SIBO Herbal Treatment: Is It Better?

Have you recently received a diagnosis of SIBO? You may be wondering about treatment and if SIBO herbal treatment is safer or more effective than prescription medication. Great question!

In this article, we’ll be covering what SIBO is, and what treatment options are available. You may be surprised at which ones we recommend for our clients.

SIBO 101

What is SIBO exactly? SIBO stands for Small Intestinal Bacterial Overgrowth. Basically, this means that the colony of bacteria that should be in your large intestine has gone on a field trip and set up camp in your small intestine.

And although this sounds like an infection, SIBO actually isn’t considered to be one. We need a diverse colony of organisms thriving in our gut, we just need them to be in the right place: the large intestine.

Unfortunately, those displaced organisms are causing a ruckus: they’re consuming and fermenting the carbohydrates in your small intestine before they have been absorbed by your body. In addition, these bacteria are able to absorb vitamins and minerals from your food and degrade the lining of your small intestine, making it more leaky.

Enter your SIBO symptoms of bloating, gas, diarrhea, and belly pain – ugh!

You can read our comprehensive overview of SIBO here.

There is much overlap between having SIBO and IBS (1) – yikes!

Let’s get this taken care of, shall we? The first step to an effective game plan is an accurate diagnosis.

Diagnosis of SIBO

There is no perfect method to diagnose SIBO, but breath testing is one of the most common. Breath testing is also the least invasive. Other SIBO diagnostic methods include taking fluid samples from the small intestine – not as easy as a breath test!

The bacteria and other organisms require nourishment to survive and thrive. They eat our food, our nutrients and when they get really surly, they can eat our protective mucus lining (seriously, so rude). The bacteria also produce waste as a normal part of their digestion. Good news: we can measure the waste gasses hydrogen, methane and hydrogen sulfide to identify which critters are taking over.

For example, the bacteria can ferment lactulose and glucose – two sugars that are used in SIBO breath testing.   When the bacteria ferment either lactulose or glucose they release hydrogen, methane and/or hydrogen sulfide.  This is one example of how breath testing can help us know who is living in your digestive system: what are they exhaling (7). We can measure it!

There are three categories of SIBO that we know of today and can diagnose with breath testing: hydrogen dominant, methane dominant, and hydrogen sulfide dominant.

The Belly Bliss approach to SIBO treatment

Many of our clients want to avoid antibiotics. They assume that herbal antimicrobials are a better option because they are natural. 

What is our preferred SIBO treatment?

The treatment that works the best, the fastest and with the fewest side effects.  

We recommend using what is going to help our client resolve SIBO. Nope, we don’t have a preference for SIBO herbal treatment over prescription SIBO treatment. We stay agnostic and don’t advocate one approach over the other: we just want you to feel better and not relapse in the future. Best practices are to have many tools in the toolbox and to work with a knowledgeable practitioner.

What helps SIBO treatment be more effective is first addressing the digestive dysfunction. This means figuring out why have SIBO to begin with. SIBO is easier to treat and the treatment is better tolerated when you know the root cause.

Ready for SIBO Relief?

Match your SIBO treatment to your type of SIBO

Now that you know that there is more than one kind of SIBO, and your breath testing has identified your specific type, we get to dive into SIBO antibiotic and herbal treatment options.

But let’s not forget, we must also address the root cause of your SIBO. Ultimately, SIBO is a symptom of something else going on, not the root cause.

We are going to say this again because it’s so important…The most effective SIBO treatment is the one that also addresses the root cause of your SIBO as well as your specific type. Unfortunately, it’s not always as simple as taking pills to make the problem go away.

Antibiotic treatment for SIBO

Prescription antibiotics and antimicrobials may be your doctor’s first choice for treating your SIBO.

The benefit of antibiotic therapy is that the course of treatment is shorter and is more likely to be covered by your health insurance plan. But that is not guaranteed: Xifaxan (the brand name is called Rifaximin) is one of the main antibiotics used in SIBO. It is expensive and not always covered by insurance.

