Healthy Hormones

The 6 Step SIBO Natural Treatment Guide

Do you struggle with stomach issues like gas, bloating, abdominal cramps, diarrhea and/or constipation, or nausea? 

Does it seem like you have a lot of sensitivities to food that you haven't always had?

Do you struggle with chronic skin rashes, fatigue, asthma, and other symptoms for which you have never gotten relief?

If so, there is a good possibility that you are suffering from small intestinal bacterial overgrowth, also called SIBO.

In this article I will discuss SIBO - what it is, what causes it, and how to diagnose it.

I will also give you a 6 Step SIBO Natural Treatment Guide that will help you resolve the problems and improve your quality of life.

Here we go...


What Is the Purpose of the Small Intestine?

So what exactly does the small intestine do?  A lot actually.

This 20 foot long tube helps us digest our food and absorb vital nutrients.

It also helps fight off infections and regulates our immune system.

The muscles in the walls of the small intestine contract in an organized fashion which pushes the contents further down.  That action helps to clear bacteria before they have a chance to multiply excessively.  This is called peristalsis.

What Is SIBO?

There is bacteria in our entire GI tract, from our mouth to our anus.

The amount of bacteria, however, varies in different parts of the GI tract.

Normally, the amount of bacteria in the small intestine is very low (less than 10,000 bacteria per mL of fluid).  Compare that to the large intestine (colon) where there is normally over 1 billion bacteria per mL of fluid!

Also, the bacteria that live in the small intestine are different kinds than the ones found in the colon.

We have several natural mechanisms that prevent excessive bacteria from growing in the small intestine.  These include:

  • Ileocecal Valve - the valve between the small intestine and colon that prevents the backflow of bacteria from the colon.
  • Stomach Acid - kills the bacteria in the stomach and small intestine.
  • Digestive Enzymes - these also have an antimicrobial effect.
  • GALT - the immune system of the small intestine that will attach and remove foreign materials including bacteria.
  • Gut Motility (peristalsis) - keeps the contents of the intestine moving through before the bacteria in it have a chance to multiply excessively.

If one or more of these protective mechanisms fail, bacteria can begin growing in the small intestine. This is called small intestinal bowel overgrowth, or SIBO.

SIBO is usually not caused by the overgrowth of a single bacteria.  Rather, it is usually many different bacteria that begin growing that are normally present in the colon.

There can also be opportunistic organisms like yeast that can take over that normally are held in check by our healthy bacteria and protective mechanisms.

This increase in bacteria or yeast damages the mucosa of the small intestine which affects its normal function.

The result is digestion is impaired and nutrients are not absorbed as well, such as vitamin B12, iron, vitamin D and vitamin A.  

The mucosal damage can also cause gaps to occur between the cells of the protective lining of the small intestine which allows proteins and bacteria to pass into our bloodstream that would not normally be allowed.  This is called "leaky gut" or intestinal permeability.

The foreign proteins trigger our immune system to react which can cause food allergies or sensitivities, generalized inflammation, and autoimmunity.

SIBO Risk Factors

Several things increase our risk of getting SIBO.  They include:

SIBO Symptoms

SIBO symptoms seem to mirror those seen with irritable bowel syndrome (IBS).  In fact, there is a strong association with IBS and SIBO.

Researchers even recommend that SIBO should be ruled out before giving any person a diagnosis of IBS.

SIBO and Thyroid

Since such a huge part of this blog focuses on thyroid disorders, I believe it is import to discuss the connection between SIBO and thyroid disorders.

Hypothyroidism is an extremely common cause of SIBO that is frequently missed by doctors.

One study found a high risk of SIBO in patients taking levothyroxine, most likely because of decreased gut motility and lack of stomach acid commonly found in hypothyroidism.

If you have hypothyroidism, please study this article closely to see if you have any symptoms that could indicate the presence of SIBO.

On the other hand, if you have been diagnoed with SIBO, it is important that you get a complete thyroid panel drawn from a doctor that is comfortable managing hypothyroidism and Hashimoto's Thyroiditis.

To learn more about hypothyroidism, read my articles here and here.  To learn about Hashimoto's, read my articles here and here.

How to Diagnose SIBO

The most common tests for diagnosing SIBO measure how much hydrogen, glucose, or lactulose the bacteria in your small intestine are producing.

