Small intestinal bacterial overgrowth (SIBO) can cause constipation, diarrhea, malnutrition, unexplained weight loss, and fatigue. Find out what causes it, how to test for it, and what you can do to treat it. Fixing SIBO can greatly improve your health in addition to other biohacks and healthy life choices.

What is SIBO?

The small intestine is designed to have a lot fewer bacteria compared to the large intestine (colon). The upper two-thirds of the small intestine usually contains less than 10,000 bacteria/mL.

In healthy individuals, bacteria in the small intestine provide many benefits [1]:

  • protecting the gut from bad bacteria
  • boosting the immune system
  • keeping the gut lining healthy
  • producing nutrients such as vitamins B9 and K

SIBO is defined as an increase in the number of bacteria or the presence of abnormal bacteria in the small intestine. Currently, >100,000 bacteria per mL are considered to be the cutoff for a diagnosis [1].

In most cases, SIBO is caused by multiple strains that live in the colon. It is less common for SIBO to be a result of an increase in the number of bacteria already found in the small bowel [2].

Bacteria can cause damage by stealing nutrients and releasing toxins. This leads to malabsorption and malnutrition.

SIBO patients are often deficient in vitamins A, D, E, B12, B9 (folate), calcium and iron [1, 3].

The bacteria can also steal protein before it is absorbed, leading to protein deficiency.

Symptoms of SIBO

SIBO can cause a variety of diverse symptoms which include [1]:

Because these are general, nonspecific symptoms, it can be hard to tell the difference between SIBO and other conditions such as IBS, lactose intolerance, or fructose intolerance.

It is not known how frequent SIBO is in the general public. A study in 34 healthy young adults found the syndrome in ~6% of them [4].

Does SIBO Cause Other Diseases?

SIBO is linked to several other diseases, including IBS and autoimmune diseases. In many cases, the severity of these diseases also relates to the number of bacteria.

1) May Cause Irritable Bowel Syndrome (IBS)

SIBO is present in 30 – 85% of patients with irritable bowel syndrome (IBS) [1, 5]. In 111 patients with IBS, treatment with the antibiotic neomycin improved their symptoms (DB-RCT) [6].

The prevalence of SIBO in celiac patients varies between 50 – 75% [7, 8].

2) Inflammatory Bowel Disease

SIBO is present in 25 – 33% of patients with Crohn’s disease [9, 10, 11].

Small bowel overgrowth is also linked to ulcerative colitis (UC). One study found bacterial overgrowth in ~18% of UC patients [5].

3) Rosacea

SIBO may also cause diseases outside of the gut. One study found SIBO in 46% of rosacea patients. Ten days of antibiotics completely reduced skin lesions in 20 out of 28 patients and greatly improved the condition in six of the remaining eight. Those who did not receive treatment either saw no improvement, or their skin condition got worse [12].

4) Fibromyalgia

A study showed that all 42 patients with fibromyalgia tested positive for SIBO. The severity of the overgrowth was linked to the degree of pain [5].

5) Other Diseases

SIBO is also common in people with:

  • hypothyroidism
  • non-alcoholic fatty liver disease
  • rheumatoid arthritis
  • cirrhosis of the liver

The amount of overgrowth is related to the severity of these diseases as well [13, 14, 15, 16, 17].


SIBO is usually caused by many factors and conditions.

These can be broken down into three distinct groups [1]:

  • Disorders of the gut’s antibacterial mechanisms
  • Structural abnormalities
  • Disorders that cause slow digestion

1) Disorders of Antibacterial Mechanisms

The digestive system has ways to prevent the overgrowth of bacteria, such as stomach acid, bile, enzymes, and immune cells. A lack of any of these allows bacteria to thrive, leading to SIBO [18].

Low Stomach Acid and Enzyme Production

Stomach acid destroys bacteria before they reach the small intestine [4]. A lack of acid production allows bacteria to pass through the stomach into the small intestine where they can multiply. Enzymes released from the pancreas also help destroy bad bacteria in the small intestine [1].

Lack of Bile Flow

Bile acids inhibit bacterial growth in the small intestine [19]. When bile production in the liver or flow from the gallbladder decreases, pathogenic bacteria in the small intestine increase [19].

