SIBO – Small Intestinal Bacterial Overgrowth

SIBO – Small Intestinal Bacterial Overgrowth or what we might refer to as Self Induced Bacteria Overgrowth, refers to a condition in which abnormally large numbers of bacteria are present in the small intestine, while the types of bacteria found in the small intestines are more like the bacteria found in the colon.

The small intestine is divided into 3 sections, with a surface area roughly the size of a tennis court. This area is covered in villi and microvilli designed to provide exceptionally efficient absorption of nutrients in the lumen (interior of the GI tract). The fact that the human body has invested that much length and interior space for absorption of nutrients shines a light on how crucial it is for survival.

There are many factors capable of breaking down the structure and the function of the digestive system, bacterial overgrowth being one. However, bacterial overgrowth is not a cause but an effect of hypothyroidism, or low metabolic function, being influenced by one or many chronic stressors in the environment. How this manifests in any one body (diabetes, scleroderma, etc.) is going to be specific to that individual, but the underlying cause is always the same- a breakdown in the metabolic system. As Diane Schwarzbien says, “you are your metabolism.”


Research has shown hypothyroidism, or low thyroid function, severely affects the structure and function of the digestive system by decreasing peristaltic movement, and the production of digestive enzymes, essential to the breakdown of protein, carbohydrates, and fat.

A common example of this would be the effects of low thyroid on the recirculation and absorption of estrogen back into the small intestine. This interferes with proper detoxification and can lead to estrogen dominance and progesterone deficiency. Low progesterone causes a lack of regeneration of the microvilli in the small intestine, which then leads to a decrease in digestive enzyme production and a decreased ability to absorb nutrients such as lactose. So the question now becomes, is lactose intolerance really just another symptom of low thyroid function and its effects on the GI system?

Note: Take it from someone who was never able to drink dairy and can now drink a good 10-12oz a day (this is not including yogurt, cheese, butter, etc.). The more attention you place on healing your metabolism, and away from trying to “fix” your gut, the more successful you will be long term.

What contributes to SIBO?

As we have mentioned, a decrease in peristalsis and digestive enzyme production interferes with the body’s ability to breakdown and absorb nutrients from the food we eat.

If we are consuming foods the body cannot break down, whether it due to low digestive juices or because we are eating foods we humans were not designed to eat, what is going to happen?

Bloating, gas, constipation, diarrhea, abdominal pain, fatigue, vitamin and mineral deficiencies…anyone familiar with these symptoms?

Foods such as grains, beans, an excessive consumption of cruciferous veggies and leafy greens (particularly raw), lentils, breads, nuts and seeds, and alcohol are some of your leading offenders when it comes to foods responsible for increased bacterial overgrowth in the gut. This is where the whole question of “what’s healthy?” can get very obscured.

Prepared properly, and in a body with optimal digestive function, these foods might not be such huge offenders, but in a body with compromised digestion these foods are facilitating chronic inflammation and metabolic destruction.

We have an entire population of people willing to do anything to heal their gut. Supplements, labs, detoxes, elimination, as well as consuming a large amount of these offending, so called, healthy foods. What would happen if we began taking some of these foods out of the diet and replacing them with foods the body can digest, so we can increase nutrient absorption, reduce stress and inflammation and normalize gut bacteria?

What can you do to begin balancing your ecosystem?

To begin, we suggest you avoid the foods mentioned above or at least, greatly reduce the amount you are consuming and make sure your veggies are thoroughly cooked.

Limit the intake of polyunsaturated fats from nuts, seeds, nut and seed oils, fish oils.

Consume ripe, tropical fruits and/or seasonal ripened fruits.

Consume well-cooked root veggies in combination with healthy fats and proteins.

Increase consumption of bone broth.

Include a raw carrot or bamboo shoots into your daily regimen.

Eat regularly to help balance blood sugar.

If you would like to speak with Josh and Jeanne regarding your health & nutrition needs, or to schedule a private consultation, please contact us here.

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Share Your Thoughts

  1. Kate

    Above makes perfect sense, but low thyroid symtomology most often includes excessive weight. What about us folks who are underweight and have a difficult time getting enough calories and are over anxious?

    September 17, 2015 • 10:24 am •
  2. Josh Rubin necessarily. Weight gain “can” by a symptom but not always is. Look at models who under eat, athletes that over train and are super skinny. They are hypothyroid for sure, but not overweight.

    September 17, 2015 • 10:49 am •
  3. East West Healing

    What you are saying Kate is really important and a common misunderstanding around hypothyroidism. It really has no look and most people these days (in our experience), diagnosed, undiagnosed, subclinical, primary, secondary or tertiary are experiencing some degree of metabolic suppression. The degree it which it affects someone is dependent on where one falls on the spectrum along with several other factors that make up your individuality.

    September 17, 2015 • 11:06 am •
  4. Hali

    This is really important for me. I have Hashimoto’s and am under a N.D.’s direction. But really the only guidance I received for nutrition was to follow the AIP. But, I have been eating raw salads everyday, along with a lot of cooked broccoli and cauliflower. I am taking a ton of supplements. I do believe my digestion is getting worse. Thank you for the info.

