All about SIBO: Small Intestinal Bacterial Overgrowth – NextGen Medicine

sibo test diet

Sibo test diet

All about SIBO: Small Intestinal Bacterial Overgrowth

This article serves as both an introduction and a comprehensive guide to SIBO, or small intestinal bacterial overgrowth. Whether you’ve never heard of it before or are struggling to treat recurring SIBO, this article is for you. I’ll cover what SIBO is, how to test for it, options for treating overgrowth, and the best strategies for preventing recurrence.

NOTE: For a deeper dive and the most up-to-date evidence, please see my article “What the latest research reveals about SIBO“.

What is SIBO, anyways?

A healthy large intestine is home to trillions of microbes, collectively called the gut microbiota, that are crucially important to human health. These microbes aid in digestion, outcompete pathogens, produce signaling molecules, stimulate the immune system, and synthesize vitamins, among other important roles. 1 To keep these microbes a safe distance away from the gut wall, the epithelium secretes a thick layer of mucus.

The small intestine, on the other hand, harbors relatively few microbes. It is the primary site of nutrient absorption in humans and has a thinner mucus layer to optimize the absorption of nutrients. Several mechanisms help to maintain low microbial numbers in a healthy small intestine:

  • Antimicrobial peptides and immunoglobulins secreted by small intestinal epithelial cells
  • Contractions of the smooth muscle lining the walls of the gut, which move the contents along the gastrointestinal tract to the large intestine
  • The acidity of chyme (the mixture of food and stomach juices) when it enters the small intestine
  • The ileocecal valve, located between the small intestine and large intestine, prevents backflow

When these mechanisms break down, abnormally large numbers of microbes bloom in the small intestine. This is called small intestinal bacterial overgrowth, or SIBO.

These microbes ferment food in the small intestine, producing hydrogen and other gases. They can also degrade the thin mucus layer and come in contact with the gut barrier, causing inflammation and intestinal permeability. This can lead to a variety of unpleasant symptoms and consequences.

SIBO symptoms and associated conditions

The symptoms of SIBO are diverse in nature and not necessarily limited to the gut. Here are just a few of the symptoms and conditions that have been associated with SIBO:

IBS-like symptoms: bloating, gas, abdominal pain or cramping; diarrhea, constipation, or both

GERD symptoms: belching, acid reflux, halitosis

Intestinal permeability symptoms: food sensitivities, headaches, skin conditions, joint pain, fatigue, asthma, anxiety, depression, autoimmunity, brain fog

Malabsorption symptoms: anemia, cognitive dysfunction, B12/iron deficiency, weight loss, steatorrhea (fatty stools)

Associated conditions: IBS, IBD, GERD, acne, rosacea, eczema, chronic fatigue syndrome, fibromyalgia, gallstones, gastroparesis, high cholesterol, liver cirrhosis, non-alcoholic fatty liver disease, obesity, pancreatitis, rheumatoid arthritis, positive H. pylori breath test, and restless leg syndrome, just to name a few.

UPDATE 3/26/19: It’s important to note that most of these studies were associating a positive breath test with these conditions. Given recent evidence that suggests breath testing cannot accurately diagnose SIBO, it is unknown how many of these conditions are truly associated with SIBO.

Risk factors for SIBO

Several risk factors have been associated with the development of SIBO:

  • Low stomach acid
  • Multiple courses of antibiotics
  • Alcohol consumption
  • Oral contraceptive pills
  • Proton pump inhibitor use
  • Food poisoning
  • Elderly
  • Organ system dysfunction
  • Prior bowel surgery
  • Motility disorders
  • Muscle/nerve damage to the gut from IBS, IBD, celiac disease

Perhaps the single greatest risk factor, however, is the modern processing of foods and the increase in carbohydrate density in Western diets. Consuming a diet high in sugar and refined carbohydrates is misaligned with the environment that our gastrointestinal tract evolved in:

“Whereas foods with living cells will have their low carbohydrate density “locked in” until their cell walls are breached by digestive processes, the chyme produced after consumption of acellular flour and sugar-based foods is […] suggested to have a higher carbohydrate concentration than almost anything the microbiota of the upper GI tract from mouth to small bowel would have encountered during our coevolution.” (Spreadbury, 2012) 3

Hidden consequences of SIBO: Impaired nutrient absorption and leaky gut

A little bloating and gas may seem harmless, but these aren’t the only consequences of SIBO. Bacterial overgrowth can also cause nutrient deficiency and leaky gut.

Nutrient deficiency

Food passes first through our stomach, then the small intestine, and then finally the large intestine. This means that we, the host, usually get the “first shot” at any nutrients entering the gut, and our bacterial compadres in the large intestine get the “leftovers”. When microbes colonize the small intestine, however, the pecking order changes. Microbes act in their own self-interest compete with the host for absorption of certain nutrients. Since they reside in the center of the GI tract (the lumen), and absorption by the host occurs at the edges of the gut (the epithelial wall), the microbes usually win out.