The negative is that they are not always effective. Plus, some antibiotics may take out more bacteria than just the misplaced organisms in your small intestine. And throwing off the balance of the microbiome may have unintended consequences.

Hydrogen Dominant SIBO

Typically, hydrogen-dominant SIBO is treated with Xifaxan. So far, the effectiveness of this antibiotic is as high as 70%, but unfortunately, the research studies available are pretty small (2). With time, we’ll have bigger and more robust research to further guide treatment.

What’s interesting about Xifaxan is that we don’t absorb the medication, which means it is only acting in our small intestine. It stays local, which is helpful for lowering the risk of causing dysbiosis by killing the good gut bacteria in the colon that you didn’t mean to.

Is it possible to improve the effectiveness of this antibiotic treatment for SIBO? Yes! We can boost the effectiveness of Xifaxan when combined with partially hydrolyzed guar gum (3).

Methane Dominant SIBO or IMO

Another antibiotic that may be used in the campaign against SIBO is called neomycin. Neomycin can kill bacteria, not fungi (4).

Typically, methane-dominant SIBO, which as also known as IMO (Intestinal Methanogen Overgrowth) is treated with a combination of Xifaxan and neomycin, or Xifaxan combined with metronidazole. You may also know metronidazole by the brand name Flagyl (5).  

Hydrogen Sulfide SIBO

Hydrogen sulfide SIBO is new on the scene and therefore a less researched category of SIBO.

There is not yet a consensus on treatment but typically Xifaxan is used. A clinician may also include Bismuth or Pepto Bismol (6).

An overview of SIBO Herbal Treatment

The type of herbal antimicrobials used will depend on the type of SIBO you have. We can help with guidelines based on your symptoms and diagnosis.

To date, there has been only one study comparing the herbal treatment of SIBO with Rifaximin antibiotics. The study used proprietary herbal formulas, compared the improvement in breath testing with Rifaximin treatment and found nearly identical results (8). The key takeaway? Both options are good!

The four proprietary supplement blends that were tested included a mixture of herbal antimicrobials. These included oregano oil and berberine, which are discussed in further detail below. The challenge of studies that include a mixture of ingredients is how to know if each ingredient is absolutely necessary. Further research is needed.

Potential benefits of SIBO herbal treatment

Herbal antimicrobials may be more gentle on your system than prescription antibiotics. You have the ability to slowly titrate up the dosages to reach an effective dose.  

Herbal treatments may also help address other gut health issues, including candida, parasites and other pathogens.

Potential cons of SIBO herbal treatment

Not everyone tolerates herbs, especially those with environmental allergies. Any antimicrobial, including SIBO herbal treatment and antibiotics, can cause die-off and side effects.

A typical SIBO herbal treatment course is 4 – 6 weeks. Treatment might have the unintended consequence of killing bacteria beyond the small intestine, which can cause dysbiosis in the colon, vagina, and beyond. Some herbs are contraindicated with other supplements and medications.

For an in-depth look at SIBO die-off symptoms and how to prevent them, check out our blog post: SIBO Die-Off Symptoms Explained (and How to Prevent Them).

Safety note about herbal supplements

“Natural” SIBO herbal treatment does not mean risk-free.

Just because you can purchase herbal supplements over the counter does not mean they are benign.  It’s critical to work with a knowledgeable practitioner who understands how to use herbs, which herbs are appropriate for your case, in what dose, and for how long.

It is also important to be able to select high-quality brands that are 3rd party tested for purity.

There are numerous herbs that can be used to treat SIBO, so it’s best to work with a practitioner who is well-versed in using them.

SIBO Herbal Treatment Options

We now know that the bacteria involved with SIBO include E. coli and Klebsiella.  The following herbs have been shown to effectively eradicate these bacteria and more. 


