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SIBO Part II: Natural Treatment and Therapies

Dr. Jolene BrightenPublished: Last Reviewed: Food Leave a Comment

As we talked about in the previous post, “SIBO Part I: What Is It & How Do I Know If I Have It?,” SIBO can be quite difficult to treat.

Today, in SIBO Part II, I want to share my approach to treating this condition and what steps you can take right now to heal your gut.

When treating SIBO, I first look at the factors that may have contributed to the condition in the first place. This requires a thorough understanding of your health story. In addition to the lactulose breath test used to diagnose SIBO, I order further testing to examine possible underlying causes, potential nutrient deficiencies, and health conditions that may have been caused by the bacterial imbalance.

Here are just a few tests I may consider running, depending on your symptoms and health history:

  • CBC
  • CMP
  • Ferritin
  • Celiac Panel
  • Thyroid Panel
  • Stool testing for fat malabsorption
  • Food Allergy/ Sensitivity
  • Cortisol
  • Insulin
  • HgA1C
  • Colonoscopy or Endoscopy

Now let’s break it down into the specific treatment approaches to this condition.

There are many moving parts when it comes to treating SIBO, and they all work together to heal and balance.

SIBO Natural Treatment Therapies


In my experience, diet is absolutely essential for treatment to be successful. The two diets I often recommend Fermentable Oligo-, Di-, Monosaccharides And Polyols (FODMAPS). This diet are intended to “starve out” the bacteria, but not you (although it may feel that way at first glance).

In addition to the diet, I recommend that people allow about 3-4 hours between meals. The idea behind this is to allow the migrating motor complex (the mechanism that causes a sweeping motion to occur in the small intestine during fasting states) to move food through your system and to avoid giving anything extra to the excess flora.

Diet alone can reduce the number of bacteria significantly, although it may take a couple of years to do so. So, before jumping all in on the diet, consider working with a licensed health care provider. The timing of using this diet is important and in my practice, we aim to use therapeutic diets for the shortest period of time for our patients to experience benefits.

HCl and/or Digestive Enzymes:

Hydrochloric acid (HCl) is produced in the stomach and, along with aiding with digestion, it is a powerful antimicrobial. It is also necessary for liberating nutrients from your food so they can be absorbed by the body.

SIBO is common in patients with pancreatic conditions, such as chronic pancreatitis. Because of this and the bacteria’s ability to interfere with bile, digestive enzymes can be a necessary part of therapy.

In my clinic, I use Digest with my patients because it is a combination of HCl, pancreatic enzymes and bile acids, which help with absorption and create an environment where these bugs do not thrive. This is a good thing. 😉

Herbal Antibiotics:

As noted above, diet alone does have the ability to reduce the number of bacteria, but you must be diligent and it takes quite a bit of time. I have found great success using herbal antimicrobials, often in combination, to eradicate the number of bacteria in the small intestine. Berberine, oregano oil, allicin (garlic) and black walnut are some the more common herbal antimicrobials used in SIBO.

In my practice, I begin patients with Gut Clear at 1-2 caps once to twice daily depending on the person's case, a natural antimicrobial herb, along with Digest, and a biofilm disrupter like NAC.

What is often missing from the antimicrobial treatment of SIBO is the use of biofilm disruptors, like N-acetylcysteine. Biofilms act as a form of protection against these antimicrobial agents. These biofilm disruptors can make treatment more effective, but can also create a bigger die off reaction.

I also want to note that you can also use Rifaximin, a pharmaceutical, with all cases of SIBO. However, this drug is very expensive and can be a barrier to treatment for some people. I've also seen it be ineffective in some cases, which can be very frustrating. The best way to determine what will work for you is to discuss your options with your doctor.


These are agents which stimulate the migrating motor complex, which does not function appropriately in SIBO, and prevents the “back flow” of bacteria from the colon to the small intestine. Since the core of the issues with SIBO are due to impairment of this sweeping mechanism, the use of prokinetics is often essential for treatment and prevention of recurrence.

In my practice I often recommend MotilPro because it contains an array of nutrients and herbs that support gut motility.

Please note that the use of pharmaceutical prokinetics should be supervised by a doctor and evaluation of long term therapy should be done under medical supervision.

Ileocecal Valve Function:

The ileocecal valve (IC valve) is the gatekeeper between the large and small intestine. People with SIBO have been shown to have some level of dysfunction with how this valve is functioning. Evaluation by a practitioner experienced in restoring ileocecal valve function is recommended to determine if treatment is needed.

Healing the Gut:

With SIBO, you need to be cautious with what herbs you use in restoring the integrity of the cells. For example, using marshmallow, slippery elm, aloe vera or licorice could contribute to recurrence of symptoms due to their mucopolysaccharide content, which can actually feed bacteria. Common nutrients that I use with patients include L-glutamine, N-acetylcysteine, turmeric, zinc, and vitamins A and D.

I've had great success with Gut Rebuild with my SIBO patients. It contains herbs to support healing and 75 mg of zinc to support healthy intestinal lining and immune function.


Probiotics can be very helpful in repopulating the gut with good bacteria, but in my experience, you must also work to rebuild the terrain so that the good gut bugs want to stick around. Rebuilding the gut barrier and restoring proper function also results in better regulation of bacterial numbers in the small intestine.

A word of caution on probiotics — If they make you feel worse don’t take them. And AVOID prebiotics, lactose, Fructooligosacchardies and inulin when treating SIBO, which will feed the bacteria and can make the condition worse.

What's the best choice with SIBO? I recommend my patients use Women's Probiotic as this can be beneficial and have minimal side effects in those people with SIBO.

Address Sympathetic Dominance:

This is often a large missing piece of SIBO therapy in my patients who have been treated by other practitioners. If you are stressed and residing in a sympathetic state (fight or flight), your digestion will be impacted. There is a reason why the parasympathetic nervous system is termed, “rest and digest.”

One technique I have all of my patients employ to be completely present with their meals. Enjoy all the sensations, chew thoroughly, and do not allow for distractions, such as working while you eat. There is often more to reducing sympathetic overdrive than just this, but it is great starting place and everyone would benefit from this.

I also recommend adrenal supportive supplements to help them get into a state of calm quicker while working with their body.


Being proactive in preventing recurrence is a necessary part of treatment. Generally, the diet needs to be followed for about 3 months. In addition, other therapies should be employed to support gut motility, encourage healthy levels of HCl and heal the intestines.

If you think SIBO may be an issue for you, I recommend working with an experienced health care professional to get the testing and treatment you need.

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About The Author

Dr. Jolene Brighten

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Dr. Jolene Brighten, NMD, is a women’s hormone expert and prominent leader in women’s medicine. As a licensed naturopathic physician who is board certified in naturopathic endocrinology, she takes an integrative approach in her clinical practice. A fierce patient advocate and completely dedicated to uncovering the root cause of hormonal imbalances, Dr. Brighten empowers women worldwide to take control of their health and their hormones. She is the best selling author of Beyond the Pill and Healing Your Body Naturally After Childbirth. Dr. Brighten is an international speaker, clinical educator, medical advisor within the tech community, and considered a leading authority on women’s health. She is a member of the MindBodyGreen Collective and a faculty member for the American Academy of Anti Aging Medicine. Her work has been featured in the New York Post, Forbes, Cosmopolitan, Huffington Post, Bustle, The Guardian, Sports Illustrated, Elle, and ABC News. Read more about me here.