Microbes that bloom in the small intestine particularly thrive on iron and Vitamin B12. Their human host can quickly become deficient, leading to anemia and cognitive impairment. Microbes in the small intestine can also deconjugate bile, which is crucial for the proper absorption of fat and the fat-soluble vitamins: Vitamin D, Vitamin K, Vitamin A, and Vitamin E.

Leaky gut

Remember that the small intestine only has a thin layer of mucus separating the intestinal epithelium (the gut wall) from the gut lumen (the center). Bacterial overgrowth in the small intestine can quickly degrade this thin protective lining. Direct contact of bacteria with the gut epithelial wall causes inflammation and damage to the absorptive villi of the epithelial cells. This begins a vicious cycle of impaired absorption stimulating proliferation of microbes that only cause more damage.

Inflammation of the intestinal lining can also cause “leaky gut”. The intestinal wall normally forms a tight barrier. In leaky gut, this barrier is breached, and large, non-digested food particles and bacteria can enter the bloodstream. The immune system sees these particles and bacteria as foreign invaders and launches an inflammatory immune response. Chronic damage to the gut barrier, therefore, results in chronic, low-grade, systemic inflammation. Gut bacterial metabolites can also leak through the barrier, and in excessive amounts can lead to neurological issues.

Clearly, SIBO is a serious condition with broad consequences. Next, we’ll discuss testing and treatment.

Testing for SIBO

Unfortunately, the small intestine is a hard place to get to, so testing for SIBO in a clinical setting is extremely difficult. The most popular way to test for SIBO is using a breath test. After consuming a carbohydrate substrate, the amount of hydrogen and methane gases on the breath are measured using repeated samples taken for 2-3 hours. Two types of tests are available and differ based on the substrate used.

Lactulose breath testing (LBT): Lactulose is not digestible by humans, but it is by bacteria. LBT can diagnose overgrowth at the distal end of the small intestine (the ileum), which is thought to be most common. LBT is more sensitive than glucose breath testing, but less specific, meaning there will be a higher rate of false positives.

Glucose breath testing (GBT): Both humans and bacteria use and absorb glucose. Glucose is absorbed within the first three feet of the small intestine. Therefore, GBT reflects overgrowth in the proximal end of the small intestine, and cannot diagnose distal overgrowth. GBT is more specific, but less sensitive, meaning there will be a higher rate of false negatives.

Which to choose?

Given that distal SIBO is more common, and that treatments for SIBO are relatively safe, I tend to favor the lactulose breath test. In other words, we’d rather over-diagnose SIBO than under-diagnose it, since the consequences of untreated SIBO far outweigh any risks of treating someone who doesn’t actually have SIBO. When choosing a laboratory for testing, make sure that they use the Quintron machine, as this has been validated in peer-reviewed studies, and that they test BOTH hydrogen and methane. I prefer the three-hour test, as this allows you to see what happens as lactulose enters the colon.

Preparation for SIBO testing

Preparation for SIBO testing is very important to get an accurate result. Here are the recommended test preparation steps to improve breath test accuracy: 4

  • 4 weeks before the test: avoid any antibiotics (unless retesting after eradication therapy)
  • 2 weeks before the test: complete any antimicrobial supplements
  • 1 week before the test: avoid promotility drugs and laxatives such as high dose vitamin C and magnesium if possible
  • 1 day prior to the test: avoid all fermentable foods such as complex carbohydrates, fruits and vegetables, spices, and herbs. Consume plain meat, broth, and steamed jasmine rice. Stop all non-essential supplements and medications.
  • 12 hours before the test: begin an overnight fast and consume water only. Avoid vigorous exercise and smoking the day of the test.

Limitations of SIBO testing

As discussed earlier, breath testing is not a perfect science. False negatives and false positives are common. Currently available breath tests also only measure hydrogen and methane and do not include hydrogen sulfide, which may be the predominant gas produced in some patients with SIBO. 5 Other patients may have small intestinal fungal overgrowth (SIFO), which can cause symptoms similar to those observed in SIBO, 6 and this will not be reflected in a breath test. Despite these limitations, breath testing remains the best way to clinically diagnose SIBO.

UPDATE 3/26/19: I no longer recommend breath testing for SIBO, in light of recent evidence. Please see “What the latest research reveals about SIBO” for up-to-date information on SIBO testing.

Test interpretation

For many years, different researchers, clinicians, and laboratories used their own guidelines for interpreting SIBO test results. This made it difficult to compare across studies and was unnerving for patients when different practitioners gave them different interpretations. There was a clear need for a standardized approach.

