Treating SIBO (Part 3): Causes of SIBO - Hollywood Homestead

Small Intestinal Bacterial Overgrowth (SIBO) is a condition in which you have too much bacteria or the wrong type of bacteria in your small intestines. It is important to note that bacteria is normal and even healthy in our intestines. SIBO is not caused by one type of bacteria.   In most cases, SIBO is caused by an overgrowth of bacteria which should normally be found in the large intestine, though SIBO can also be caused when bacteria which should be in the small intestine gets out of control.   SIBO has an incredibly high recurrence rate. To treat and beat SIBO for good, it is important that you understand the many factors which cause SIBO.

This is part of a series on how to treat SIBO.  Catch up on the other parts of the series:

Stress as a Cause of SIBO

The majority of SIBO cases are likely caused by stress.1  Stress is also likely what makes SIBO so likely to come back after you treat it. As we talked about in Part 2 of this SIBO series, the gut is linked to the brain in what is called the gut-brain axis.

You don’t need lengthy scientific evidence to realize this. Just think about how your stomach gets upset when you feel stressed, or how you get hungry when depressed, or how you get butterflies in your stomach when excited. Without rehashing all of the info found in Part 2, researchers have now discovered that it isn’t just our brains which communicate to the gut, but bacteria in our gut “talk” to the brain.

If you a group of healthy people, they each will have different bacterial compositions in their guts. Yet, each person’s gut bacteria stays pretty much the same – even when compositions are measured months or more apart. Yet, when you take a person and put him in a stressful situation, the bacterial composition drastically changes. This creates an imbalance in bacteria which can affect health.2

Stress can also indirectly cause SIBO in many other ways. As you will see, stress can cause many of the other conditions which may cause SIBO.

  • Stress -> Inflammation -> Low Stomach Acid -> SIBO
  • Stress -> Weakened Immunity -> Overgrowth of “Bad” Bacteria -> SIBO
  • Stress -> Weakened Immunity -> Infection -> Antibiotic Use -> SIBO
  • Stress -> Motility Problems -> Bacteria Proliferation -> SIBO

Remember, the gut-brain axis is a two-way street! This is why stress can be both a cause and symptom of SIBO. To cure SIBO for good, it isn’t enough to take antibiotics and make changes to your diet. You’ve also got to manage stress.

Antibiotic Usage as a Cause of SIBO

As someone who took entire arsenals of antibiotics during the first 2 decades of my life (including large doses of penicillin injected into my rear more times than I can count!), I can attest to how quick doctors are to prescribe antibiotics. In Argentina where I grew up, you can even get antibiotics without a prescription.  I would just call my doctor who lived in another province and tell him my symptoms.  He’d tell me what antibiotics to pick up, increasing my dosage each time.

It isn’t just in Argentina were antibiotic over-prescription is a problem. One survey found that American doctors prescribe antibiotics in about 101 million visits yearly!3 Other studies have found that these antibiotics are often unnecessary — such as when they are given when the underlying problem is actually a virus.4

It also doesn’t help that antibiotics are regularly given to animals, which is another reason to buy antibiotic-free meat (Actually, if you want to improve your gut and overall health, you should buy organic pastured meat.  For bonus points, visit the farm to confirm the quality!). Overuse of antibiotics leads to antibiotic-resistant superbugs, which is a major threat to health.  But let’s just look at what antibiotics can do to our gut health.

When you take antibiotics, they don’t just kill off the “bad” bacteria which are causing your infection. They kill off the “good” bacteria which need to be in your gut. This upsets the balance of your gut flora. Without enough good bacteria to keep the bad bacteria in check, the bad bacteria can proliferate and lead to SIBO.

Once you consider the link between antibiotic use and SIBO, it is easy to understand why SIBO has such a high recurrence rate. Doctors traditionally prescribe antibiotics for SIBO, which temporarily may solve the problem. However, the antibiotics do not address the underlying cause of SIBO.  Because the healthy bacteria are also affected when you take antibiotics for SIBO, the bad bacteria just proliferate again and SIBO comes back. This is why it is so important to follow strict diet and lifestyle protocols to prevent SIBO recurrence.

Not Enough Gastric Acid as a Cause of SIBO

Acid reflux is incredibly common: 50% of adults will experience some type of gastroesophageal reflux disease in a 12 month period and 20-30% will have weekly symptoms.