    September 17, 2015 • 6:00 pm •
  5. East West Healing

    Hali-linking the effects of thyroid function to digestion is so essential to being able to give the body proper nutrients and reduce as much of the burden as possible. Not often are we considering the properties within foods and what that might mean to where we are metabolically. We are glad you found the information helpful:)

    September 18, 2015 • 8:47 am •
  6. Josh Rubin

    Thanks for the support! You are welcome.

    September 29, 2015 • 11:53 am •
  7. Lori

    LOVED this Vlog! I never realized how your metabolic work pertaiined to my SIBO issues. The symptoms and solutions seem spot on to me! Even after all the gut thrive work I did with Christa, I’m still not right. I’ll definitely call you for a consult! Have you or your clients ever used Apple’s Swiave…an ear thermometer that records and stores all your body temps in their app?

    September 18, 2015 • 7:40 am •
  8. East West Healing

    Lori!!…We are so glad you found this helpful AND we have accomplished our goal because we are certain most people are not aware of the relationship:) Digestion is a big topic and most, if not all digestive symptoms, are a result of something having gone array metabolically. Regarding temps and pulses, we have not used the app you are mentioning. I tried looking for it and couldn’t find it? Shoot us over a link, would love to check it out and see how accurate it is. Anything we can do to make things easier for our clients:)

    September 18, 2015 • 8:56 am •
  9. Josh Rubin

    Glad you enjoyed it!

    September 29, 2015 • 11:53 am •
  10. David

    i have been battling stomach, digestion, bloating, gas, extreme fatigue, muscle weakness, nasal congestion etc.. for 14 years. However the fatigue started before stomach issues after multiple sinus infections and antibiotic treatment. I’ve never recovered. I’ve been to dozens of doctors, tried supplementation for adrenal burnout and nothing seems to work. I’ve always thought that I still carry a low grade sinus infection. I was told this isn’t possible. I think it is and I think that it could be affecting my thyroid which has been affecting my metabolic issues. I recently starting eating one clove of raw garlic at night. It seems like it is the only thing that will clear up clogged sinus and fatigue. I do use oregano oil but the garlic seems to work best. I am concerned however that chronic Rhinitis is supposedly incurable? If the Rhinitis is causing problems with my Thyroid and Rhinitis is incurable that sucks! I like you cannot eat grass fed butter or other dairy because it clogs my nose and I get a sinus infection. It would be very interested in what your thoughts are. Also its probably time to schedule an appointment to talk with you.

    Mahalo! from Hawaii

    September 19, 2015 • 6:17 pm •
  11. Josh Rubin

    go ahead and fill this out on our site and either of use would love to chat with you about your digestive issues. We hear your story all the time and the one thing that is missing is food! People are being taught to eat less, be restrictive and live in fear, eat supplements, do cleanses, etc. As you can see, it doesn’t work. Feel free to contact us anytime!

    September 21, 2015 • 9:26 am •
  12. Steven Bahr

    SIBO what foods do i eat that will keep my thyroid and body functional ?
    Does PEMF machine help?
    Candida what diet protocal works?
    Fermented veggies ok?
    I need energy taking usual abcdek2 msm methylene blue pantothenic acid ginko minerals
    Is DE diamotacious earth ok (sharp silicon with neg charge)?

    September 23, 2015 • 2:21 pm •
  13. peter

    Ray Peat’s theories are full with errors. I will give you one example – if you have fructose malabsorbtion what will happen if you eat fructose – SIBO. If his theory that sibo is caused by hypo thyroid was true people with fructose malabsorbtion should have problems will all digestive enzymes – but they can digest starches without problems. ALso how can you blame hypothyroidism when 90% of americans dont have primary hypothyroidism – they have autoimmune disease Hashimoto – all autoimmune diseases are caused by leaky gut – and it seems Ray Peat thinks that leaky gut is caused by hypothyroid – how is this possible – you can’t blame the symptom and call it a cause. If SIBO was caused by hypothyroidism that taking NDT should fix it easy – but this does not seems to happen in reality.

    October 29, 2015 • 7:12 pm •
  14. […] cause 80-90% of pancreatitis cases. The gallbladder and pancreas share a duct that enters the small intestine; if a stone blocks this duct, pancreatic juices can be trapped in the pancreas and cause […]

    December 30, 2015 • 8:39 am •
  15. I couldn’t refrain from commenting. Well written!

    April 28, 2016 • 12:00 am •
  16. […] forth by hundreds of thousands all over the world to improve digestion, rid the body of candida, SIBO, leaky gut, food intolerances among a plethora of other bacterial imbalances and other digestive […]

    August 2, 2017 • 2:02 pm •
  17. Janet

    I like the concept that food instead of nutritional supplements should keep us healthy. That said….If a person has the APOE4 gene, it is recommended by MD to consume 2000 mg of EPA and DHA per day, and for those without the APOE4 gene 1000 mg per day. Is there evidence that your program helps to prevent Alzheimer’s without using supplements? Three meals (providing 1000 mg) to six meals (providing 2000 mg) of fatty fish per week does not seem logical to me, a landlubber. 🙂


    February 24, 2018 • 2:42 pm •