Underactive Immune System in the Gut

Immunoglobulin A (IgA) is a type of antibody that helps fight bad bacteria in the gut. SIBO is common in people with a genetic condition that lack IgA (selective IgA deficiency) [20]. Bacterial overgrowth is also common in AIDS patients due to an underactive immune system [21]

2) Structural Abnormalities

Structural flaws in the small bowel can lead to SIBO. Certain structural abnormalities trap bacteria and allow them to accumulate.

Small Intestinal Inflammation

Diverticula are small pouches in the small intestine that can become inflamed. These pouches can collect bacteria and lead to SIBO.

One study found that 59% of the patients with diverticulitis had SIBO. Treatment with antibiotics decreased the SIBO and the inflammation [22].

Bad Connections Between Intestine and Organs

Intestinal fistulas are unnatural connections between an organ and the intestines. Bacteria can become trapped in these connections [4].

Ileocecal Valve Dysfunction

The ileocecal valve separates the end of the small intestine from the beginning of the large intestine. When this valve is damaged or removed, bacteria can come up from the large intestine and take over [23]. Bacterial overgrowth occurs soon after patients have their ileocecal valve removed [24].

Stomach and Gut Surgeries

Stomach and gut surgeries such as gastric bypass surgery can cause SIBO [25]. Stomach and gut surgeries that bypass parts of the gut can create sections that collect bacteria called blind loops [25]. Because SIBO often develops in people who have these blind loops, it is often referred to as Blind Loop Syndrome (BLS).

3) Disorders Causing Slow Digestion (gut flow disorders)

Normally, the muscles lining the stomach and small intestine will contract and relax in waves. This process is known as the migrating motor complex (MMC). The MMC stops bacteria in the colon from coming up into the small bowel [26].

Peristalsis is the movement of food down the gut caused by wavelike contractions of muscles lining the gut. It occurs whether food is present or not.

Any disease or disorder that stops the MMC or slows peristalsis will let bacteria from the large intestine travel into the small intestine.

Diabetic neuropathy

Diabetic neuropathy is damage to the nerves of the gut from diabetes. When the nerves become damaged because blood sugar is too high, gut movement slows down and bacteria are allowed to accumulate.


Scleroderma is a chronic connective tissue disease. It partially blocks the intestines, slowing down the movement of food. This also allows bacteria to accumulate.

Research has found SIBO to be present in 43 – 56% of scleroderma patients [27, 28].

Other Causes

Overconsumption of Alcohol

If you have SIBO, you may want to keep the drinking to a minimum. Heavy alcohol use has been associated with SIBO [R]. Even moderate alcohol consumption (1 drink/day for women, 2 drinks/day for men) can lead to SIBO [29]. Alcohol damages the gut in many different ways, including:

  • Decreases enzymes
  • Damages the villi
  • Thickening of the gut wall with connection tissue (fibrosis)
  • Slows gut movement
  • Decreases immune system in the gut

Some bad bacteria may even be able to feed off alcohol [30]. All of these factors lead to bacterial overgrowth.

Overconsumption of Refined Carbohydrates

Diets rich in refined sugars tend to increase the growth of bacteria, both good and bad [31]. The body can only absorb so much sugar at once and any extra can be used by opportunistic bacteria [32, 4]. SIBO patients also have less of the enzymes needed to break down and absorb sugars, allowing leaving them to be absorbed by bacteria [4].

Common Risk Factors

The following increases the risk of developing SIBO:

  • Use of proton-pump inhibitors (PPIs) and other antacids [33]
  • Use of painkillers [33]
  • Lack of breastfeeding [34]
  • Antibiotic use [4]
  • Age [4]
  • Celiac Disease [35]
  • Crohn’s Disease [35]
  • IBS [4]
  • Liver diseases [4]
  • Kidney Failure [4]
  • Inflammation of the pancreas [4]
  • Leaky Gut [36]
  • Immunodeficiency [33]
  • Diabetes Mellitus (type I and type II) [33]

Birth Control Medications

Use of birth control medications has been associated with IBD and IBS [37, 38]. Given the strong link between these conditions and SIBO, it is likely that birth control pills are also associated with SIBO.