These tests are far from perfect and can result in a high percentage of false-negative results.

For this reason, I don't test every patient that I think has SIBO.  If they have many of the common symptoms, in my opinion it is okay to start treating them for suspected SIBO.

If their symptoms aren't as clear cut, then testing them before beginning treatment may be a good idea.

Testing them after treatment to make sure the SIBO has been eradicated is often a more practical plan.

The 6 Step SIBO Natural Treatment Guide

Before we start with the different treatment options, it's important to remember the primary rule of functional medicine - find the root cause of the problem and correct it.

If you just clear the bacterial overgrowth in the small intestine but you don't address what caused it in the first place, it is likely that the bacteria will eventually return and you will be right back where you started.

For example, if your SIBO is linked to the fact that you eat a ton of sugar and processed carbs, you must address your diet while you are clearing the bacterial overgrowth.

If you have uncontrolled hypothyroidism, you must get your thyroid in balance in order to prevent the SIBO from returning.

There are several steps to successfully eradicating SIBO.  The basic concept is to:

     1.  Reduce or eradicate the invading bacteria in your small intestine 

     2.  Re-populate the small intestine with beneficial bacteria

     3.  Heal the intestinal lining

     4.  Take the right supplements

     5.  Eat the right foods.

1.  Diet -

Diet is the critical first step in healing SIBO.

The bacteria that have overgrown in your small intestine prefer certain foods that they need to grow and multiply.

The fermentation of these foods is what leads to the symptoms that SIBO causes.

That's why your goal should be to remove these foods so that you can "starve" those bacteria.

Several diets have been shown to treat SIBO.  Each has its positives and negatives.  The ones that seem to work the best with SIBO include:

To ensure the best chance at success, I would suggest picking one of the diets and sticking to it and the treatment protocol very strictly for at least 2-3 months.

If you aren't seeing symptomatic improvement, then you can switch to one of the other diets.

If the reintroduction of foods causes a flare in your SIBO symptoms - bloating, gas, diarrhea, etc. - you may need to continue on the treatment protocol for longer or you may even have an undiagnosed food sensitivity.

- Fermented Foods

Once the bacterial overgrowth has been reduced through the diet, fasting, and herbal antibiotic treatment, the next step should be the reintroduction of fermented foods.

Fermented foods contain healthy bacteria that are essential for normal gut health.  They are the ultimate natural probiotic.

Fermented foods can help to repopulate the GI tract with healthy strains of bacteria.

Common types of fermented foods include:

Fermented foods can be a bit of an "acquired taste."  However, I think the benefits they offer make it worth the effort for you to learn how to enjoy them.

Remember, fermented foods should be added LATER in your treatment.  If your SIBO is active, the healthy bacteria in the food can increase the fermentation in your small intestine which can worsen your symptoms.

2.  Probiotics -

Probiotics are an essential component in the treatment of SIBO.

At first, it may not make sense to treat a condition caused by an overgrowth of bacteria with a bacterial supplement.

It is important to realize that the herbal or prescription antibiotics kill both the good and bad bacteria.  For example, in this study, a low carb diet caused a reduction in bifidobactera, one of the good guys.

That is why it's critical to replenish the good guys in the GI tract so you can return to normal gut function.

With that in mind, there are some things you should consider when using probiotics:

  • Not all probiotics work for every person
  • Some probiotics contain prebiotics which can make SIBO worse
  • Some patients do better when probiotics are added AFTER the SIBO has been treated with antibiotics
  • As a general rule, soil-based probiotics are better tolerated in SIBO than lactobacilli and bifidobacteria based probiotics
  • It is usually best to change up the probiotics periodically instead of using the same product all of the time
  • Probiotics are not a substitute for fermented foods and will not work as well

As a general rule, I would suggest using soil-based probiotics during the treatment phase of SIBO.  

In the repopulation phase, I add lactobacilli and bifidobacteria based probiotics if the patient can tolerate them.  This is also when fermented foods should be added.

- Soil-based Probiotics

Soil-based probiotics are usually much better tolerated in SIBO patients than lactobacilli or bifidobacteria based probiotics.

That is why they should be used early during the treatment of SIBO, even when antibiotics are being used.