Allicin is an active component of garlic. It’s found to have antimicrobial properties against a range of organisms, including fungi, bacteria and parasites (9).

While there is currently no study looking uniquely at Allicin and SIBO to date, Allicin shows promise with how many different organisms it can fight against.  We have found Allicin to be effective with both hydrogen and methane dominant SIBO. 


Berberine is a natural part of the Chinese herb Coptidis Rhizoma, kind of like how curcumin is one of the active ingredients of turmeric. Sometimes abbreviated as BB, berberine may be a helpful SIBO herbal treatment for its ability to reduce inflammation, as measured by several blood markers (10).

One small study found that berberine is helpful for reducing symptoms including abdominal pain and diarrhea in IBS sufferers (and remember that there is a high probability of overlap with SIBO and IBS) (11).

Berberine may also be beneficial for those with an H Pylori infection (12).

And lastly, berberine has been studied in patients with E. coli and Vibrio Cholera infections (poor things). The berberine treatment group felt better and had improvement in their diarrhea (13).


Oregano oil may also help in the fight against your rogue pathogens. Be careful, because too much oregano can cause an upset stomach.

Oregano can be taken medicinally as an essential oil in an enteric coated capsule. While not enough to be considered treatment for SIBO, you can also enjoy adding fresh oregano to your Mediterranean-inspired dishes year-round.

Oregano oil has demonstrated antimicrobial (meaning, it kills microbes, such as bacteria) activity against several species of bacteria (14, 15). Oregano oil can also fight against candida, a yeast that is a normal part of our body’s ecosystem but can grow too much if the balance is upset (16).

In addition, oregano may assist in the fight against parasites (17). One small study showed promising results. Verification with further research would strengthen the state of the science.

Note of caution: Oregano oil can inhibit copper, iron, and zinc absorption (18).  Something to think about if you have iron-deficiency anemia.


Neem is an herbal remedy originating in India. It is used in a wide variety of applications, including as an oral hygiene option (chewing on neem tree twigs) and the oil is used as a pesticide.

Neem is used as one option for treating SIBO, alone or in combination with other herbals, such as allicin (see above) (19). Unfortunately, there is no peer-reviewed research to support this use of neem just yet. Currently, the published research on neem is focused on gingivitis and other measures of oral health.

Safety note: high doses of neem oil come with the risk of neurotoxicity and hepatotoxicity.

How to work with your gastroenterologist

What may be news to you, is that there are a few different types of SIBO, based on which organisms have gone rogue. Your doctor can be a valuable resource in your SIBO diagnosis and treatment if they’re familiar with the condition. And unfortunately, not all doctors are experts in SIBO.

Your gastroenterologist may be able to order your SIBO breath testing. Additional providers for this testing can include chiropractors, naturopathic doctors, clinical nutritionists (that’s us!) as well as functional nurse practitioners.

The best breath testing is comprehensive, meaning that it measures all potential gases: hydrogen), methane and hydrogen sulfide (20).   Trio-Smart is a new SIBO breath test that measures all three gasses.  If you have diarrhea, which is associated with both hydrogen and hydrogen sulfide dominant SIBO, then you may want to consider using this test. 

SIBO herbal treatment: key takeaways

Herbal treatment may help you to recover from SIBO. But matching the right treatment to the right type of SIBO is important, as is working to prevent unintended consequences such as SIBO die-off symptoms.

We don’t necessarily recommend herbal treatment over prescription antibiotics. Either can be effective options.  Regardless of which option you choose, we highly recommend working with a provider who is very knowledgable about choosing which herbs or antibiotics to use to treat SIBO. Unfortunately, we have had clients who were provided with cookie-cutter protocols and they ended up feeling worse.

We recommend getting an accurate diagnosis, identifying your root cause (or causes) of SIBO and working with SIBO experts to develop the most effective plan that resolves your current symptoms and prevents a SIBO relapse.

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