How To Test

There are two popular tests used to diagnose SIBO:

  • jejunal aspiration
  • hydrogen breath test (HBT)

Hydrogen/Methane Breath Test

The challenges of jejunal aspiration led to the invention of another type of test called the hydrogen breath test. It is the most popular way to diagnose SIBO due to its low risk, simplicity, and noninvasive nature.

The test involves the patient fasting overnight and then eating a sugar that is fermented by the bacteria in the small intestine. The gases from the bacteria are then captured and used to see if there is an overgrowth [4].

HBT has its drawbacks. In about 15 – 30% of people with SIBO, the bacteria will produce methane instead of hydrogen [39].

It is necessary to also test for methane if the hydrogen breath test is negative. People who test positive for methane tend to have constipation [40, 6, 41].

The HBT also has a high false negative rate. This means that the test turns up a negative result when in fact the person does have SIBO [36].

Lastly, there is no consensus as to what determines a positive result. The only way of being confident in the results is to treat SIBO and see if symptoms disappear [4].

Despite these drawbacks, most doctors still prefer the use of the HBT [42].

Some practitioners even prefer using a stool or urine testing (organic acids), but there isn’t any scientific support for these tests.

Hydrogen breath tests can be administered by a gastroenterologist. They can also be purchased online and performed in the comfort of your home. Results are sent into a lab to be tested for the presence of SIBO.

Sampling The Small Intestine

The gold standard for SIBO testing is a jejunal aspiration. This involves taking a sample from the small intestine and counting the number of bacteria per mL.

It is a costly and invasive procedure that requires a tube to be inserted into the small bowel. Another issue is the risk of contamination of the tube as it is passed through the stomach [4].


Many different antibiotics, diets, and supplements are effective in eradicating SIBO. Most conventional doctors will treat the condition using antibiotics. However, SIBO often returns.

1) Pharmaceutical Antibiotics

The standard therapy for SIBO is antibiotics such as tetracycline, vancomycin, metronidazole, neomycin, and rifaximin (mainly individually) [43]. This is counterintuitive, as antibiotics can cause SIBO. However, certain antibiotics like rifaximin actually reduce bacterial overgrowth.

Rifaximin’s effectiveness has been thoroughly studied. It is also poorly absorbed so it stays in the gut and doesn’t lead to bacterial resistance [44].

This table is a summary of trials for rifaximin and other antibiotics for the treatment of SIBO.

Subject typeSubject numberDrugsDurationEffectivenessSource

Children with IBS


33600 mg RifaximinDaily for 1 week21 children tested negative for SIBO45

SIBO patients


191,200 mgDaily for 10 days8 patients have a normal breath test, but no symptom resolution46

IBS and SIBO patients


106800 mg (200 mg, 4x daily) RifaximinDaily for 14 daysImproved digestive symptoms in all patients and eliminated overgrowth in 55 out of 64 patients that were re-tested.47

SIBO and IBS patients


83500 mg neomycinDaily for 10 daysImproved symptoms by 35% (11% for placebo), 20% of patients tested negative6
SIBO patients1421200 mg rifaximin or 500 mg metronidazole7 days63% eradication rate for rifaximin, 44% for metronidazole48
Methane-positive SIBO patientsNo. of patients taking:

Neomycin = 8

Rifaximin = 39

Both drugs = 27

500 mg 2x/day neomycin and/or

400 mg 3x/day for rifaximin

10 daysEradication rates

33% neomycin alone

28% rifaximin alone

87% both drugs


Although rifaximin is safe and effective, it is very expensive. A month’s supply retails for ~$1,300 and is not usually covered by commercial health plans in the U.S. [50].

2) Probiotics

Probiotics are helpful in managing and even eliminating SIBO, even more so than antibiotics like rifaximin. Probiotics help with gut disorders such as bacterial overgrowth by [51, 52, 53, 54]:

  • competing for nutrients with bad bacteria
  • producing compounds that fight against bad bacteria
  • preventing leaky gut
  • reducing inflammation
  • boosting the immune system

This table is a summary of studies of probiotic therapies for SIBO.

