Do you think you have small intestinal bacterial overgrowth (SIBO)? Or perhaps you’ve been treated for it, or for irritable bowel syndrome (IBS), and you’re still experiencing symptoms. Diagnosing SIBO can be challenging because its symptoms vary so widely. You may not even experience bloating, one of the hallmark SIBO symptoms. In fact, SIBO can be so tricky that it’s often misdiagnosed as IBS, and research suggests that 50% of those diagnosed with IBS actually have SIBO. 

This is why testing, particularly breath testing, for SIBO can be useful. Read on to learn about SIBO’s main symptoms, the types of testing available, and why I recommend breath testing if you do choose to test. Or, you can find out if your symptoms are SIBO by taking this simple quiz, and get started on the road to optimal health right away with my free training.

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What is SIBO?

So, what is SIBO? Although there is some beneficial bacteria in your small intestine (sometimes called the small bowel), most of your gut bacteria is meant to be located in your large intestine and colon. In fact, this is where they help break down food, synthesize vitamins, and eliminate waste. When the “healthy” bacteria normally found in the large intestine and colon begin to colonize the small intestine, SIBO occurs. However, it can also be caused by an overgrowth of otherwise normal bacteria in the small intestine itself.

This can be caused by high-carb diets, nerve and muscle damage from diabetes or certain autoimmune conditions, Hashimoto’s, physical obstructions such as diverticula, scarring from surgeries or Crohn’s disease, and from medications such as antibiotics, acid-blocking drugs, and steroids.

The excess bacteria then feed off the undigested food in your small intestine. They particularly love to feed on foods such as sugar, simple and complex carbohydrates, starches, and alcohol.

This might not be a huge issue if food is moving through your system at the ideal rate. However, if you have an under-active thyroid, as is the case with hypothyroidism, your body processes—including digestion—slow down. This often causes constipation. When you are constipated and food lingers in your intestines, it ferments and becomes a breeding ground for bacteria.

Foods that are fermenting in your gut produce hydrogen as a byproduct. Hydrogen can feed single-celled organisms in your small intestine called archaea, which then produce methane as a byproduct. When you have SIBO, you have excess levels of hydrogen or methane, or both in your digestive system.

The Main Symptoms of SIBO

SIBO’s symptoms can range from digestive imbalance to chronic illness and autoimmune conditions. Here are the main ones you might experience.


You’ve gone to your doctor with frequent diarrhea, constipation — or both — gas, bloating, and abdominal pain. After extensive lab testing, studies, and procedures, everything comes back normal. In what’s known as a diagnosis of exclusion — when she or he can’t find anything wrong — your doctor diagnoses irritable bowel syndrome. However, many doctors don’t test for SIBO even though the symptoms are alike. In fact, 50% are misdiagnosed and actually have SIBO instead.

Intestinal Issues

SIBO can cause embarrassing gas, painful bloating, diarrhea, and stomach pain.1 You might also be constipated, or experience mixed symptoms that can change from day to day and week to week.2,3 You might wake up with a flat tummy, only to appear 6 months pregnant by mid-morning. Or you may have no digestive symptoms at all.4

Leaky Gut

Leaky gut occurs when the tiny openings in your gut wall that normally allow nutrients and water to pass into your bloodstream become too large and allow foreign matter to escape into your body. This includes proteins found in common foods and toxins that trigger your immune system, cause inflammation, and can lead to food sensitivities (especially to dairy products as many adults are already lactose intolerant), allergies, and even autoimmune disease.

Chronic Issues

Many chronic issues are all linked to SIBO. In fact, SIBO is more common in people who suffer from fibromyalgia, diabetes, celiac disease, chronic fatigue, and Hashimoto’s disease.5,6,7,8  

I often saw in my clinic that my Hashimoto’s patients had reduced bowel motility, which leads to SIBO. This is because people with low levels of thyroid hormone experience slowed transit time. That is, undigested food remains in the gut for longer than usual. This food can ferment, overfeeding bacteria and causing SIBO, along with the uncomfortable gas and bloating associated with it.9 In fact, it’s estimated that 50% of all people with hypothyroidism also have SIBO.10

However, you don’t need to have one of these health problems to have SIBO. You might simply feel weak and fatigued because SIBO can cause malabsorption of nutrients, particularly fats, in your digestive tract.11 Malabsorption occurs for a variety of reasons including changes in your mucosal lining and in your bile salts. This commonly leads to nutrient deficiencies such as B12 deficiency, which causes fatigue, among other things.12

Skin Issues

Rashes, rosacea, and other skin issues also often appear when you have SIBO because the leaky gut that SIBO causes can lead to skin inflammation. In fact, in a recent study of 113 rosacea patients, 46% tested positive for SIBO.13 This is a powerful connection!

I saw in my clinic that the inflammation leading to my patients’ rosacea was frequently caused by undigested proteins in food that got into their bloodstream and cause an inflammatory reaction.14,15

Histamine Intolerance

My patients would also commonly have rashes caused by histamine intolerance triggered by leaky gut. In addition to the histamine produced inside your body as part of your immune response, there are also a variety of foods that naturally contain histamine, cause the release of histamine, or block the enzyme that breaks down histamine, diamine oxidase (DAO).

Common symptoms of histamine intolerance include rashes, as well as headaches, flushing of the face and skin and low blood pressure. Resolving SIBO often resolves histamine intolerance issues as well.

Vitamin and Mineral Deficiencies

As I mentioned above, SIBO can lead to vitamin B12 deficiency because SIBO causes malabsorption of the nutrients in your food. Signs of vitamin B12 deficiency include anemia, fatigue, diarrhea, and headaches.16 However, that isn’t the only deficiency it can cause. The malabsorption that SIBO causes can prevent your body from taking in vitamins A, D, E and K, as well as iron, which are some of the major nutrients your body needs to survive and stay healthy.17,18

Do you think you have small intestinal bacterial overgrowth? Take this short quiz to find out!

