small intestine. Archae then produces methane. Excess gas contributes to many symptoms of SIBO. It also leads to a whole host of other issues, such as digestive problems and chronic illness.

What Causes SIBO?

After enzymes break down our food, it travels from the stomach to the small intestine. In a healthy gut, bacteria travel with our food to its final destination: the colon. Unfortunately, several risk factors can disrupt this process, including:1

  • Damaged nerves or muscles in the gut resulting in leftover bacteria in the small intestine. For example, type 1 and type 2 diabetes can affect the muscles in the gut, leaving room for SIBO to develop.
  • Physical obstructions in the gut, such as scarring from surgeries or Crohn’s disease and diverticula (tiny pouches that can form in the wall of the small intestine) can collect bacteria instead of passing it on to the colon, where it belongs.
  • Medications that influence or disrupt the normal gut flora including antibiotics, acid-blocking drugs, and steroids. 
  • A diet high in sugar, refined carbohydrates, alcohol, and other high-carb foods you eat or drink.

If you’ve done the work and addressed your root causes, then why would symptoms of SIBO return? Well, let’s talk about the causes of SIBO relapse.

What Is Causing My SIBO Relapse?

You might be thinking, “I followed the three-step protocol and eliminated the overgrowth.” I bet it worked! However, if you go back to eating the way you did before the SIBO protocol, don’t be surprised if you have a relapse. Diet is only one of the reasons why you have a SIBO relapse. Here are the three primary reasons for SIBO recurrence.

What are The Causes of SIBO Relapse? - Infographic - Amy Myers MD®

1. Your Diet

Diet is never a quick fix. It’s why I call my program The Myers Way® because it truly is a way of life. You can reintroduce certain foods once you’ve finished the SIBO protocol. If you are susceptible to gut infections, you might have to be more careful with what you put on your plate or in your cup.

As I mentioned, the food you eat is one of the root causes of SIBO. So it makes sense that it can also cause SIBO relapse. Here’s a look at the biggest culprits of a SIBO recurrence.  


Sugar is the number one offender when it comes to SIBO. If you’ve ditched refined sugar and your SIBO still won’t go away, ease off all-natural sweeteners as well. Yes, this includes coconut sugar, honey, and maple syrup. Save sweet treats for special occasions, and try to stick to ones made with stevia or monk fruit.

Pure Stevia is 200-300 times sweeter than regular sugar. Pure monk fruit is 150-200 times sweeter. Using them in small quantities makes them less likely to feed an overgrowth.


You may also have to watch out for fruit in addition to added sugars. Although fruit contains plenty of nutrients, it’s also very high in natural sugars. Keep it to a minimum if you’re struggling with SIBO relapse. Keep it to one cup or less of low-sugar fruits such as berries per day.


Liquid sugar can be just as bad – if not worse – than sugar itself. Certain types of alcohol are not only packed with sugar but they’re fermented as well. Beer, wine, and champagne are among the top alcohols you should avoid. Even one to two drinks per day can lead to symptoms of SIBO. Bloating, gas, abdominal pain, constipation, and diarrhea can be worse as well.3

Alcohol is also a toxin, so I recommend ditching it completely. If you feel like you have to be a social drinker, try a mixed drink with tequila or a vodka made from potato.

Starchy Vegetables

Sweet potatoes, squash, and other starchy vegetables are high in carbs. While healthy, these get converted into sugars in your gut. These seemingly harmless foods may be behind a SIBO relapse. Instead, fill your plate with non-starchy vegetables. Some of the best include leafy greens, broccoli, cauliflower, cucumber, asparagus, and zucchini.

Cutting out refined sugar and alcohol is the first step in addressing your SIBO relapse. I recommend Leaky Gut Revive® Strawberry Lemonade for curbing sugar cravings. It works so well and tastes amazing when made into a Strawberry Cooler

Take this simple symptoms quiz to determine which foods contribute to SIBO relapse. It also tells you which foods help restore the balance of bacteria in your gut.