Bacteria strainSubject typeHow the bacteria was takenEffectivenessSource

Lactobacillus casei


IBS patientsDaily yogurt drink; 6.5 billion CFUEliminated SIBO + improved symptoms in 9 out of 14[55]


Lactobacillus casei and Lactobacillus acidophilus



22 Chronic diarrhea related to bacterial overgrowth, 12 treatment, and 10 control21-day supplementationReduced number of stools and hydrogen levels in the breath test, although the effects did not last after stopping(DB-RCT)




Bacillus coagulans



30 stomach pain or diarrhea with SIBO2x daily for 3 weeks93% negative breath test vs 67% controls, 100% stomach pain and other digestive symptoms resolved vs 50% controlled[57]


3 Bifidobacterium strains



Stomach and gut cancer patients (200)250 mg, 2 tablets 3x/d for 4 weeksBreath test decreased and digestive symptoms improved in 51/63 probiotic group vs 16/63 control group[58]

Combination of:

50 liver disease patients with SIBO4-week supplementation of 5 billion CFU capsule dailyEradicated in 6 out of 25 patients with probiotic vs 0/25 in control group. Digestive symptoms improved with probiotic only.(DB-RCT)



Why SIBO or IBS Patients React Poorly to Probiotics

In many SIBO patients gut movement is slowed down. Normally, the movement of the gut sweeps bacteria and food down, preventing them from collecting in the small intestine. Decreased gut movement allows bacteria to grow in the small intestine [60].

In addition, giving more bacteria to someone that already has too much may make the issue the worse.

Many probiotic products also contain prebiotics, which can be fermented by the bacteria in the small intestine. This can worsen SIBO symptoms.

3) Herbal Antimicrobials

Herbal antibiotics may be cheaper and have fewer side effects than drugs [50].

Herbal formulas FC Cidal and Dysbiocide, or Candibactin-AR and Candibactin-BR were more effective (46% vs 34% eradication rate at 4 weeks) than 1200 mg daily rifaximin [50]. The formulas contained extracts of well-studied antibacterial herbs such as thyme, wormwood, olive leaf, ginger, and oregano, in addition to other less-studied ones [61, 62, 63, 64, 65].

Herbal extracts that may help with SIBO include:

  • Oregano oil kills or inhibits many strains of bacteria in the intestines [66].
  • Berberine prevents the growth of several bacteria in the gut [67].
  • Red thyme essential oil prevents the growth of Escherichia coli and Staphylococcus aureus, both of which have been found play a role in SIBO and IBS [68, 69, 70].
  • Olive leaf prevents the transfer of bacteria from the large to the small intestine [71].

A combination of nine different herbs called Iberogast® has been studied for its treatment in gut disorders such as IBS. One trial (DB-RCT) found that Iberogast improved IBS symptoms compared to placebo [72]. It is believed to work by improving gut flow and killing bad bacteria [73].

4) Elemental Diets

An elemental diet is a liquid diet that consists of the individual nutritional parts of food such as:

  • amino acids
  • fats
  • sugars
  • vitamins
  • minerals

It’s given to patients with inflammatory bowel diseases because the nutrients don’t need to be digested and are absorbed easily.

Elemental diets starve bacteria because they are low in carbohydrates that the bacteria in the small intestine eat.

In IBS patients with SIBO, 15 days of an elemental diet resulted in normal breath tests for 80% of the patients [74].

While these results are great, it is important to recognize that there are downsides to the diet. Elemental formulas do not taste pleasant and can be challenging to stay on for long enough. Indeed, 25% of subjects refuse to stay on the diet for more than 2 – 3 weeks [75].

If you have tried other treatments without success, an elemental diet may be worth trying.

5) Low FODMAPs, Specific Carbohydrate Diet, and GAPS Diets

A diet called the low-FODMAP (Fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet has been shown to treat symptoms of irritable bowel syndrome [76, 77, 78]. The diet limits carbohydrates that are poorly absorbed by humans but easily eaten by bacteria.

Given the link between SIBO and IBS, it is likely that the effectiveness of the low-FODMAP diet is due to its ability to starve bacteria.

Another diet called the Specific Carbohydrate Diet (SCD) restricts all carbohydrates besides glucose and fructose, as they do not need to be broken down to be digestive. The diet is based on the fact that many people with gut disorders don’t have the enzymes necessary to break down carbohydrates and therefore can only tolerate simple sugars.

