You’ve tried everything. An elimination diet. A low-FODMAP diet. Yet somehow your small intestinal bacterial overgrowth (SIBO) symptoms relapse! Trust me, you’re not alone.

As a functional medicine doctor, I helped dozens of patients in my clinic overcome SIBO and take back their health. 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, have your symptoms go away just to see them return.  

The good news is that you have the power to reverse your symptoms and say goodbye to recurring SIBO infections once you 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. 

Contents hide

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, with many different species living together in harmony. Together, these species play a vital role in your immune system, thyroid function, bone health, and overall health. 

Most of your gut bacteria are meant to be located in your large intestine and colon, where they help break down food, synthesize vitamins, and eliminate waste. However, external factors such as medications or a poor diet can cause your rainforest to become unbalanced. When this happens, the bacteria normally found in the large intestine and colon overgrow and colonize in your small intestine.

While colonizing in your small intestine, the group of overgrown bacteria can thrive by feeding off the undigested food passing through. This process of fermenting carbohydrates produces hydrogen, which can feed the single-celled organisms in your small intestine called archaea, which then produce methane. All that excess gas in your GI tract is what contributes to the severe bloating people experience with SIBO, in addition 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 through our digestive system from the stomach to the small intestine. In a healthy gut, bacteria gets passed through the digestive tract along with our food to its final destination: the colon. Unfortunately, this process can be disrupted by a number of risk factors, 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 on Earth would SIBO come back? Well, let’s talk about the causes of a SIBO relapse.  

What is Causing My SIBO Relapse?

You might be thinking, “I followed the 3-step protocol and eliminated the overgrowth.” I bet it worked! However, if you go back to eating the way you did before did the SIBO protocol, it should not be a surprise you had a SIBO relapse. However, diet is only one of the reasons why you have a SIBO relapse. Here are the three primary reasons for a SIBO recurrence. 

What are The Causes of SIBO Relapse? – Infographic – Amy Myers MD®What are The Causes of SIBO Relapse? - Infographic - Amy Myers MD® 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 and be a little more flexible once you’ve finished the SIBO protocol. However, 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 a 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, you might also have to ease off all-natural sweeteners such as 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, while pure monk fruit is 150-200 times sweeter, meaning you’ll use them in such small quantities that they’ll be less likely to feed an overgrowth.2

In addition to added sugars, you may have to watch out for fruit. Although fruit is filled with plenty of nutrients, it’s also very high in natural sugars and should be kept to a minimum if you’re struggling with a SIBO relapse. Keep it to 1 cup or less per day of low-sugar fruits such as berries.


Liquid sugar can be just as bad – if not worse – than sugar itself. Certain types of alcohol such as beer, wine, and champagne are not only packed with sugar, they’re fermented as well. Just 1 to 2 drinks per day can lead to SIBO, and make symptoms such as bloating, gas, abdominal pain, constipation and diarrhea worse.3

Not to mention alcohol is a toxin, so I recommend ditching it completely. If you feel like you absolutely have to drink alcohol socially, try a mixed drink with tequila, or a vodka you know was made from potato.

Starchy Vegetables

Sweet potatoes, squash, and other starchy vegetables are high in carbs, which get converted into sugars in your gut. Although you may not think of these seemingly harmless foods when fighting SIBO, they may be behind a SIBO relapse. Fill your plate with non-starchy vegetables instead, including leafy greens, broccoli, cauliflower, cucumber, asparagus, and zucchini.

Cutting out refined sugar and alcohol is certainly an adjustment, however it’s the first step in addressing your SIBO relapse. I recommend Leaky Gut Revive® Strawberry Lemonade for curbing sugar cravings while you ease your way into this low-sugar way of eating. It works so well and tastes amazing when made into a Strawberry Cooler

For more information, take this simple symptoms quiz to determine which foods contribute to SIBO relapse, and 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 of SIBO, and subsequently a 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 a slew of immunosuppressive medications and invasive surgeries. By ignoring the upstream factors that led to Crohn’s disease, these methods don’t address the thing that caused the inflammation in the first place such as leaky gut, stress, or diet. 

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. Gluten is the number one culprit of several gut infections such as leaky gut and SIBO because it triggers the release of zonulin in your intestines, a chemical that tells your gut lining to “open up”. It is also highly inflammatory, meaning it can cause stress to your immune system.

The gluten protein has a similar chemical structure to some of your body’s tissues (specifically your thyroid), which can lead to molecular mimicry, where your body mistakes your tissues for gluten and attacks them. 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 and interfere with their ability to send signals. High blood glucose weakens the walls of the small blood vessels that supply the nerves with oxygen and nutrients. Remember, damaged nerves in the gut can result in leftover bacteria in the small intestine and a decline in gut mobility, leaving room for a SIBO relapse to occur. 

