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what causes SIBO

9 SIBO Causes Your Doctors are Forgetting to Address

SIBO, short for Small Intestinal Bacterial Overgrowth, is a condition where bacteria is overpopulating the small intestine. I’ve talked about SIBO in detail before in episode 16 of Thank Gut It’s Fixed; what it is, the symptoms, how do you know if you have it, and what you can to do get rid of it.

The problem with SIBO isn’t that the bacteria is pathogenic (this may be the case for some but not always). Rather, it’s the accumulation of bacteria in the wrong place. In a healthy gut, the majority of bacteria populates the large intestine. For several reasons that I will be sharing here, bacteria migrate to the small intestine and ferment or eat up food higher up in the digestive tract. This will result in gas production, bloating, excessive burping, acid reflux, stomach pain, diarrhea, or constipation.

With SIBO, the bacteria disrupt digestion and compete with your body for nutrients. Many people end up with nutrient deficiencies, which can manifest in fatigue, brain fog, low energy, hair loss, dry skin, or others. SIBO also causes gut inflammation and leaky gut, leading to a cascade of events like food sensitivities, bacteria endotoxicity, brain-gut axis imbalance, autoimmunity, and others.

Studies are finding that 78% of people who have been diagnosed with IBS test positive for SIBO. We’re finally trying to find the root cause of IBS, but it doesn’t just stop at SIBO! If you don’t have an official diagnosis of IBS or SIBO but you have the symptoms, keep on reading and investigating because this may be exactly what you need.

Why is it Important to Understand SIBO Causes?

SIBO doesn’t just happen overnight and it tends to come back. If you identify the root cause and work on correcting it, you improve your chances of long-term prevention and gut health success. That’s a key step I can’t ignore when working with my patients who have SIBO. If you’re working with a doctor or health practitioner (conventional or functional) and they aren’t searching for root causes or suggesting comprehensive strategies to boost healthy gut function, then they don’t really know enough about SIBO.

In this video, I talk about the common SIBO causes. Make sure you also read below as I go into more depth and add a few points in writing.


After you get diagnosed with SIBO, your conventional doctor, most of the time, will prescribe an antibiotic. If you’re working with an integrative medicine doctor, they may recommend an antibiotic or go with an herbal protocol instead. An herbal protocol will consist of certain products that are known to kill bacteria such as berberine, oregano, or others.

It’s important to kill the bacteria, there’s no doubt about that. As an integrative medicine dietitian, I do support herbal products. Research finds that herbal protocols are as effective as antibiotics and have fewer side effects, and even one round of antibiotics can damage your gut flora for up to a year. I’ve seen repeatedly SIBO tests coming back negative for my patients after the herbal protocol. You can do more research to decide what is better for you and talk with your practitioner. I don’t recommend products like these online without knowing my patient’s medical background and usually caution people from DIY-ing healing SIBO as you can do more harm on your own.  

What comes after killing the bacteria is crucial for long-term success. As I said, SIBO does not come out of nowhere. If you have SIBO, there’s usually an underlying issue or dysfunction that has been going on for a few months or even a few years.

If you just kill the bacteria without supporting gut function and eradicating the root cause, SIBO will come back again. I’ve definitely worked with patients who went on multiple 14-day antibiotic rounds because symptoms disappear for a little bit and then return. They finally decided later on that this is nonsense and that they needed to find a different solution. SIBO is a very stubborn condition and if you don’t heal from the inside out, you’re just wasting your time.

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SIBO Causes

You may be searching for SIBO causes and expecting to find evidence for having the ONE clear thing that lead to it. However, SIBO usually happens as a result of a combination of factors. It’s important to address every one that you possible could. 

1. Getting Older


Unfortunately, you really can’t do much about this. We’re always growing older, and SIBO is more prevalent in older adults.

2. Structural Issues


Some people have different or abnormal structural issues in the small or large intestine that interfere with food and waste flow. If that’s your case, you can’t really change that. But you can support your gut muscle contraction and digestion so they functions better.

3. Low Stomach Acid


Stomach acidity, through the production of hydrochloric acid, keeps the stomach and upper GI tract sterile. That helps kill the bacteria entering our bodies through our food. When you don’t have enough stomach acid, they have a higher chance for overpopulating the small intestine.

What causes stomach acid production to be low? Acid blocking medications. This includes proton pump inhibitors and H2 Blockers, prescription or over the counter. This also includes short and long-term use. I talk about these in details on episode 13.  Low stomach acid may also be caused by H Pylori infection in the stomach. More on that at later episodes. H Pylori can predispose someone to developing SIBO.

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4. Motility Problems


Your digestive tract is made of smooth muscle cells that contract to push food from the esophagus all the way out. Peristalsis is the motion that pushes food through the intestines so we can digest it and absorb nutrients. The migrating motor complex (MMC) is the muscle contraction wave that is responsible for pushing waste and by-products AFTER you finish eating to get rid of them. You may have motility issue where one (or both) of these motions don’t fully complete or work properly.

When food is not pushed down the pipe properly or fast enough, it stays in the small intestine for too long, allowing bacteria to fest on it and grow. Similarly, when undigested food, waste, bacteria and their by-products are not swept down and cleaned up properly, bacteria can overpopulate the small intestine.

On episode 21, I talk about why grazing is bad for your gut and how it can cause motility interruptions. I encourage you to read more about that. If your eating style involves meals and snacks (or grazing) constantly throughout the day, it can be one of the contributing factors to SIBO.

