Have you ever heard that before you treat your methylation problem, that you must heal the gut first?  Well I am here to share with you more information that supports that idea. As you will see, SIBO is a problem that is caused by several major issues which plague our society – poor nutrition, stress, toxicity and excessive dependence on pharmaceutical drugs.  Combine all that with less-than-optimum methylation genetics and you get a recipe for disaster.  In support of this concept I will show you studies which highlight how the “standard of care” in our medical system is destroying our digestive tracts.  But lets not get ahead of ourselves.

In my previous video I shared with you what SIBO is and how it can interfere with the methylation cycle.  That video explains how excess bacteria growing in the small bowel not only makes us malnourished, but it is the main reason why people get weird symptoms from taking methylation support or b vitamins.  Because SIBO increases levels of folic acid inside the body it creates a big issue for those of us with methylation SNPs.  As I have pointed out, people with MTHFR, MTR, COMT, MAO, GAD, ACE and other SNPs are more sensitive to elevated levels of folic acid.  Having a SIBO problem predisposes you towards having a methylation problem.  If someone has SIBO, then treating SIBO and restoring gastro-intestinal health has to be the first place you start when dealing with a methylation issue.  For without a healthy GI tract, it is impossible to know if the vitamins and foods we are eating are helping or hindering us.

While it is very important to know what SIBO is (Part I), we still haven’t answered the question of what actually causes SIBO?  And if you were wondering how that problem starts, then you are in luck!  We now know that SIBO can only occur in the gut when certain conditions are met.  When I meet a new patient and begin working with them to heal their methylation issues, the first thing we have to look at is their gastrointestinal health.  This is to say it is very important to know if the gut is healthy before you begin working on methylation.

If you don’t have a properly functioning gut, then taking vitamins and eating healthy, nutritious food may not give you the benefit you were looking for – it may make you feel sick!  Without a healthy gut, throwing vitamins and food into your mouth is like pouring fertilizer onto weeds.  This is the #1 reason why someone gets side effects and negative reactions from taking methylation supplements.  To rule this problem out I ask many questions, but the most important ones are:

  • Have you ever been on any antibiotics? If so, how long ago and for how long did you take them?
  • Have you had any issues with yeast or yeast infections?
  • Do you have any constipation? or diarrhea?
  • Any issues with acid reflux?
  • Do you suffer from any abdominal pain? If so, is it above the belly button, or below? Right or left side?
  • Do you see any undigested food in your stool?
  • Do you have any gas, bloating, or discomfort following a meal?
  • Etc, etc…

Believe me, these issues above are very common!  Its not a stretch to say that many of the people reading this article and watching this video have at least one of these issues right now.  The reason these problems are so common is that modern life is VERY hard on our digestive system.  GI complaints are a leading cause of doctors visits, and drugs that treat these issues are top sellers, grossing billions for the pharmaceutical industry.  But just having the symptoms listed above doesn’t mean you have a SIBO problem, it just means you need to rule it out.

In order for SIBO to become a problem in your body, you need to have a combination of altered gut motility, low stomach and a poor balance of gut bacteria.  The latest studies are crystal clear that this is the real cause of SIBO. The following list outlines in more detail these causes of SIBO:

The Three Root Causes of SIBO

  1. Low stomach acid
    1. Long-term PPI usage – using Nexium, Prilosec or other omeprazole-type drug for heartburn effectively shuts off stomach acid production.  Long term these drugs have dangerous effects not just on the gut, but the entire body.
    2. Low blood sugar – as outlined here, skipping meals and allowing the blood sugar to quickly drop lowers stomach acid production; people with chronically low blood sugar have very poor stomach acid levels – they simply don’t digest their food very well.
    3. Aging – 30% of people over 60 have hypochlorhydria or low stomach acid.
    4. Chronic fatigue/Fibromyalgia – mitochondrial dysfunction caused by heavy metal burden, chemical exposure, or elevated metabolic toxins lowers stomach acid.  The cells which make stomach acid have a huge number of mitochondria; anything that poisons our mitochondria impairs the stomach’s ability to make hydrochloric acid.
    5. Hiatal hernia – the valve called the lower esophageal or cardiac sphincter can become dysfunctional and get pulled up above the diaphragm; this leads to loss of stomach acid into the esophagus, resulting in less stomach acid in the stomach.
  2. Altered Gut Motility
    1.  Dysfunction of the ileocecal valve (ICV) – the ICV is a muscle located at the junction of the small and large intestine.  This muscle opens and closes all day long, helping the peristaltic waves of digestion push our food from the kitchen (small intestine) into the bathroom (large intestine).  Problems arise when this muscle gets stuck open, and bacteria that normally lives only in the colon, migrates up towards the stomach as is seen in SIBO.
    2. Food allergies – poor food choices – dairy, gluten, soy, corn, GMO, etc. – cause increased levels of inflammation in the ileum and colon, forcing the valve to stay open.
    3. Constipation – Stool builds up in the colon, restricting peristalsis and causing toxins to leak back into the body; lack of magnesium in the diet is the main cause of constipation, but any kind of constipation interferes with gut motility.
    4. Irritable Bowel Syndrome or IBS – while the term IBS is a “garbage can” diagnosis, partly because it is very common and the causes are not medically understood.  IBS sufferers often have either increased bowel transit or decreased bowel transit time, both of which can disturb digestion and promote bacterial overgrowth.
  3. Imbalanced Gut Flora
    1. Antibiotic usage – kills healthy bacteria while allowing aggressive bacteria to grow rapidly, often colonizing areas of the small intestine leading to SIBO.
    2. High sugar diets – excess carbohydrates provide fuel for candida albicans and other intestinal parasites to grow rapidly.
    3. Chronic yeast issues –  either from antibiotics, stress, or poor dietary choices, aggressive yeast species create fermentation in the gut, often causing bloating, gas, pain and malabsorption.  Yeast also produces aldehydes and alcohols that impair brain focus and concentration.