The soil-based probiotics that I recommend include:

- Lactobacilli and Bifidobacteria Probiotics

The probiotics may actually WORSEN symptoms in the early stages of treatment, but they are generally well tolerated once the bacterial load has been reduced.

I generally recommend adding these probiotics later in the treatment and AFTER treating with soil-based probiotics.

My favorite brands include:

- Beneficial Yeast

Some patients are extremely sensitive to probiotics and have a hard time tolerating any of them.

In those situations, treating them with saccharomyces boulardii can be helpful.

This beneficial yeast competes with the bad bacteria and can help inhibit their growth in the small intestine.

My recommended brand can be found here.

3.  Herbal Antibiotics and Supplements

Herbal antibiotics are essential for treating SIBO.

At times it may be necessary to use prescription antibiotics, but it is preferable to start here.

On this treatment you should usually start seeing a reduction in SIBO symptoms within 2 weeks.  If you aren't seeing benefit by 2-4 weeks you need to reassess your treatment plan and consider going a different direction.

Phase 1 - Reduce Bacterial Burden

There are several herbs that have been shown to have antibacterial and antifungal properties:

  • Berberine 500mg daily - studies
  • Oregano Oil 600mg daily - studies
  • Caprylic Acid 400mg daily - studies
  • Undecylenic Acid 125-250mg daily - studies
  • Thyme Oil 100-200mg daily - studies
  • Grapefruit Seed Extract 100-200mg daily - studies

These herbs are grouped into the following products that are available online:

- Candibactin AR

- Candibactin BR

- AC Formula II

The recommended dosages and treatment lengths are:

  • Candibactin AR/Candibactin BR x 30 days (maximum dose recommended on bottles, titrate up as tolerated.
  • Candibactin AR/BR + AC Formula II + Diflucan x 30 days
  • Candibactin AR/BR x 30 days + Prescript assist + AC Formula II x 30 days at maximum dosages or until symptoms decrease (you should notice a decrease within 2 weeks)
  • For constipation predominant SIBO or IBS - consider adding Antratil - study here

Repeated doses may be necessary for complete eradication.

Phase 2 - Rebuilding and Reducing Inflammation

After 1-2 rounds (or more) of Phase 1, you can move into Phase 2 which will rebuild the normal gut flora and heal the mucosal damage in the small intestine.

- Rebuild the Intestinal Mucosa

Glutamine helps close the tight junctions in the intestinal mucosa which heals leaky gut.

My favorite brand is available here.  Take 1 scoop in water 2-3 x daily.

- Support the Immune System

Several supplements help to support the immune system.  These include:

     Zinc - get my preferred brand here.

     Selenium - get my preferred brand here.

     Vitamin D - get my preferred brand here.

     IgG from Bovine Colostrum - get my preferred brand here.

- Promote liver detoxification

These supplements boost liver function which helps rid the body of toxins.

     Curcumin/tumeric - get my preferred brand here.

     Ginger - get my preferred brand here.

     Milk Thistle - get my preferred brand here.

     This is a great combo supplement with all of them.

- Exercise

Exercise itself can have a positive effect on the gut bacteria.

It is therefore important for you to exercise consistently throughout your SIBO treatment.

4.  Prokinetics

Prokinetics are very helpful in the treatment of SIBO by helping to propel the bowel contents through the GI tract.

This is important because the methane gas produced by the intestinal bacteria actually slows down gut transit.

Keeping things moving through the GI tract prevents constipation.  That is important because each bowel movement helps dump (no pun intended) excessive bacteria from our body via the stool.

It is important to have at least 1 large bowel movement each day.  Anything less is going to cause problems.

Many people have NEVER had regular BMs, so that seems like an impossible goal.  It needs to happen, however.

It will be hard to get your SIBO under control if you are constipated.

If you are chronically constipated, you should have a workup for hypothyroidism which is a common cause of it.

Some natural prokinetics include:

Triphala - this herb has the advantage of helping gut motility but it also helps balance the intestinal bacterial flora which makes it a perfect supplement for SIBO.

- In cases of severe constipation, it is helpful to use Triphala in combination with magnesium.

- In later stages of SIBO treatment, it's better to use this supplement which has other nutrients that help to heal the gut.

At times, it may be necessary to use magnesium citrate (200-2000mg per day) in order to increase your bowel movement frequency.  Vitamin C crystals (ascorbic acid) can also be added to the magnesium citrate if needed.

