Herbs for SIBO Protocols: Do They Work?

Small intestine

Does using herbs for SIBO protocols work?

First off, if you have SIBO, you already know it can be a beast to beat. From conventional prescription drugs to herbal protocols and other supplements for SIBO, patients now have a lot of options to consider.

But when discussing herbs for SIBO, which are usually not recommended by gastroenterologists, the question is, what are those options, and more importantly, do they work?

If you are new to SIBO, let’s start with a quick primer.

What is SIBO?

Small intestinal bacterial overgrowth, also known as SIBO, is a condition in which pathogenic bacteria populate in the small intestine. While we normally want a variety of healthy bacteria in our gut, an overgrowth of bad bugs in the small intestine, a section of the digestive tract that doesn’t normally host a large amount of bacteria, is not ideal.

For starters, bacteria love to ferment certain carbohydrates and produce gas … and gas is normal!

The problem is, when these bacteria produce gas in the small intestine, which does not expand as readily as the large intestine, the gas can feel painful and “stuck.”

And given how long and winding the small intestine is, all that poor trapped air has a long journey to get out, and so it ends up causing a lot of discomfort.

As you can see from this diagram, the small intestine is not an ideal place for gas to collect.

Small intestine

Complications from SIBO

Additionally, this bacteria overgrowth can cause more problems. One important role of the small intestine is to absorb nutrients from our food. When SIBO is present, the small intestine cannot do this nearly as effectively.

First, the overgrowth of bacteria reduces the output of digestive enzymes. That means we can’t break down our food as efficiently, and our food is easier for the bacteria to then ferment. Excessive fermentation = gas.

Brilliant on SIBO’s part, but bad for us and our ability to absorb nutrients from our food.

Second, poor digestion can then cause the gut to either move food through our system too quickly, causing diarrhea, OR can cause the opposite and stop us up completely. In many cases, people will have both. It can feel like a no-win game.

Third, poor digestion can also cause upward pressure as all that gas builds up. This gas pushes on the sphincter between the stomach and esophagus, allowing air and acidic liquid to move upwards. This is why many with SIBO may also experience reflux and/or frequent burping.

As you can see, there are many unpleasant downstream effects that come with this condition, and these are just a few. SIBO can cause so many symptoms and present in so many different ways, which makes it very tricky to identify and treat.

Thankfully, we do have many treatment options for SIBO, including many herbs for SIBO sufferers.

But first, we need to figure out which “type” of SIBO a person has, aka, what type of bacterial overgrowth is happening.

How to Test for SIBO

If you didn’t already know, we DO have tests for SIBO. And they do not involve getting your blood drawn or sending in a stool sample! Good news, right?

Breath testing options are available, and these tests help us figure out if a person produces primarily one (or multiple) of three gasses: methane, hydrogen, or hydrogen sulfide.

“Typically” (and I put this in quotes because there are always those outliers), methane producers have constipation, hydrogen producers experience diarrhea, and hydrogen sulfide producers tend towards diarrhea but may experience both.

Because of these generalities, testing is key because the type of gas someone produces helps determine the most effective treatment options.

If you need testing, reach out to a practitioner. Gastroenterologists can order these tests, although they may or may not offer, so ASK. Additionally, dietitians and naturopaths can usually order these tests as well. Our office can order these tests for our clients or refer out to options locally.

Traditional Treatment Options for SIBO

Now, I realize we discussed using the most effective treatment option based on SIBO testing results. Unfortunately, many GI docs are only going to offer one treatment: Rifaximin (aka Xifaxan). Most are not offering herbs for SIBO treatment.

First off, I’m not going to downplay this drug. Rifaximin is pretty amazing. Once a discarded antibiotic, it was soon discovered that this forgotten drug had impressive actions in the digestive tract BUT did not get absorbed elsewhere.

That fact made it useless in many respects, but the realization that it could kill unwanted bacteria specifically in the gut without going systemic like most antibiotics do, was a lightbulb moment for SIBO researchers.

Now prescribed to many SIBO patients, it’s actually most effective for hydrogen producers. If you are in the methane or hydrogen sulfide camp, you may or may not see much help.

Aaaaand, that is why we are talking about herbs for SIBO …. Because Rifaximin only works for certain people.

And if you didn’t know, a notable study back in 2014 showed that herbal treatments for SIBO were just as effective as prescription options, and in many cases, MORE effective.

Herbs for SIBO

Let me preface this by saying, herbs are effective. They can be so effective, much like drugs, that they should always be used in conjunction with advice from a practitioner. PLEASE do not self-treat.

The options and advice given here are for informational purposes only. Seek professional guidance to know which herbs and in which combinations would be ideal for you. In some cases herbs for SIBO treatment can do more harm than good when used incorrectly.

With that said, let’s dive into some common herbs used for SIBO. While of course you should work with a practitioner on the exact regimen, I truly believe patients should be informed about what they are taking and why. Use this as information to stay informed and involved with your own care.

Herbs for SIBO: Berberine

Berberine is a compound from a number of plants (Goldenseal, Oregon Grape) that has been used medicinally for hundreds of years to treat a variety of conditions, from nausea to high cholesterol to diabetes. It may also have a role in gut health and is often one of the herbs used to treat SIBO.

Several studies have shown that berberine has anti-microbial properties. It appears berberine may work by inhibiting the growth of unwanted bacteria. Berberine may also reduce inflammation, which can allow the gut to heal and restore more quickly.

However, because berberine can change the microbiome, it should only be used under the guidance of a health professional and only for a set amount of time. We have very little data on the long-term use of berberine and its impact on the gut.