2. Underlying Gut Condition

As I mentioned earlier, physical obstructions in the gut can be a cause symptoms of SIBO. They can also lead to SIBO relapse. Here are the most common gut conditions that can lead to a SIBO relapse.

Crohn’s disease

The connection between Crohn’s disease and SIBO is a result of structural abnormalities of the gut.4

Studies have shown an increase in the prevalence of SIBO among patients with Crohn’s disease. Conventional medicine treats Crohn’s disease with immunosuppressive medications and invasive surgeries. By ignoring factors that led to Crohn’s disease, these methods don’t address the root cause. Leaky gut, stress, or diet lead to chronic inflammation, a precursor to autoimmue diseseas.

Celiac disease

Celiac disease is an autoimmune disease caused by a reaction to eating gluten. Gluten is a protein found in wheat and certain grains. It’s the number one culprit of several gut infections, including leaky gut and SIBO. Gluten triggers the release of zonulin, a chemical that tells your gut lining to “open up”. It is also highly inflammatory, meaning it can cause stress to your immune system.

Gluten protein has a chemical structure similar to that of some of your body’s tissues. Because of this, your body mistakes your tissues for gluten and attacks them. Molecular mimicry is the name of this process, and it happens a lot in the thyroid. I recommend everyone remove gluten from their diet.


Neuropathy is one of the most common complications of diabetes. Over time, uncontrolled blood glucose levels damage nerves. Signal interference occurs, causing a lot of problems. High blood glucose also weakens the walls of the small blood vessels. Nerves are unable to receive enough oxygen and nutrients, leading to cellular death.

Damaged nerves in the gut can result in a decline in gut mobility, increasing your risk for SIBO relapse.

Leaky Gut

Leaky gut is actually one of the symptoms of SIBO and one of the most common ones I saw in patients struggling with SIBO. Inflammation in your gut loosens the tight junctions holding your intestinal wall together. Left unchecked, it leads to intestinal permeability. From here, toxins, microbes, and undigested food particles can pass through and into your bloodstream. Your immune system marks them as pathogens and attacks them. This can allow bacteria to overgrow in your small intestine. If you have addressed your leaky gut symptoms and they return, you could have a SIBO relapse. 

3. Medications

The truth is that some medications, such as antibiotics and NSAIDs, do more harm than good. These types of medications disrupt gut mobility and can lead to a SIBO relapse. However, they aren’t the only ones. Let’s talk about the medications that might be behind your SIBO relapse. 


Antibiotics have one job: kill bacteria and stop them from multiplying. However, this simple task is what leads to an overgrowth of bad bacteria. Antibiotics do not discriminate between good bacteria and bad bacteria. Their job is to travel to your gut and simply kill bacteria. 

You might be thinking, “Don’t you want to kill overgrown bacteria?” Yes, but antibiotics can lead to an imbalance in your gut. Remember, the bacteria normally found in the large intestine and colon overgrow and colonize in your small intestine. If you must take antibiotics, I recommend taking a soil-based probiotic. Soil-based probiotics do not colonize the small intestine. They also do not feed on the bacteria already growing there.


If you occasionally get a runny nose, itchy eyes, unexplained anxiety, or sinus headaches, you’ve likely been told it’s allergies. Conventional medicine tells you to take antihistamines to treat these symptoms. Be careful, though, because antihistamines block your body’s natural production of histamines. Histamines are chemicals produced by your immune system. Their job is to create inflammation in response to an outside invader. Over time, the use of antihistamines can cause a histamine intolerance. In time, histamine bacteria can overgrow in your small intestine.


Conventional medicine uses non-steroidal anti-inflammatory drugs (NSAIDs) treat inflammation, reduce pain, and decrease fever. Unfortunately, many people don’t realize their troubles are just beginning when they reach for these little pills. NSAIDS not only cause leaky gut, but they can be one of the greatest barriers to recovering from it. NSAIDs increase intestinal permeability and can increase your risk for SIBO relapse.5

Now that you understand the causes of a SIBO relapse, let’s talk about ways you can treat symptoms of SIBO recurrence.