In 2015, a group of SIBO experts convened for the North American Consensus to review current literature, reconcile differences between studies, and develop standardized diagnostic criteria for SIBO. 4

The updated criteria are as follows:

Hydrogen: a rise in hydrogen of 20 ppm from baseline in the first 90 min is considered a positive result 4

[Rationale: There is no part of the gut that does not have bacteria, so the previously used “double peak” criteria for diagnosing SIBO doesn’t really make sense (i.e. there is no trough of bacteria between the small intestine and the colon). Additionally, the colonic peak always happened at 105 minutes or later in normal patients. Since some patients have more rapid transit time, 90 minutes was suggested as a fair guideline.]

Methane: a methane level of 10 ppm or higher at any time during the test is considered a positive result 4

[Rationale: The devices currently used for measuring methane have an error rate of ±2 ppm, and 98% of patients that start at 5 ppm eventually surpass 10 ppm. While prior guidelines focused on the increase in methane, the real issue is whether a patient produces methane at all, since most of the methane being produced is from the previous day, not from consumption of the substrate.]

Hydrogen sulfide: the missing gas?

In some cases, a relatively flat-line across the three hours despite obvious symptoms of SIBO may be indicative of hydrogen sulfide (H2S) production. Dr. Pimentel has said that he will be releasing new data on a commercial test for hydrogen sulfide (H2S) in June 2018.

Different forms of SIBO

Based on the results of the breath test, there are three primary forms of SIBO.

Hydrogen only: overgrowth of bacteria in the small intestine ferment fibers to produce hydrogen.

Methane present: about 45% of people with SIBO will also have elevated methane on the breath test. This is indicative of excessive bacteria and archaea present in the small intestine. In particular, a group of archaea called methanogens selectively feed on hydrogen produced by other bacteria and produce methane. Reflux and belching are more common in patients with elevated methane, and methane production is highly correlated with constipation. 7

Hydrogen sulfide present: some people with SIBO will have elevated hydrogen sulfide production. In this case, bacteria called sulfate-reducers feed on hydrogen produced by other bacteria and produce hydrogen sulfide. It’s thought that this type of SIBO may be more common in those with diarrhea-predominant IBS. 5

Now that we have some background on testing and the types of SIBO, let’s move on to treatment.

Treating SIBO: antibiotics and antimicrobials

In treating SIBO, the overall goal is to reduce bacteria in the small intestine, repair the intestinal lining, and prevent relapse by addressing the underlying causes that led to SIBO in the first place. To do this, we take a comprehensive approach that includes several interventions.


Antibiotic treatment seeks to address the bacterial overgrowth itself and is the first choice for most gastroenterologists. Rifaximin is the antibiotic of choice for most cases of SIBO, though a combination of rifaximin and neomycin may be used if a positive result for methane is detected in the breath test.

Both rifaximin and neomycin are poorly absorbed, meaning that they remain in the intestine and do not have systemic side effects. Rifaximin also works via a different mechanism than most antibiotics and does not result in antibiotic resistance. 8 Studies have shown that a two-week course of rifaximin does not have long-term negative effects on the composition of the gut microbiota, and may even increase levels of Bifidobacteria and Lactobacillus. 9 Meanwhile, it’s quite effective at reducing overgrowth in the small intestine.

According to a 2017 meta-analysis, a single dose of rifaximin successfully eradicated SIBO in 71% of patients, with improvement or resolution of symptoms in 68%. Even if the first course of antibiotics doesn’t work, repeated courses of rifaximin may be successful. 10,11 Unfortunately, despite its effectiveness, rifaximin still isn’t yet approved by the FDA for SIBO and must be ordered by a physician for IBS-D. 11 In patients with elevated methane, rifaximin is only 28% effective, but a combination of rifaximin and neomycin was able to eradicate methane in 87% of individuals. 12

*Important note: restrictive diets such as GAPS or low FODMAP are not recommended during antibiotic or antimicrobial treatment, since microbes may transition into a dormant state when food is not available and will be less susceptible to treatment. In fact, feeding the microbes may significantly increase the efficacy of antibiotic treatment. 13


Like antibiotics, herbal antimicrobials seek to address the bacterial overgrowth. One multi-center study found that herbal therapies are at least as effective as rifaximin, with similar response rates and safety profiles. 14 Herbal therapy is often a good first-line treatment, since herbal antimicrobials can also correct other dysbiosis issues, such as fungal overgrowth, parasites, and overgrowth of pathogenic bacteria in the colon. These can also be ordered without a physician.

Common antimicrobial protocols use oregano, berberine derivatives, neem, garlic, and other herbs alongside a biofilm disruptor and a monolaurin supplement.

SIBO Diets

Several diets have been suggested for the management and treatment of SIBO.