Based on all those heartburn medicine ads you see on TV, you would think that acid reflux is caused by having too much gastric acid and that antacids are the solution to all your problems. Really, heartburn is caused by too little acid.7    I talk about this in my post about the chronic GERD my son had for the first year of his life and how to beat heartburn


The symptoms of acid reflux are caused not from having acid, but rather occur when acid gets into the esophagus. This can happen when there is too much pressure (such as from inflammation and excess stomach gas) causes stomach acids to be pushed up into the esophagus.  Antacids do wonders for suppressing the symptoms of acid reflux but, because you need acid, they just don’t address the underlying problem and actually make the problem worse in the long run.8

Our bodies need gastric acid to digest food and break it down.   Without enough stomach acid, you end up with undigested carbohydrates in your digestive tract. Bacteria in your small intestines love carbohydrates and they start to feed off of them.

Not only do the bacteria proliferate, leading to SIBO, but the bacteria produce hydrogen gas as a byproduct of digesting carbs. You end up with a belly full of gas, which in turn creates intra-abdominal pressure and pushes your stomach acid up into your esophagus – causing acid reflux.  According to researchers Suarez and Levitt, just 1 ounce of carbohydrates that escapes absorption in a day could produce more than ten quarts of hydrogen gas in small intestine. This gives you an idea of how much pressure undigested carbs can produce!9

Treating SIBO (Part 3): Causes of SIBO - Hollywood Homestead

Gastric acid not only helps digest food, but also suppresses ingested bacteria naturally. So, low gastric acid is a double-edged sword. Bacteria proliferate because there is so much undigested carbs to feed off of, and they continue to proliferate because there isn’t enough gastric acid to suppress growth.10

Why Would You Have Low Stomach Acid?

The obvious answer to this question is that you have been prescribed proton pump inhibitors or are taking antacids for acid reflux.   But what caused you to have the acid reflux symptoms in the first place?

Though the drug industry would rather you didn’t know about it, research shows that ulcers are caused by a bacteria called h. pylori which is present in as many as 2/3 of the population. I personally battled with this infection, which I talk about in my post about how to treat h. pylori naturally.

There are many other reasons why your stomach acid production might be low. Some of these include old age, stress, adrenal fatigue, chlorinated water, and alcohol consumption.Treating SIBO (Part 3): Causes of SIBO  A big contributing factor though, is diet. The junk foods and carbs which make up the Standard American Diet are very inflammatory. As Dr. Myhill explains:

“The stomach is lined with cells that are proton pumps – that is to say they pump hydrogen ions from the blood stream into the lumen of the stomach. Stomach acid is simply concentrated hydrogen ions. There is a natural tendency for these hydrogen ions to diffuse back from where they came but this is prevented by very tight junctions between stomach wall cells. However, if the gut becomes inflamed for whatever reason, there is leaky gut and hydrogen ions leak back out.”12

In this way, SIBO is linked to leaky gut syndrome.

In recap, you may have low stomach acid which caused SIBO if:


Poor Immunity as a Cause of SIBO

Our immune systems are a heck of a lot smarter than antibiotics at controlling “bad” bacteria. A healthy immune system will control bacteria in the small intestines by secreting mucus containing immunoglobulins. When your immune system becomes compromised, SIBO can occur. SIBO has been linked to many immunodeficiency syndromes.13

Instead of asking how impaired immunity causes SIBO, we should be looking at the root cause: why is your immune system not functioning in the first place? Of course, there are many possible reasons for this, such as stress and poor diet.  Do you see a recurring theme here?  Stress and poor diet are at the root of most causes of SIBO!

Dysmotility as a Cause of SIBO

Another cause of SIBO is dysmotility, which is a condition in which the muscles of the digestive system become impaired and are no longer able to empty contents efficiently. The contents become trapped in the small intestine. Motility is incredibly important for protecting against SIBO: the movements in the bowl prevent organisms from attaching to the wall of the small intestines. When you’ve got food waste sitting in your small intestines instead of exiting through the large intestine, bacteria can start to proliferate as it feeds on the waste.14

The movements of our digestive system are actually on a rhythmic schedule which is known as the migrating motor complex. 