There are several prescription prokinetics that can be used (erythromycin, Reglan, Propulsid), but they have significant side effects and should only be used when Triphala has failed.

5.  Intermittent Fasting

and terms

There are 2 main ways to kill the unwanted bacteria in the small intestine that you get with SIBO:

- "Starve" them out by selectively avoiding the foods that they feed on, like I discussed earlier under diet.

- Don't eat anything at all for periods of time to really starve them out, otherwise known as intermittent fasting.

Intermittent fasting can be an extremely effective technique for multiple conditions, including SIBO.

Intermittent fasting not only decreases the bacterial load by reducing the amount of food we eat, it also has other benefits:

Start by going without food for 14-16 hours for 2-3 days per week.  

That means eating dinner one evening, then not eating again until lunch the next day.

Make sure you eat the same amount of calories the next day with lunch and dinner that you would have if you had eaten breakfast so you don't damage your metabolism by eating too few of calories.

In other words, make sure your lunch and dinner have at least 1200 calories total.

This technique can go a long way toward improving your symptoms of SIBO.

6.  Antibiotics

I know that this article is about natural treatments for SIBO, but it's important to mention that many SIBO patients may need prescription antibiotics to help eradicate the bacteria in their small intestines.

I recommend almost always starting with the herbal therapies, but if symptoms persist despite 2 or more treatment rounds, it may be time to consider a prescription antibiotic. This could be needed in up to 15% of people.

Also, some people just have difficulty tolerating the herbal therapies.

If you do end up needing a prescription antibiotic therapy for your SIBO, make sure you also request a prescription antifungal medication.

The herbal therapies treat fungal infections, but the prescription antibiotics don't.

My preferred SIBO antibiotic regimen is:

Rifaxim 1200mg + Neomycin 1000mg x 10-14 days plus Diflucan 100mg x 30 days

If patients use this regimen in conjunction with all other therapies I have mentioned in this article, re-treat is usually not necessary.


SIBO is a serious condition that is often misdiagnosed as IBS.

IBS should not be diagnosed until SIBO has been ruled out.

Untreated, SIBO can lead to chronic inflammation, gut issues, and the development of autoimmune conditions.

If you have classic symptoms, it is reasonable to consider treatment even without a diagnostic test.

You can consider testing later to determine if the SIBO has been eradicated.  If your symptoms are not classic, testing may be warranted before starting treatment.

The complete eradication of SIBO can be difficult, but if all steps in this treatment guide are followed, long term success is possible.

This SIBO Natural Treatment Guide includes diet, herbal antibiotics, probiotics, prokinetics, intermittent fasting, and possibly prescription antibiotics.

It is also critically important to identify the root cause of your SIBO and correct it, or else long term success may be difficult.

Now it's your turn...

Have you been diagnosed with SIBO?

What treatments have you tried?

Were the treatments successful?

Did you learn anything from this article that will help you?

About the Author Dr. Jeff Whelchel

Dr. Whelchel is a family physician who specializes in functional medicine, especially hormone optimization. He has over 20 years experience in private practice managing patients with various medical issues. His passion is helping patients reach their full potential of wellness and quality of life. He grew up in the Texas Panhandle where he currently lives. He is married and has 3 awesome children.

Leave a Comment:

Jessica Holley says November 10, 2017

Dr Whelchel, you just nailed all of my sysmptoms that have been destroying my life the last year! I can no longer tolerate magnesium, vit c or my probiotics. My chronic constipation has not been resolved even with 3 hospital stays and 2 surgeries. You have given me hope again! I am so grateful you are on the path of helping your patients regain their health. I need an appointment with you ASAP!

    Dr. Jeff Whelchel says November 10, 2017

    I glad the article helped, Jessica. Try the treatments I listed. If you need help let me know.

honer says June 14, 2019

Great article! We will be linking to this paгticularly great content on our website.
Keep up the good writing.

Emily K says March 23, 2020

I just got diagnosed with SBO and am debating going on Xifaxan as it can worsen symptoms. I usually try the natural route and am hoping your methods help.. have you heard anything about Xifaxan?

    Dr. Jeff Whelchel says April 1, 2020

    I have used it on several of my patients. Overall they typically tolerate it very well. It can be quite expensive so check around on pricing before you buy it. Good luck!

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