Leaky Gut

Leaky gut is actually a symptom of SIBO and one of the most common ones I saw in patients struggling with SIBO. Inflammation in your gut leads to intestinal permeability, where the tight junctions holding your intestinal wall together become loose. When you have a leaky gut, toxins, microbes, and undigested food particles can escape through the holes and into your bloodstream, where 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 do more harm than good such as antibiotics and NSAIDs. These types of medications disrupt the 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 the good bacteria and bad bacteria. Their job is to simply go to your gut and kill bacteria. 

You might be thinking, “Don’t you want overgrown bacteria to be killed?” The issue is that the imbalance in your gut caused by antibiotics leads to bacterial overgrowth. Remember, when your gut flora are out of balance the bacteria normally found in the large intestine and colon overgrow and colonize in your small intestine. If you must take antibiotics and struggle with recurring SIBO symptoms, I recommend taking a soil-based probiotic. Soil-based probiotics do not colonize in the small intestine or feed on the bacteria already growing there. 


If you suffer from the occasional runny nose, itchy eyes, unexplained anxiety, or sinus headaches it’s likely you’ve been told it’s just allergies. Conventional medicine tells you to take antihistamines to treat these symptoms, which blocks your body’s natural production of histamines. Histamines are chemicals that are produced by your immune system that create inflammation in response to an outside invader. Over time, the use of antihistamines can cause a histamine intolerance, which can allow the histamine bacteria to overgrow in your small intestine. 


Non-steroidal anti-inflammatory drugs, or NSAIDs, are used in conventional medicine to treat inflammation, reduce pain — especially in the joints — and decrease fever. Unfortunately, many people will never even realize their troubles may be just beginning when they reach for these little pills. NSAIDS not only cause leaky gut, they can be one of the greatest barriers to recovering from it because they increase your intestinal permeability, which means they make SIBO worse, or cause a SIBO relapse.5

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

How to Treat a SIBO Relapse

I take the same approach to treating a SIBO relapse the same way I recommend treating SIBO –  a 3-step approach that works to eliminate the overgrowth and restore your gut’s natural balance. My SIBO Breakthrough™ Program is a step-by-step process to help you beat small intestinal bacterial overgrowth for good. It includes the three step approach outlined below as well as the strategies you need to create a gut-healthy lifestyle you can stick with.

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 all sugar and alcohol and limiting carbohydrates such as fruit, starchy vegetables, grains, and legumes. 

While some inflammatory foods can be reintroduced after getting your gut bacteria back in balance, I recommend ditching gluten and dairy for good, particularly if you have an autoimmune or thyroid condition.

Step 2: Attack the Bacteria

In my clinic I typically used the antibiotics Xifaxan and Neomyacin to attack the bad bacteria. Xifaxan is more effective with hydrogen-dominant SIBO and Neomyacin with methane-dominant SIBO. These antibiotics kill the pathogenic bacteria with the least amount of disruption to the good bacteria in your microbiome.

If starving the overgrowth and attacking the bacteria have little effect on your recurring SIBO symptoms, it could be because a biofilm has formed around the overgrown bacteria, making it more difficult to eliminate. In these cases, I recommend treating bacterial overgrowth with a biofilm disruptor such as Microb Clear®. It is a blend of magnesium caprylate, berberine, and extracts from tribulus, sweet wormwood, barberry, bearberry, and black walnut. These ingredients work to kill off the bacteria naturally.

The ingredients are not as harsh as broad-spectrum prescription antibiotics which can wipe out good and bad bacteria alike. 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 your SIBO symptoms.

When you have an overgrowth of bacteria in your small intestine, it is often lactobacillus or bifidobacterium species. The majority of probiotic supplements contain these species, so using them adds to the bacteria in your small intestine. Consequently, one clue that you may have small intestinal bacterial overgrowth is that probiotics containing lactobacillus or bifidobacterium exacerbate your symptoms.

As I mentioned earlier, soil-based probiotics don’t colonize the small intestine or feed the bacteria already growing there. In short, they do not contain lactobacillus or bifidobacterium strains, yet 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 SIBO relapse and keep it away for good. By following the 3-step approach, eliminating sugars and alcohol, and supplementing with soil-based probiotics to maintain a bacteria balance in your gut, you can start living a fruitful life. 

Memorial Day Savings - Up to 40% OFF - Stock Up on All Your Favorites This Weekend Only! Offer ends May 30th at Midnight Pacific Time.

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<br>. 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.