The typical berberine dosage for most conditions is 500 mg, three times per day, although dosages for SIBO are often much higher.

One thing to note: Berberine may interact with other medications, so always consult with your practitioner before starting any new supplements.

Herbs for SIBO: Oregano Oil

Oregano oil, a traditional medicine used in numerous cultures over the centuries, has a wide range of health uses. The oil’s active ingredients, carvacrol and thymol, have well-established anti-viral, anti-fungal, and antimicrobial properties.

In addition, oregano oil appears to have anti-inflammatory and antioxidant benefits, all of which could be helpful in SIBO.

The oils from oregano help eradicate SIBO by breaking down the cell membranes of pathogenic bacteria while keeping beneficial strains intact.

Naturopaths often recommend dosing at 50 mg, three times per day, however some go much higher than that. Make sure to work with a knowledgeable SIBO practitioner to determine the right dose and for how long.

One thing to note: The oils from oregano and other herbs can be irritating to the mucosa of our digestive tract. Make sure to take in an encapsulated form that releases the oils where they need to be. Avoid taking oregano oil or other essential oils orally as a liquid. Liquid forms are usually recommended for topical use only.

Herbs for SIBO: Neem Oil

Neem oil is extracted from the Neem tree. Used for centuries in Ayurvedic medicine, it is known to have potent anti-inflammatory and antimicrobial effects while also providing support to the immune system.

Often combined with other anti-microbial oils, neem oil on its own is quite strong. In fact, it’s often been used as a natural pesticide and human cases of toxicity have been reported.

Naturopaths commonly recommend somewhere around 300 – 500 mg, three times per day. While you can easily find neem oil capsules online, remember to consult with a practitioner before using and only purchase from trusted sources.

One thing to note: Neem oil may act as a form of contraception. If you are trying to get pregnant or thinking of doing so, avoid neem oil and consult your doctor before trying ANY herbal protocols.

Herbs for SIBO: Allicin

Allicin is a compound found in garlic that has been well-studied. Much like the aforementioned oils, it also has antioxidant, antimicrobial and anti-fungal properties. It has been used for a variety of health conditions from treating high blood pressure and cholesterol, to cancer and infections, and to treating gut issues, especially SIBO.

Currently there is no standard dosing for allicin, but naturopaths often use 600-900 mg per day, divided into 2-3 doses.

Toxicity is rare, but some may experience side effects such as stomach upset and occasionally diarrhea.

One thing to note: Allicin is not the same as taking straight garlic. If you experience bloating or other unpleasant side effects when eating garlic and other high FODMAP foods, you will likely not experience that with allicin supplements.

Other Herbs for SIBO: Herbal Blend Products

Below are listed a couple of common herbal blend products that are used for SIBO protocols. These products combine many of the herbs for SIBO we just discussed so there are fewer products to purchase and fewer pills to take.

Let’s take a look at a few of these popular formulations.

Candibactin AR and Candibactin BR

These products by Metagenics are some of my favorites. They were used as one of the treatment protocols in the 2014 study previously mentioned that showed herbs could be just as useful for SIBO as prescription antibiotics.

Together, they cover most of the herbs discussed. The usage and protocol differs by practitioner, but I often have my clients doing Candibactin BR twice a day and Candibactin AR 1-2x per day, depending on their needs.

I have noticed that sometimes burping or a slight twinge of indigestion is often reported with Candibactain AR, which includes a decent dose of oregano oil, but that usually resolves within a week.

Dysbiocide and FC Cidal

Both of these products offer a wide range of herbs, some of which we have discussed here and some of which we haven’t.

Combined, they appear to have very potent anti-bacterial effects.

This was also one of the protocols used in the 2014 study that found herbal treatments were just as effective as Rifaximin.

I do not use these products as often, but the standard dose is 2 capsules, twice per day, for both products.

How to Use Herbs For SIBO?

The recommended length of time to take herbal products often varies, but it is typically advised to stay on the regimen for at least 30 days.

Occasionally a practitioner will keep someone on a protocol for longer, but it depends on the type of SIBO and severity.

Also, treatments may vary depending on how long someone has had SIBO and whether or not this is the first time being treated.

With any protocol, however, NEVER use these herbal treatments long term unless advised to do so by a practitioner who specializes in SIBO.


Because these herbs, as described, DO change the microbiome. In most cases this is beneficial, but long-term outcomes are unknown. Additionally, these herbs may begin to impact the microbiome negatively, ie affecting the GOOD bacteria, over time.

Once the SIBO has been cleared or the recommended time of the protocol has ended, it is always good to taper off the products and re-assess.

This, again, is where working with a skilled practitioner is key. DO NOT self-diagnose or self-treat. More often you will do more harm than good, and you waste a whole lot of money in the meantime.

In Summary

If you are suffering from SIBO and the standard pharmaceutical recommendations are not working, there are herbs for SIBO that you can consider.

Because diagnosing the type of SIBO you have and assessing other symptoms are so critical to choosing the right herbal protocol, always consult with a practitioner specializing in gut health first.

Otherwise, you risk wasting a lot of money and potentially worsening or prolonging your symptoms.

Questions? Please reach out! I am a registered dietitian specializing in gut health. Our office has access to many SIBO testing options and herbal protocols. Additionally, I have a network of naturopaths and gastroenterologists I refer to routinely to make sure my clients get the breadth of care they need.

SIBO is NOT something you have to live with. Reach out and determine your next step today.


Danielle VenHuizen, MS, RDN

Registered Dietitian, Certified LEAP Therapist