How to Treat a SIBO Relapse

I take the same approach to treating a SIBO relapse the same way I recommend treating symptoms of SIBO. You can work to eliminate bacterial overgrowing by using a three-step approach. My SIBO Breakthrough™ Program is a step-by-step process to help you beat small intestinal bacterial overgrowth for good. It includes the steps below, along with strategies to create a gut-healthy lifestyle!

SIBO Relapse – 3 Steps To Get Rid of SIBO – Infographic – Amy Myers MD®SIBO Relapse - 3 Steps To Get Rid of SIBO - Infographic - Amy Myers MD® Relapse – 3 Steps To Get Rid of SIBO – Infographic – Amy Myers MD®

Step 1: Starve the Overgrown Bacteria

Starve the overgrown bacteria by removing the foods that feed it from your diet. This means cutting out all sugar, alcohol, fruit, starchy vegetables, grains, and legumes. 

While you may reintroduce some inflammatory foods after getting your gut bacteria back in balance, I recommend ditching gluten and dairy for good. I mean this especially if you have an autoimmune or thyroid condition.

Step 2: Attack the Bacteria

In my clinic, I typically prescribed antibiotics Xifaxan and Neomycin for bad bacteria. Xifaxan is more effective with hydrogen-dominant SIBO and Neomycin with methane-dominant SIBO. These antibiotics kill pathogenic bacteria with the least harm to the good bacteria in your microbiome.

If starving the overgrowth and attacking the bacteria doesn’t stop recurring symptoms of SIBO, it could be due to a biofilm over the overgrown bacteria. Biofilm makes it more difficult to eliminate. In these cases, I recommend treating bacterial overgrowth with a biofilm disruptor such as Microb Clear®. This blend of magnesium caprylate, berberine, tribulus extracts, sweet wormwood, barberry, bearberry, and black walnut work to kill off the bacteria naturally.

These ingredients are not as harsh as broad-spectrum prescription antibiotics. Microb Clear® is a natural and gentle way to support your journey to optimal gut health.

Step 3: Restore Your Good Bacteria

The final step is to restore the good bacteria in your gut. This will help support a strong immune system, optimal digestion, and nutrient absorption. Moreover, when it comes to a SIBO relapse you want to be particularly careful. Certain probiotics can add fuel to the fire and exacerbate symptoms of SIBO.

When you have bacterial overgrowth in your small intestine, it’s often either lactobacillus or bifidobacterium. Most probiotic supplements contain these species, so using them adds to the bacteria in your small intestine. Consequently, probiotics containing lactobacillus or bifidobacterium may make your symptoms worse.

As I mentioned earlier, soil-based probiotics don’t colonize the small intestine. They also do not feed the bacteria already growing there. In short, they do not contain lactobacillus or bifidobacterium strains. Even so, they still provide all the benefits of a probiotic.Getting to the root cause of your SIBO relapse is the first step in treating it. The empowering part is that you can put an end to your symptoms of SIBO and keep it away for good. By following the three-step approach, eliminating sugars and alcohol, and supplementing with soil-based probiotics, you can find relief from symptoms of SIBO.

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Article Sources

  1. What is Small Intestinal Bowel overgrowth (SIBO). Health Insight. 2021.
  2. Development of Rebiana, a Natural, Non-Caloric Sweetener. I. Prakash. British Industrial Biological Research Association, vol. 46, sup 7 . 2008.
  3. Moderate Alcohol Consumption is Associated with Small Intestinal Bacterial Overgrowth, Study Finds. . American College of Gastroenterology. 2011.
  4. Prevalence and Factors Associated With SIBO: A retrospective Study at a Referral Center. Erika Ruback and Júlio Maria Fonseca. Scielo Brazil. 2020.
  5. Role of Non-Steroidal Anti-Inflammatory Drugs on Intestinal Permeability and Nonalcoholic Fatty Liver Disease. Erika Utzeri and Paolo Usai. World Journal of Gastroenterology vol. 23. 2017.