Having low stomach acid or an irritated and inflamed ileocecal valve doesn’t automatically mean you have SIBO – but it does mean you are more likely to get it if you don’t fix these problems.  And drugs such as proton-pump inhibitors, aka the little “purple pill”, and oral antibiotics are proven to cause damage to our digestive systems.  SIBO is caused by antibiotics because these dangerous drugs don’t just kill “bad” bacteria, they also kill the “good” bacteria.  Without the healthy bugs in our gut, we don’t digest our food and our immune system becomes progressively inflamed.  By taking antibiotics we may make the symptom go away temporarily, but we create even bigger issues later on.

Just like a forest fire destroys the trees on the side of a mountain, antibiotics kill bacteria.  But not all bacteria is dies when antibiotics are given.  The good guys are mostly killed – lactobacillis and bifidobacteria – but the aggressive, antibiotic-resistant strains usually survive.  And just like on a mountain when the trees are killed, the weeds and invasive plants grow crazy since there is no longer competition for sunlight, nutrition, and space.  It is exactly the same in the gut.

Studies now show that when antibiotics kill the good bacteria, it simply allows the aggressive bugs access to more nutrition, more fertilizer and they grow faster.  When those aggressive bugs begin to grow and spread they don’t stay in one place; they start to grow into the upper small bowel.  This is how antibiotics give rise to SIBO.  Aggressive bacteria are kept in check by our good flora.  When antibiotics kill our good bacteria, there is nothing left to keep the aggressive bacteria from growing rapidly into the small intestine.  But don’t expect to hear this explanation next time a doctor prescribes that you take antibiotics.

In my opinion, taking a PPI drug is also very risky.  I say that because low stomach acid is a risk for bacterial overgrowth; and without acid in the stomach, the environment in the small intestine changesWithout acid from the stomach, the pancreas and the gall bladder do not release their digestive juices.  Normally the pancreas releases enzymes and bicarbonate that helps digest our food and raise the pH of the SI.  When the stomach acid is absent, the pancreatic juices are absent.  This is why laboratory testing routinely shows low elastase and an acidic pH – two consequences of the pancreas not releasing digestive juices.  This is one of many examples of how shutting of stomach acid by taking PPI drugs greatly disrupts the digestive process.  In a future video, I will elaborate more on this idea and show you exactly what happens to the body when stomach acid is shut off – scary stuff!


SIBO is a growing problem that is caused by bad food choices and side effects of commonly-used medications.  The standard of care in the US still relies heavily on antibiotics and proton-pump inhibitors (PPI) to treat gastrointestinal complaints.  If all you are trying to do is make the symptoms go away, then these approaches work well.  Ask anyone who takes Nexium or omeprazole (the generic name for PPI drugs) for heartburn and they will tell you how well it “makes the burning go away”.  And we can’t argue that point – if you shut off acid production completely in the stomach, then there will be no burning.  Unfortunately, these toxic substances (aka pharma drugs) also make if very difficult to absorb nutrients from your food and promote the growth of pathogenic bacteria.

Research now proves that dangerous and unnecessary drugs used to treat gastrointestinal complaints are responsible for causing SIBO.  The fact of the matter is that we over-use drugs in our society.  Whenever drugs are used, in almost every case, there exists a natural alternative that works often better than the drug, has zero side effects, and promotes rather than hinders our overall health.  If you or someone you know is suffering from SIBO, please reach out.  I have been helping many patients heal their gut naturally and balance their genetics.  Through diligent research and application of methylation science, we have been getting great results.