Gut motility issues can be a result of food poisoning. One in five people who get food poisoning may end up with an autoimmune attack that affects gut motility without even knowing it. If you get infected with some types of microbes (such as salmonella, E. Coli, virus, or parasite, etc), they will  produce a toxin called CDT. As your immune system develops antibodies to fight this toxin, an autoimmune attack may get triggered where your immune cells start to attack a protein in your gut called “vinculin”. This protein activates a type of cells called ICC that act as a pacemaker for your gut muscle contractions. If this protein and your ICC stop working, you will have problems with motility and can be the seed that starts SIBO and other digestive issues.

5. Gastroparesis


Gastroparesis is another muscle and/or nerve issue where the stomach’s motility is slow or not working at all. This will prevent the stomach from digesting (think grinding) food adequately and then emptying properly.

Gastroparesis can be caused by connective tissue disorders, nerve tissue disorders, Parkinson’s disease, or uncontrolled diabetes (diabetes causes nerve damage). Since the stomach and a lot of the digestion contractions are controlled by the central nervous system, any nerve problems can lead to SIBO.

6. Inadequate Digestion


In addition to chewing your food properly (mechanical digestion) and your stomach churning the food and starting protein digestion, your intestine needs a variety of enzymes to properly break down foods to their small individual components. Think of food as a large block of attached Legos and only the individual pieces can pass through the gut lining to get absorbed. For digestion to be complete, your pancreas, gallbladder, and intestinal cells need to produce several types of enzymes that interact and work together. Any liver issues, gallbladder removal, or small intestine inflammation will interfere with digestion and contribute to SIBO.  We also tend to produce less enzymes as we age so this may be one of the reasons SIBO is common in older people.

Learn how to identify the REAL causes of your gut problems.

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7. Constipation


This is another one where we might ask, which came first, the chicken or the egg. Constipation can lead to SIBO, and SIBO can lead to constipation. If you’ve always been slow, have fewer than 5 bowel movements per week, strain too hard to pass, or your poop looks like pebbles or small rocks, then you’re constipated. And if you’ve been like this for years or since you were a child like what some of my patients tell me, then it’s possible that constipation lead to SIBO. When that happens, bacteria in the small intestine have plenty of time to eat up your food and grow. If you have hypothyroidism, it can lead to constipation and eventually SIBO. I talked about the link between constipation, bloating, and hypothyroidism before on this episode.

At the same time, SIBO can cause constipation, especially if you have methane-dominant SIBO. You will need to kill the bacteria, but you can’t forget about a comprehensive approach to improve both texture and frequency of your bowel movements so things keep moving and not get backed up.  

8. Stress and Anxiety


This seems to show up in almost every “root cause” post! When you’re under a threat, your nervous system will put you in a fight-or-flight mode that will shut or slow down digestion, reduce stomach acid production, and slow down the muscle contractions that push food and waste through your digestive tract. That’s because the body doesn’t prioritize digestion when it’s about to be killed by a bear or tiger! Your body needs to pump blood to your skeletal muscles so you can run for your life!

However, we don’t experience bouts of acute stress followed by calm and relaxation anymore. Our modern day stress doesn’t go away. We’re chronically in a state that doesn’t support proper digestion. If we’re not intentional about finding ways to activate the rest-and-digest state by activating the vagus nerve, bacteria accumulate in the small intestine leading to SIBO. 

If you have already developed SIBO, stress management alone is not going to reverse it. The damage has happened and you must treat and eradicate the bacteria to overcome SIBO symptoms. That being said, I still discuss mediation, breathing, yoga, stretching, humming, gargling, epsom salt baths, and anything that helps activate the vagus nerve and relax with my patients as they are important parts of their healing journey.

9. Ileocecal Valve Dysfunction


The ileocecal valve is a group of muscles that connect the small with the large intestine. This valve needs to be shut most of the time and only open up when whatever is left from digestion needs to exit the small intestine. However, if it’s open too frequently, bacteria in the large intestine (where they normally should be) can migrate to the small intestine (where they shouldn’t). In the small intestine, they start to ferment carbohydrates and fibers, overgrowing, and leading to bloating, constipation, inflammation, and so on.

It’s also possible that SIBO is causing loosening of the ileocecal valve (just like it would with LES in heartburn). The gas chronically being produced by too much bacteria in the small intestine will place pressure on the ileocecal valve and keep it open, contributing to this migration of microbes into the small intestine. Which came first, the chicken or the egg? Sometimes we don’t know. If you suspect you have this issue, you can talk to a chiropractor or physical therapist who are versed in gut issues. They may be able to help you with certain exercises or adjustments to “close” these muscles properly.


SIBO Causes: Take-Home Message

If you have SIBO and just kill it off with an antibiotic or herbals, without solving the root issue or the underlying cause, it will come back.

There are several root causes and some may apply to you more than others. There are other causes as well that are less common that I didn’t get into. Once you find out the root cause, there may be several potential solutions to help re-balance the gut and return normal function.

If you’re tired of trying to figure it out on your own, and if your healthcare providers are not versed in SIBO as much you are, and if they’re not going into that much depth with your treatment plan, consider working with me privately and signing up for my program. You can read more about it here, and if you think it may be what you’ve been missing all along, you can book a Strategy Consultation call with me so we can discuss how I can help you best. 

Nour’s guidance and expertise was the key to dramatically halting our son’s [Crohn’s] disease progression! His pediatric gastroenterologist is now in agreement of our choice to treat solely with diet and supplements. All his labs have improved and his inflammatory markers are so low they are practically nonexistent.

Before working with Nour, I experienced intestinal pain off and on for for 54 years with minimal success on medications. I have benefited 100% from Nour’s program as I am now pain free!

A lot of time and money was wasted on foods that I thought would help my digestive struggles [diarrhea, bloating, hunger], but in fact I was making it worse. The main benefit is getting a handle on what negatively affects my digestive symptom. Doing a total 180 to my eating habits has been pretty amazing.