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Natural Treatment Options for SIBO - Small Intestinal Bacterial Overgrowth

Updated: Nov 12, 2022

An overgrowth of bacteria in the small intestines can lead to bloating, abdominal discomfort, excessive gas, constipation or diarrhea and malabsorption. SIBO is a common cause of irritable bowel syndrome (IBS) and linked to an array of diseases and disorders. (Visit Your Guide to SIBO for more information on the causes, symptoms and triggers).


Treating SIBO typically involves killing the excess bacteria with antibiotics or natural herbal antibiotics. However, SIBO can be challenging to address and recurrences are common.


This article outlines the therapeutic treatment options available.

Woman holding her abdomen

There are 5 options for the treatment of SIBO.

1. Prescription Antibiotics - specifically Rifaximin (brand name Xifaxan). This antibiotic is used to kill the excess bacteria.

2. Natural Herbal Antimicrobials - oral supplements that contain natural herbs, oils and spices that also have the ability to kill bacteria and other microorganisms.

3. Special low carbohydrate diets - to starve the bacteria.

4. Probiotics - certain types can reduce symptoms.

5. Prokinetics - supplements or drugs that improve the motility of the gut and sweep the bacteria from the small intestine back down into the colon.


Typically a combination of these options is used.


Antibiotics for the treatment of SIBO - prescription or natural?

The standard treatment for SIBO is prescription oral antibiotics, given for 2-4 weeks, depending on dose and symptom response.


A specific antibiotic called Rifaximin (brand name Xifaxan) has the most research to support its use in the treatment of SIBO.

Another drug, Neomycin, is often given alongside Xifaxan to improve outcomes in those with methogenic-dominant SIBO.


Metronidazole (brand name Flagyl), an antibiotic and anti-parasitic medication, is also sometimes used. However, it is known to have a large range of potential side effects from depression and irritability, to headaches, dizziness, thrush, nausea, vomiting and even stomach pain, constipation and diarrhea. Alcohol needs to be strictly avoided strictly while taking and for a few days before and after. Some of the rarer side effects of Metronidazole are potentially life threatening. (Medsafe data sheet)


Side effects with Xifaxan are rare, but headaches, diarrhea, nausea, vomiting and swelling are some of the symptoms that can occur.


Other prescription antibiotics have the potential to aggravate the condition, rather than improve it, so care needs to be taken.


Xifaxan works well for treating SIBO because it is not absorbed systemically. It stays in the gut where it can kill the overgrown bacteria and is less likely to cause side effects. Studies also suggest it does not have negative effects on healthy bacteria that live in the colon.


Its success rate at normalizing SIBO breath tests is 50 to 70%. Though recurrence can occur many months later.


Unfortunately Xifaxan is expensive and not easily available in some countries (including New Zealand). Metronidazole may be used instead.


What are the natural options to treat SIBO?

Herbal anti-microbials (also called herbal antibiotics) are oral supplements that contain natural herbs, oils and spices that kill bacteria and other microorganisms.


Unfortunately herbal antibiotics have not been well studied. However, there is research to suggest that herbal therapy is just as effective as Rifaximin for the treatment of SIBO.


Examples of common anti-microbial herbs and products used are:

  • Berberine (found in goldenseal, Oregon grape, barberry, coptis, phellodendron)

  • Oregano essential oil

  • Olive leaf extract

  • Thyme essential oil

  • Neem oil (Azadirachta inidca)

  • Allicin (from garlic)

  • Grapeseed extract

  • Atrantil (contains quebracho, conker tree, and M. balsamea Wild extracts) - more for methogenic bacteria

  • Candibactin by Metagenics (contains Thyme and oregano oil, berberine, oregon grape and other herbs)

  • SIBO guard by Bioceuticals (combination herbal supplement)

  • Biocidin by Bio-Botanical Research (combination herbal supplement)

  • Happy Belly by Metabolic Maintenance (combination herbal supplement)

Branch of ripe red barberry after a rain with drops of water
Branch of ripe red barberry (source of Berberine)

Products used by functional medicine practitioners and other holistic practitioners to treat SIBO usually contain one or more of these herbs and the top quality products are typically only accessed through a practitioner.


Combining several herbs during treatment can be beneficial since different ones target different bacteria and have synergistic effects.


Treatment length can be anywhere from 4 to12 weeks.


Many practitioners prefer herbal anti-microbials because they are affordable, can address other issues in the gut such as a fungal overgrowth and parasitic infection, and they are less likely to contribute to antibiotic resistance.


What diets are used to treat SIBO?

Since the bacteria primarily eat carbohydrates, all SIBO diets aim to reduce carbohydrates and therefore their food supply, effectively starving them.

The only carbohydrate that bacteria do not eat much of, is insoluble fiber.


