SIBO Autoimmune Oakland Portland | Dr. Jolene Brighten |

SIBO Part II: Natural Treatment and Therapies

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 are the Specific Carbohydrate Diet (SCD) and Fermentable Oligo-, Di-, Monosaccharides And Polyols (FODMAPS). These diets 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.

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.

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. Oregon grape, oregano oil, allicin (garlic) and cinnamon are some the more common herbal antimicrobials used in SIBO. I often use Candibactin AR and Candibactin BR successfully with my patients.

That said, I do not recommend that people begin treating themselves for SIBO with herbs because some of these herbs can be dangerous if used improperly, with other medications, or in the case of certain medical conditions.

What is often missing from the antimicrobial treatment of SIBO is the use of biofilm disruptors, like N-acetylcysteine or Interfase. 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.


These are agents which stimulate the migrating motor complex, which does not function appropriately in SIBO, and prevents the backflow 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.

Please note that the use of 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.


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.

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.


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.


Think you may have SIBO? Contact my office to meet with one of my skilled practitioners.


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About The Author

Dr. Jolene Brighten

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Dr. Jolene Brighten is a licensed Functional Medicine Naturopathic Doctor, best selling author, speaker, and mother. Dr. Brighten specializes in women’s health, from fertility to postpartum care, adrenal and thyroid support, autoimmune conditions, and digestive disorders. In her patient centered practice, Dr. Brighten thrives on navigating the space between conventional and alternative medicine, all while working with patients to help them achieve optimum balance, health, and happiness.