Types of Testing

As I mentioned above, a simple way to find out if your symptoms are likely SIBO related is by taking this simple quiz, which I developed after treating thousands of patients in my clinic over a decade of practice. If you find you do have SIBO you can reverse this condition naturally, without harsh treatments such as antibiotics or other prescribed medications.

Additionally, there are a number of different types of SIBO testing, some of which are only available through functional medicine practitioners, and others that are generally available through traditional doctor’s offices and generally covered by insurance. Bear in mind that traditional doctors are likely to treat SIBO with antibiotics, so if you prefer to treat your symptoms without harsh medications, taking matters into your own hands or finding a functional medicine practitioner may be your best option. Here are the most common tests:

  • Dysbiosis test: This test, specially ordered and administered by a functional medicine practitioner, measures the urine levels of organic acids that are produced by the bacteria in your gut. The results may show high levels of acids such as hydroxyphenylacetate and cresol which could indicate SIBO.19 This test, while valuable, is generally not covered by most insurance.
  • Comprehensive Functional Medicine Stool test: This test allows lab technicians to see what bacteria, yeasts or fungi are present in your stool. Your practitioner will be looking for changes in bacteria composition and fat malabsorption to try and diagnose SIBO. I want to stress that this must be a comprehensive test so that a complete data set is available for analysis. Comprehensive tests are generally only ordered by functional medicine practitioners. If your traditional doctor orders a stool test, it will likely not be comprehensive, and not give the full picture.
  • Breath test: This is the gold standard of testing for SIBO if you’re determined to get diagnosed by a doctor. It can be administered by a functional or traditional medicine practitioner, and is often actually covered by insurance. The breath test measures the amount of hydrogen and methane in your breath. You’ll breathe into a special balloon, or collect your breath into small glass tubes over several hours, so your doctor can see the levels of key gases in your breath, some of which may indicate a bacterial imbalance. The most comprehensive tests measure both methane and hydrogen, as well as carbon dioxide. The sugar solution these tests come with should contain 10g of lactulose, 75g of glucose and 25g of fructose.

Less common testing types available through traditional doctors include jejunal aspiration, which involves taking fluid from your small intestine to measure its bacteria content.20 You may also find that the antibiotic Rifaximin, used to stop the growth of bacteria and to treat IBS as well as other digestive problems such as diarrhea21 may be prescribed based on your symptoms. If those symptoms improve, you will be deemed to have had SIBO.

Who Do I Recommend Testing For and Why

If you’ve been diagnosed with IBS, which is often a diagnosis of exclusion, it’s a good idea to investigate the possibility that you have SIBO. As I mentioned before, almost half of IBS patients have actually been found to have SIBO.22

If you have been treated for certain diseases (such as inflammatory bowel disease, as well as diabetes, chronic fatigue, fibromyalgia or another autoimmune disease) and you haven’t experienced much or any relief, I recommend you get tested for SIBO. If you do have it, treating it is likely to lead to big improvements in your symptoms. 

If you’re gassy and bloated despite positive dietary changes, such as eliminating gluten and dairy, testing for SIBO may also be right for you.
While I usually preferred to diagnose based on symptoms (such as those found in here in my SIBO Quiz), if you do choose to test for SIBO with your doctor, I recommend breath testing. It is the gold standard of lab testing for SIBO. It is inexpensive, non-invasive, and relatively accurate, although it is dependent on how quickly food travels through your body and requires a lengthy office visit.

What to Expect for the Breath Test

Prior to the test, you will follow a two-part diet to minimize your exposure to fermentable carbohydrates, which can cause a false positive test results. For the first 12 hours you will eat foods such as eggs, clear broth, plain steamed white rice and broiled or baked chicken, turkey or fish. No fats (with the exception of minimal olive oil for cooking), fruits, vegetables, or starches other than plain white rice are permitted. Those who are constipated will follow the diet for longer. 

In the second part, you will fast for 12 hours, generally overnight is fine. Usually, you may drink water and take your prescription medicines, however, check with your healthcare provider as they’re requirements may differ. 

For the test itself, you’ll breathe into a tube to measure your baseline methane and hydrogen levels. Next, you’ll drink a sugar solution and then breathe into a tube again every 20 minutes for three hours so your practitioner can collect a breath sample at regular intervals.23

SIBO breath tests are not yet standardized, but I’ve found the three-hour test is the best because each person’s digestive process happens at a slightly different rate. The longer test also allows your practitioner to see the pattern of gas production for both the large and the small intestines. A typical cut-off between the small intestine and large intestine is 100 minutes and results after that time don’t usually reflect what’s going on in the small intestine. Currently, the general consensus is that a rise in hydrogen of ≥20 p.p.m. by 90 minutes during glucose or lactulose breath testing for SIBO is considered positive.24 

Further, studies show that high methane production is associated with constipation and that patients treated for SIBO saw an improvement in their bowel regularity.25 So if you have SIBO and are dealing with constipation (which is less common), you likely have methane-producing SIBO. During testing, methane levels ≥10 p.p.m. are considered positive for this type of SIBO. 

Whether or not you decide to breath test for SIBO or to investigate treatment based on your symptoms alone, I recommend you watch my free training. I developed this training based on 10 years of clinical practice where I helped thousands of patients overcome SIBO naturally. I share detailed information about what SIBO is, why it occurs, the symptoms, and what you can do to eliminate it naturally in three easy steps. It also includes a simple SIBO diet that will get you back on track fast. My free training is the perfect first step in taking back your health!

SIBO Training - Promo Image - Amy Myers MD

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