Small intestinal bacterial overgrowth (SIBO) treatment may include antibiotics, which reduce bacterial overgrowth, as well as vitamin, calcium, and magnesium supplements, which help address nutritional deficiencies. Specific diets, such as the elemental diet and the low-FODMAP diet, may also be used to help individuals avoid symptom-triggering foods.

This article explains the options you and your healthcare provider can discuss for treating SIBO including taking antibiotics and adjusting how you eat.

Antibiotic Therapy

For now, the “gold standard” treatment for SIBO is using antibiotics to reduce bacterial overgrowth in the small intestine. These medications are also thought to ease inflammation in the small intestine lining, which could cause malabsorption.

SIBO can be categorized in two ways:

  • Methane-dominant SIBO usually results in constipation.
  • Hydrogen-dominant SIBO causes diarrhea.

Antibiotics are used to treat both types of the disease, but along with antibiotics, methane-dominant SIBO may require you to take fiber.

Unfortunately, there are no clear SIBO treatment guidelines, and more research on the use of antibiotics for SIBO is still needed. Several types of antibiotics are used to treat SIBO, but which is best for a specific individual and at what dosage is still not clearly understood.

Xifaxan: First Course of Treatment

For now, the primary antibiotic used to treat SIBO is Xifaxan (rifaximin) since most patients seem to benefit from it. Research indicates that Xifaxan, a brand name for the generic drug rifaximin, kills various strains of bacteria, improving symptoms.

Antibiotics Commonly Prescribed to Treat SIBO

Your healthcare provider may start treatment with one type of antibiotic. If symptoms persist or reoccur, you may be prescribed a different one.

  • Flagyl (metronidazole)
  • Cipro (ciprofloxacin)
  • Tetracycline
  • Amoxicillin-clavulanate
  • Neomycin
  • Norfloxacin
  • Xifaxan (rifaximin)

In the body, Xifaxan is not absorbed into the bloodstream. This reduces side effects and improves the drug’s ability to act directly on the bacteria in the small intestine.

Another benefit is that Xifaxan has little impact on bacteria in the large intestine. This lowers the risk of gastrointestinal symptoms and yeast infections, which are common with other antibiotics.

Despite the promising research, Xifaxan has not been approved by the FDA for the treatment of SIBO (although it is approved for treating diarrhea-predominant IBS and travelers’ diarrhea). Therefore, prescribing Xifaxan for SIBO is considered “off-label” use.

While some side effects are possible, in general, Xifaxan is considered a safe medication.

With incomplete research, there’s no definitive consensus regarding the proper dosing and duration for using Xifaxan for SIBO. In most clinical trials, higher dosages are more effective than lower doses. In clinical practice, Xifaxan is most often prescribed in courses of two weeks. Other antibiotics may be prescribed simultaneously or in tandem with repeated courses prescribed as needed.

Dietary Interventions

In addition to using antibiotics to regulate intestinal bacteria, you may be able to manage SIBO symptoms by addressing nutritional deficiencies or avoiding foods that cause symptoms.

Nutritional Deficiencies

If you are diagnosed with SIBO, you should work with your healthcare provider to identify and address any possible nutritional deficiencies. Supplements should be taken for any or all of the following vitamins and minerals if a deficiency is found:

  • Vitamin AVitamin B12Vitamin DVitamin ECalciumMagnesium

If your healthcare provider believes that steatorrhea and/or another type of fat malabsorption is present, they may recommend that you take a pancreatic enzyme supplement.

Elemental Diet

The elemental diet is a diet restricted to medically formulated liquids. Nutrients are consumed in their most elemental form so it’s easy to digest and absorb them.

Some health practitioners recommend an elemental diet along with antibiotics to help people with SIBO because it reduces the amount of food that bacteria can work on. It also may lower your overall gut bacteria, which will improve symptoms.

More research is needed to understand the benefits of this hard-to-follow dietary plan. Meanwhile, it’s recommended that you do not try this at home with homemade formulas because there’s a risk of nutritional deficiency.