Low-FODMAP diet

The low FODMAP diet is an excellent choice for short-term therapeutic relief. FODMAPs stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. These are specific types of carbohydrates that are highly fermentable and stimulate the growth of microbes. In controlled studies, a low FODMAP has been shown to reduce symptoms in 76 percent of patients compared to 54 percent of patients given standard dietary advice. 15 However, it doesn’t necessarily eradicate the bacteria.

Furthermore, Low FODMAP may be detrimental to the colonic gut microbiota in the long-term. Most FODMAPs are prebiotics, meaning that they selectively feed and promote the growth of beneficial bacteria in the large intestine. Cutting all FODMAPs out of your diet may starve microbes in the small intestine, but it also starves beneficial bacteria in the colon. It also may alter colonic pH and interfere with proper vitamin absorption. For these reasons, I do not recommend a low FODMAP diet for more than 2-3 months. It should only be used as short-term symptom relief and should not be used in place of antimicrobial or antibiotic treatment.


The Gut and Psychology Syndrome (GAPS) Diet was designed by UK practitioner Dr. Natasha Campbell McBride and is loosely based on the Specific Carbohydrate Diet (SCD). GAPS focuses on removing all potentially inflammatory and fermentable carbohydrates (including but not limited to FODMAPs), healing and sealing the gut barrier, and restoring healthy digestive function and microbiota.

GAPS is an extreme diet and is not recommended as a first course of treatment for most patients with SIBO, but may be worth considering in patients with severe neurological and/or gastrointestinal issues. The therapeutic bone broth that is considered a staple of the GAPS diet should also be a staple in any SIBO treatment or prevention protocol.

Elemental Diet

An elemental diet is another extreme approach that seeks to starve the bacteria by replacing all meals for two weeks with an elemental formula of powdered nutrients in pre-digested, easily absorbed form.

There are several disadvantages to this method, including not being able to eat solid food for 2-3 weeks, unintended weight loss, and the unpleasant taste of the formula. Like the low FODMAP diet, it will also effectively starve the bacteria in your colon. However, it has a surprising 80-84% success rate in eradicating SIBO, and is safe and well-tolerated.

Because of its extremity, the elemental diet should only be used as a last resort if other SIBO treatments have failed. If you go this route, I recommend a homemade formula. Commercially available elemental formulas are expensive and incredibly high in carbohydrates, sugar, and artificial ingredients.

Preventing SIBO recurrence

Despite treatment, recurrence of SIBO develops in almost half of patients. This is because SIBO itself is a “symptom” of underlying causes. If these underlying causes are not addressed, bacteria can regrow within as little as two weeks of finishing antibiotics or antimicrobials.

The three major mechanisms that seem to contribute most to SIBO are impaired motility, poor gastric acid secretion, and colonic microbial dysbiosis. There are several risk factors that I discussed earlier that you want to be sure to address as well.

With these in mind, here are six key steps to preventing SIBO recurrence:

  • Eat a lower carbohydrate diet: Avoid large amounts of carbohydrates and eliminate refined carbohydrates entirely from your diet. Replace them with non-starchy vegetables. This will significantly reduce the chance of overgrowth recurring.
  • Use prokinetic agents: In many cases, SIBO relapses because eradicating the bacteria does not correct deficiency of the migrating motor complex (MMC). The MMC is responsible for moving bacteria down into the large intestine every 90 to 120 minutes during periods of fasting at night and between meals, clearing them from the small intestine. Many conditions, such as diabetes mellitus and scleroderma, can affect the muscles in the gut and impair MMC function. Therefore, prevention should include motility agents such as the herbal formulation Iberogast or the prokinetic drug Low Dose Naltrexone, particularly in cases of SIBO with constipation.
  • Restore stomach acid: Restoring the acidity of chyme entering the small intestine is crucial for inhibiting bacterial overgrowth. This can be accomplished using betaine HCl supplements. You should also check for nutrient deficiencies, as zinc, iodine, potassium, sodium, and chloride are required for gastric acid production.
  • Try intermittent fasting: Fasting stimulates the MMC and sends “housekeeping” waves through the small intestine, sweeping food or bacteria into the large intestine. Constant eating or snacking, on the other hand, results in the constant presence of food in the small intestine – the perfect environment for SIBO.
  • Avoid alcohol consumption and use of medications that promote SIBO: Alcohol, proton pump inhibitors, and oral contraceptives have all been associated with an increased risk of SIBO.
  • Support a healthy gut microbiota: Dysbiosis in the colon can disrupt gut motility and is therefore a predisposing factor to SIBO. Consuming plenty of fermented foods, prebiotic fibers, and taking a probiotic of soil-based organisms can help to reseed a healthy microbiota after eradication therapy.

And there you have it – everything you need to know about SIBO! If you appreciated this article, be sure to subscribe to my weekly newsletter to get updates on my latest posts and health-related research.

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