The established SIBO treatment diets are:

  • The Specific Carbohydrate Diet (SCD),

  • The Gut and Psychology Syndrome Diet (Gaps Diet),

  • The Low FODMAP Diet (LFD)

  • SIBO Specific Food Guide (a combination of SCD + LFD) and it's variant the SIBO Bi-Phasic Diet.

  • The Elemental Diet (a meal-replacement beverage that contains only the simplest forms of nutrients, used for just 2-4 weeks)

These restrictive diets can be used as a main treatment for SIBO, or in conjunction with natural or prescription antibiotics.

They can also be used after anti-microbials to give the gut time to heal or used to prevent a recurrence.

Though there is some debate as to whether long term use of these diets is a good idea given they can be very restrictive and fermentable carbohydrates are needed to feed beneficial gut bacteria in the colon.


Disagreement also exists around following these diets while taking anti-microbials as some believe reducing carbohydrates simply causes bacteria to “go into hiding” inside biofilms and become more difficult to kill. Others believe it is an additional tool to starve and kill the bacteria.


Some practitioners use other food restrictions, such as removing gluten and dairy, in order to reduce die-off symptoms and aid gut healing. As the bacteria die, toxins can be released and temporary, often flu-like symptoms, can develop. The Herxheimer or die-off reaction is a natural response to the destruction of harmful bacteria and other threatening microorganisms.


The success rate of the elemental diet is around 80%.The Specific Carbohydrate Diet (SCD) has a 75% to 84% success rate if followed strictly. However recurrence often occurs once stopped.


Probiotics for the treatment of SIBO?

Research suggests that taking oral probiotics can reduce the symptoms of SIBO and interfere with the growth of bacteria in the small intestine.

Probiotic supplement

Treatment of SIBO with probiotics along with antibiotics gave an 82% symptom improvement, compared to those only receiving antibiotics, in one small study.


In another study, specific probiotics given twice a day for 30 days reduced symptoms by 70% in people with IBS and SIBO, compared to just 10% symptom reduction in people who had IBS but no SIBO.


Probiotic strains that may help include:

It pays to note that some probiotic strains may actually increase symptoms, and although certain probiotics may reduce symptoms, it is not clear if they prevent a SIBO recurrence.


What are Prokinetics and how can they be used to treat SIBO?

Prokinetics are drugs or supplements used to improve the motility of the gut and sweep the bacteria from the small intestine back down into the colon.


It is thought that the main cause of SIBO is a disturbance in the migrating motor complex (MMC), a pattern of contractions that occur in the gastrointestinal tract between meals.

This cyclic, recurring wave of movement clears food and bacteria out of the small intestines. It occurs every 90 minutes or so when your stomach is empty.


When this doesn't occur frequently enough, due to underlying conditions, abdominal scar tissue, frequent sitting and even stress, the bacteria can build up or even migrate up from the colon into the small intestines where there is even more food to digest and ferment.

It's this fermentation process that produces a release of gas.

Excessive amounts of gas leads to bloating, abdominal distension and pain.


What are popular prokinetics?

Iberogast herbal supplement
  • Iberogast - a herbal liquid available at many pharmacies which has been found to be effective with minimal side effects.

  • Tegaserod - a prokinetic pharmaceutical drug

  • Ginger

  • Artichoke extract

  • 5HTP - the precursor to the neurotransmitter serotonin that can be given as a supplement. It can also be helpful for low mood symptoms, but is not always appropriate for those on SSRI anti-depressants.

Because prokinetics do not kill or starve the excess bacteria, it is often used in addition to dietary changes and antimicrobials.


Which treatment option is right for me?

I've found that those SIBO sufferers who get the best results and do not need multiple rounds of treatment have used a combination of natural anti-microbials and prokinetics with dietary and lifestyle changes. Probiotics and other gut healing supplements are then used after the antimicrobials.


The challenge is knowing the dose, type and duration of the anti-microbial supplement, as the severity of overgrowth and type of bacteria present is different for everyone.


A comprehensive stool test can give an indication of the type of bacteria present in the colon which is more than likely to also be in the small intestine, but is not guaranteed.


Some stool tests even evaluate which antimicrobial is likely to be most effective at killing a specific pathogenic bacteria. This is helpful if pathogenic, disease-causing bacteria are also present.


Extended use of antimicrobials may reduce the amount of beneficial bacteria in the colon, so this must be considered when deciding dose and duration of an antimicrobial.


For some an overgrowth of bacteria or fungi can additionally occur in the large intestine, so antimicrobials that impact different types of microbes and in the lower intestines can be highly beneficial.


Since relapses are high, multiple rounds of treatment may be necessary.


What tends to improve outcomes are lifestyle and dietary changes, avoiding certain medications, addressing structural issues and improving gut motility.


You can learn more about how to prevent SIBO and a relapse by heading here.


Looking for help to address your SIBO or IBS symptoms? Check out our "work with me" page.



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