Those of us with changes to our MTHFR, MTR, COMT, MAO, GAD, ACE and other SNPs are more sensitive to digestive problems.  This partly has to do with the excess folic acid that comes from bacterial overgrowth.  It also has to do with the fact that methylation imbalances make us more sensitive to inflammation, malnutrition, and malabsorption.  With methylation genes in our bodies, just being average won’t work.  To be truly healthy, we have to do better than average, we have to strive for excellence.  And that is what I do.

Yours In Health,

Dr. Rostenberg

By studying the current peer-reviewed research, Dr. Rostenberg has discovered powerful, natural strategies to restore your gut and heal your body.  He can help you uncover the genetic or root causes of your health problem and find a natural solution!  If you would like help with your methylation genetics to improve your gut function and reduce/eliminate your symptoms, please contact Dr. Rostenberg at Red Mountain Natural Medicine today. Phone 208-322-7755. Email redmountainclinic@gmail.com. Website http://www.redmountainclinic.com








  • March 27, 2015 Reply


    How to heal SIBO then

  • October 14, 2016 Reply


    Hi Dr. Rostenberg,

    Interesting points and great article. But this is where it gets confusing as a patient. As a person who suffers from SIBO, it seems to me SIBO can be a secondary symptom or a cause (eg. which came first? the chicken or the egg). Here are a few scenarios demonstrating my point:

    (1) So let’s say low stomach acid causes SIBO. Then wouldn’t b-12 help with the generation of stomach acid. In that case, one should take methyl b12?
    (2) Does SIBO make mitochrondira dysfunction worst since it is release toxins into bloodstream. Then treating the SIBO will inevitably help the mitochdrondia dysfunction, and thus help a person make stomach acid? I have had practitioners say to me that oxidative stress is caused by SIBO, which is causing a person’s chronic fatigue, and not the other way.
    (3) Yeast causes SIBO or SIBO allowed the yeast to proliferate? The same with food allergies. Does SIBO cause food intelorance/allergies or was it the food that caused the SIBO?
    (4) Emotional stress can cause SIBO to flourish. But then SIBO can give a person mental health issues (increased anxiety etc), which leads to more emotional stress.

    So my question for you: How does know whether SIBO was just a secondary symptom or not? It seems almost cyclical. Where does one begin? or when can you tell if SIBO was the secondary symptom?


    • October 17, 2016 Reply


      Hi Frank,

      Thanks for your comment. SIBO can only occur when conditions are just right. It is an environmental problem in the gut itself, which then impacts systems all over the body. The main causes of SIBO, per the peer-reviewed literature, as as follows: low stomach acid, poor gallbladder function, weak pancreas function, ileocecal valve dysfunction, high stress, and antibiotic exposure. Add all those up and you will get a big environmental problem in the gut itself. Our treatment is always directed at treated all those factors at once. We have seen really good results with our comprehensive approach. If you would like help navigating this frustrating gut-based problem, please reach out and contact my office. You may reach us at 208-322-7755 and care@redmountainclinic.com.

      Yours in Health,

      Dr. Rostenberg

    • April 4, 2017 Reply


      It may not be this clear-cut for everyone, but my cycle began with retaking my childhood vaccines to get into nursing school, ironically. The diarrhea began then and I lived with it for 13 years. I finally was able to stop it with MSM and TMG, but I am still working on correcting the damage. ( Adrenal exhaustion, hypothyroid, tooth loss, peripheral neuropathy, arthritis, bone loss, duodenal ulcers, getting off the Prilosec)

  • November 24, 2016 Reply


    Which side does pain present with SIBO? I eat a very strict PALEO diet, but splurged on some ice cream for the first time in a few years. I got pain in my lower right side and have felt that pain before. Is this indicative of SIBO? It appears I can never slip up with my diet. I have not been on an antibiotic in over 16 years, maybe only a one time usage in my life that I recall. Do you know of any mold toxin connection? I have had water damage in my newish home. Thanks for the informative article.

  • December 11, 2017 Reply


    Which side does pain present with SIBO? I eat a very strict PALEO diet, but splurged on some ice cream for the first time in a few years. I got pain in my lower right side and have felt that pain before. Is this indicative of SIBO? It appears I can never slip up with my diet. I have not been on an antibiotic in over 16 years, maybe only a one time usage in my life that I recall. Do you know of any mold toxin connection? I have had water damage in my newish home. Thanks for the informative article.

    • December 18, 2017 Reply

      Dr. Rostenberg

      Hello Sanatan,

      Thanks for your comment. There is no definitive Right or Left side which SIBO causes pain. Pain in the abdomen has many different causes, one of those being SIBO. Without performing an in-depth consultation and history/work-up it would be very hard to guess what is the best treatment for you. If you are interested in getting a personalized approach to optimize your health and well being, then please contact my office care@redmountainclinic.com and 208-322-7755.

      In Health,

      Dr. Rostenberg

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