It is thought that MMC has a “housekeeping” role.  One of the biggest mistakes I made when first attempting to treat SIBO was thinking that I could just take a laxative to help empty the contents of the intestines.  But you’ve really got to address MMC with methods such as prokinetics if you want to get the unhealthy organisms out of your gut and restore balance.15

Dysmotility can be a genetic problem. In genetic cases, it is common for family members to also have other muscle contraction problems, such as incontinence from not being able to control the bladder. Dysmotility can also be caused by problems like:

  • Parkinson’s Disease
  • Diabetes
  • Scleroderma
  • Thyroid disorders
  • Lupus
  • Amyloidosis
  • Muscular dystrophy
  • Inflammation of the intestines17

This last point is very important. Note the recurring theme occurring here. Stress and bad diet can cause gut inflammation. This can then led to low stomach acid, which in turn leads to bacterial overgrowth. This in turn leads to more stress, which creates a vicious cycle. Again, this is why it is so important to treat SIBO with a comprehensive strategy which includes diet and stress management.

Heavy Metals as a Cause of SIBO

Another possible cause of SIBO is heavy metals toxicity. Every day, we come into contact with a barrage of toxic heavy metals. For example:

  • Aluminum found in toothpaste, baking soda, and aluminum cans
  • Cadmium in drinking water, plastics, and paint
  • Lead in car exhaust, eating utensils, and canned foods
  • Mercury in air conditioner filters, certain fish, and floor waxes
  • Arsenic in wine, household detergents, and preservatives

Even if you take steps to eliminate heavy metals from your life (like making your own toothpaste and cleaning products), it is still impossible to completely avoid toxic heavy metals. These heavy metals have been shown to have adverse effects on your body, including on your digestive tract. 19

Even “healthy” heavy metals can be harmful to your gut health. For example, your body needs heavy metals like iron to be healthy. But, if your gut is damaged (such as from inflammation and leaky gut), then you won’t be able to absorb these nutrients into your body.  “Bad” bacteria use some heavy metals to form biofilms. Biofilms are basically mesh-like structures where bacteria live.

To form biofilms, bacteria use iron, calcium, and magnesium (amongst others). The biofilm acts as a shield which protect the bacteria and makes it very difficult for probiotics or antibiotics to kill the bacteria.   This is obviously a Catch-22 because you need those metal nutrients to stay healthy, but they also can help the bad bacteria thrive.20  We will get more into this later in the section about how to do a heavy metals detox.

UPDATE: There is now a heavy metals test that you can order without a doctor.  While I’m a HUGE fan of doctor guidance, I understand that you sometimes need lab results before you invest in a practitioner.

On a Personal Note…

The truth is that I don’t know what the cause of my SIBO was. For me, there were probably numerous underlying causes of my SIBO… chronic antibiotic use in my formative years, a damaged gut from the junk food diet I used to eat, heavy metal exposure (mercury and lead to be specific), h. pylori, chronic stress…

SIBO can be a vicious cycle. It is caused by stress. Trying to figure out SIBO makes you more stressed. The SIBO comes back and you get more stressed.

 Understanding that cycle is the easy part.  Breaking it is the tricky part.

All of the causes above are issues that I have personally struggled with. It is hard to pin down, but you’ve got to do your best to attack SIBO with a multidimensional approach. Just taking antibiotics probably won’t cure you if you don’t make major changes to your lifestyle and diet. The good news is that, once you master these changes, it isn’t just your gut health which will be better – you entire health and happiness will improve.

Want to find out if you have SIBO?  Read the next part of this series, How to Diagnose SIBO

Ready to eliminate SIBO once and for all? Get your copy of The SIBO Solution: Your Comprehensive Guide to Eliminating Small Intestinal Bacterial Overgrowth by clicking HERE. You’ll also receive a BONUS SIBO Detox Support Guide mini ebook with your purchase.

  Treating SIBO (Part 3): Causes of SIBO - Hollywood Homestead

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Sylvie McCracken is a former celebrity assistant in Hollywood turned full time entrepreneur currently living in Ashland, Oregon with her kids. She writes about treating and preventing health conditions with real food and natural remedies, as well as anything else she feels like writing about because she's a rebel like that. 😉 he also mentors health professionals turned entrepreneurs on her other site,