The effectiveness of SCD in treating SIBO is questionable. One study found that the low FODMAP diet, but not the SCD improved symptoms of IBS after three months. A potentially worrying result was that patients on the SCD saw their vitamin D drop by 42% and their folic acid levels drop by 67%.

The Gut and Psychology Syndrome (GAPS) diet is another diet that resembles the low FODMAP and SCD diets. It restricts complex carbohydrates like those found in grains, and starchy vegetables and potatoes. The GAPS diet incorporates lots of fermented foods and bone broth. Bone broth helps heal the gut due to its gelatin content and provides minerals that are often deficient in SIBO patients.

Note: Some people may respond negatively to the bone broth as it contains certain carbohydrates that can feed bacteria in the small intestine, potentially making SIBO worse. If this is the case, it is recommended to eat meat broth instead, which contains less of these carbohydrates but still helps heal the gut with gelatin and minerals.

6) Lectin Avoidance Diet

Following the lectin avoidance diet may help with SIBO. The diet excludes grains, beans, nuts, seeds, most potatoes, and all dairy. These foods may feed bacteria in the small intestine and damage the gut lining, making SIBO worse.

How to Prevent Relapse

A difficult aspect of treating SIBO is that it often comes back after treatment has stopped [56]. This is because there is usually an underlying disorder or disease causing it.

If there are other disorders, those should also be treated to prevent the overgrowth from coming back. Otherwise, it may be necessary to continually treat SIBO.

In patients who tested negative for SIBO after taking rifaximin, 44% of them tested positive for it nine months later. Symptoms also returned during this time [43].

Prokinetic Drugs

Prokinetic drugs are drugs that stimulate gut movement (peristalsis). These include:

  • Octreotide
  • Low-dose naltrexone
  • Tegaserod
  • Low-dose erythromycin.

Tegaserod is a prokinetic drug that activates serotonin (5-HT) receptors in the gut, increasing gut movement [79].

Researchers tested tegaserod or low doses of the antibiotic erythromycin (also a prokinetic) in preventing SIBO from returning in 64 IBS patients. These patients had eliminated SIBO with antibiotics and were symptom-free.

The time until SIBO returned was 60 days in those who didn’t take a prokinetic. Erythromycin extended this time to 139 days and tegaserod extended it to 242 days [56].

Vagus Nerve Stimulation

Improving the function of the vagus nerve (vagal tone) may also help prevent SIBO from coming back. The vagus nerve plays a key role in digestion by causing the release of stomach acid and digestive enzymes [80].

The vagus nerve also plays a role in the wavelike movements of the bowels that push food along the gut (peristalsis). Peristalsis helps prevent the buildup of bacteria [81].

Read this post to learn how to improve the vagus nerve function.

Stress Management

Stress is likely to play a role in SIBO [1].

A review of 15 randomized controlled trials showed that psychological therapies aimed at reducing stress improved IBS symptoms and quality of life in IBS patients [82].

You can learn how to take control of your stress in this post.


The migrating motor complex (MMC) that helps push bacteria down the intestines is only active in the absence of food, so fasting and not eating between meals may also help stop SIBO from returning [26].

User Experiences with Antibiotics, Supplements, and Diets

A blogger with SIBO noted that treatment with rifaximin allowed him to stay symptom-free, but symptoms returned when he stopped antibiotic treatment. He eventually eliminated SIBO by eating a diet low in fermentable carbohydrates (GAPS diet), taking oregano and ginger pills, and using betaine HCL and digestive enzymes with meals [83].

Another SIBO sufferer had constipation and bloating after stopping rifaximin treatment, but was able to reduce these symptoms by taking digestive enzymes, bile, and low-dose erythromycin.

One person blamed multiple relapses of their SIBO on probiotics and finally found relief by using ginger, grape seed extract, and glutamine [84].

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About the Author

Will Hunter

BA (Psychology)
Will received his BA in Psychology from the University of California, Los Angeles. 
Will's main passion is learning how to optimize physical and mental performance through diet, supplement, and lifestyle interventions. He focuses on systems thinking to leverage technology and information and help you get the most out of your body and brain.

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