The Low-FODMAP Diet

The low-FODMAP diet was designed to reduce the symptoms of IBS. The idea is to temporarily restrict your intake of carbohydrates, or high FODMAPs, that contribute to IBS symptoms.

With SIBO, two of the five FODMAP types, lactose, and fructose, may be poorly absorbed due to inflammation along the lining of the small intestine. In addition to these two, other non-absorbed FODMAPs may be fermented by the bacteria residing inappropriately in the small intestine, leading to bloating and other digestive symptoms.

Therefore, the low-FODMAP diet may be helpful for SIBO because eating fewer carbohydrates might “starve” the bacteria in the small intestine. However, as of yet, there are no clinical studies on the subject.

Not much is known about the appropriateness of the low-FODMAP diet for a person taking antibiotics for SIBO. Some experts think the diet may reduce the effectiveness of the antibiotic treatment because it makes bacteria dormant. Instead, it’s recommended that you eat a normal diet while on antibiotics. After the course of antibiotics, you can follow the low-FODMAP diet to prevent future SIBO recurrences.

Before You Change Your DIet

It is best to follow a FODMAP diet under the guidance of a registered dietician or nutritionist.

Address Underlying Issues

Before prescribing antibiotics, your doctor will do a complete physical exam and medical history to see if your SIBO symptoms could be due to an underlying condition.

Diseases that Affect the Small Intestines

Certain diseases can contribute to the onset of SIBO  and may impair digestion in the stomach or small intestine. These include:

  • Gastroparesis, which affects the nerves in the stomach, causes a slow down in the digestive process. It’s often related to diabetes, and if blood sugar is regulated it may go away.
  • Celiac disease, an autoimmune disease that affects the small intestines, causes problems with absorption in the digestive tract. People with celiac disease are at higher risk for SIBO. For these individuals, strict adherence to a gluten-free diet is essential for improving symptoms and overall health.

Structural Problems

In addition to disease, abnormalities in the digestive system’s structure can lead to the development of SIBO. Some of these defects may be correctable through surgery. They include:

  • Blind loops
  • Bowel obstruction
  • Diverticula present in the small intestine
  • Fistulas
  • Crohn’s disease of the small bowel
  • Strictures

SIBO may also be experienced by those who have undergone a partial colectomy (removal of the colon), which can result in colonic bacteria flowing backward into the small intestine.

Medication Side Effects

Sometimes, a medication used to treat a different health problem may cause conditions that foster SIBO. These medications include:

  • Opiate medications typically prescribed for pain
  • Proton pump inhibitors (PPIs) typically prescribed for GERD

Discontinuing these drugs may help to reduce SIBO symptoms.

The Future of SIBO Treatment

As more research is done on SIBO, more treatments are likely to emerge. A particularly exciting avenue of research is the development of advanced technology which will accurately identify the presence and type of bacteria present in a person’s small intestine. In the meantime, other possible options are being explored as possible safe, effective treatments for SIBO.

Herbal Formulations

In one published study, the herbal formulation was found to be at least as effective as Xifaxan for treating SIBO.

Herbal formulations also promise to avoid the side effects of antibiotic medication and treat those for whom antibiotics are not working. They may also prevent the recurrence of SIBO.

Prokinetic Medications

Prokinetic medications are used to treat gastrointestinal disorders and acid reflux. They may also help with SIBO. Preliminary research suggests that these medications may be especially helpful for those with SIBO and scleroderma.

Prokinetic medications may be helpful because they potentially enhance the power of the small intestine’s own “cleansing wave” to wash bacteria out.

Probiotics

In theory, probiotic supplements may be helpful for treating SIBO because they have been shown to have a positive effect on bacterial makeup, to improve the health of the gut lining, and to reduce inflammation. However, there is a lack of significant research on the effectiveness of probiotics in treating SIBO.

Preventing Relapse

Despite success in treating SIBO with medication, relapses are common. Not much is known about the best way to prevent SIBO symptoms from returning. The recommended course of action is to prescribe a course of antibiotics rather than have people modify their diet. If necessary another course of antibiotics is prescribed.

It can be difficult to understand what those diet modifications would look like. It may be helpful to follow the low-FODMAP diet for a short time. It may also be helpful to avoid foods containing artificial sweeteners such as aspartame, saccharin, and sorbitol, which hold the potential for interacting with bacteria present within the small intestine.

Summary

SIBO can be extremely painful and reduce your quality of life, but it doesn’t have to be that way. Antibiotics are often completely effective at treating SIBO. However, it may take multiple antibiotics, or you may need repeat treatments if SIBO recurs.

If you have found, through a breath test or elimination diet, that you have either lactose intolerance or fructose malabsorption, you may want to avoid foods containing these sugars for the same reason.

Along with taking medication, it’s recommended that you modify your diet to ensure you are getting adequate nutrients and to prevent inflammation.

SIBO can be complicated by other medical conditions that affect digestion. Taking care of these diseases and conditions can reduce the amount of bacteria in your intestines and stop inflammation. 

Researchers continue to look for treatments that help with easing SIBO symptoms. The hope is to reduce side effects and lower the risk of SIBO returning after antibiotics clear up the bacteria.

Frequently Asked Questions

  • What is the root cause of SIBO?
  • Bacterial overgrowth in the small intestine is believed to be caused by a change in acidity in the small intestine that makes it easier for bacteria to grow. Decreased movement in the organ causes that bacteria to sit, altering the balance of digestive enzymes.
  • What does SIBO poop look like?
  • Most commonly, SIBO causes loose, watery stools. The condition interferes with the absorption of different nutrients, including fat. Fat malabsorption can result in oily, smelly stools that float.
  • What is the best treatment for SIBO?
  • SIBO is treated with antibiotics to reduce bacteria overgrowth. Xifaxan (rifaximin) is considered the best antibiotic for treating SIBO. It is not absorbed into the bloodstream, so it act directly on the bacteria and minimizes side effects.
  • How long do I have to take antibiotics for SIBO?
  • SIBO is typically treated with a two-week course of antibiotics along with lifestyle changes.
  • How can I naturally cure my SIBO?
  • Dietary changes can help hinder bacteria growth, reduce inflammation, and address nutritional deficiencies. A 2014 study found that herbal remedies like oregano oil, berberine extracts, and lemon balm may be as effective as standard SIBO treatment, but more research is needed.
  • Does SIBO ever come back after antibiotics?
  • Yes. Studies estimate that about 44% of people with SIBO experience symptoms again within nine months of initial treatment.
  • How long does SIBO take to heal?
  • This depends on what caused it, and if it’s being managed, as well as how much bacterial overgrowth there is. Many people will feel better within four weeks of treatment, but others will require continued treatment or will need to be treated again.

Bacterial overgrowth in the small intestine is believed to be caused by a change in acidity in the small intestine that makes it easier for bacteria to grow. Decreased movement in the organ causes that bacteria to sit, altering the balance of digestive enzymes. 

Most commonly, SIBO causes loose, watery stools. The condition interferes with the absorption of different nutrients, including fat. Fat malabsorption can result in oily, smelly stools that float. 

SIBO is treated with antibiotics to reduce bacteria overgrowth. Xifaxan (rifaximin) is considered the best antibiotic for treating SIBO. It is not absorbed into the bloodstream, so it act directly on the bacteria and minimizes side effects.

SIBO is typically treated with a two-week course of antibiotics along with lifestyle changes.

Dietary changes can help hinder bacteria growth, reduce inflammation, and address nutritional deficiencies. A 2014 study found that herbal remedies like oregano oil, berberine extracts, and lemon balm may be as effective as standard SIBO treatment, but more research is needed.

Yes. Studies estimate that about 44% of people with SIBO experience symptoms again within nine months of initial treatment.

This depends on what caused it, and if it’s being managed, as well as how much bacterial overgrowth there is. Many people will feel better within four weeks of treatment, but others will require continued treatment or will need to be treated again.