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Small Intestinal Bacterial Overgrowth

Updated: Jul 21, 2022


Do you ever feel bloated after eating, even if you've only had a small amount of food? Do you have trouble losing weight, regardless of how much you diet and exercise? Do you have irritable bowel syndrome? If so, you may have Small Intestine Bacterial Overgrowth (SIBO).


SIBO is a condition in which too many bacteria grow in the small intestine, causing gas, bloating, and other digestive problems. There are many different root causes and risk factors for developing SIBO. The underlying cause, and then obviously the treatment as well, is different for different people, however diet and lifestyle factors play a role for everyone. In this post, we'll discuss what SIBO is, its symptoms and causes, and how to treat it naturally. So read on to learn more about small intestinal bacterial overgrowth also known as SIBO.


1. What is Small Intestine Bacterial Overgrowth (SIBO)?

SIBO is a condition in which too many bacteria grow in the small intestine. It becomes bothersome particularly when types of bacteria which are not commonly part of the normal small intestinal bacterial microbiome in this part of the digestive tract overgrow.

The small intestine is normally home to a diverse population of bacteria. This is normal, and we need these bacteria to help us digest our food. However, SIBO occurs when there is an overgrowth of some of the harmful bacteria. The exact cause of this overgrowth differs from person to person. Sometimes good bacteria get killed off when we use antibiotics for another sickness. Sometimes bad bacteria which grows on sugar grows too much and overpopulates our gut because we are eating a diet with too much sugar and processed food.

Most often SIBO starts when your small intestine doesn't move food along the way it should. Bacteria grow and stick around too long. If the good bacteria that help you digest food can't keep up with the harmful bacteria, you might notice symptoms such as discomfort, bloating, diarrhea, decreased absorption of nutrients, vitamin deficiency and other digestive problems.

In my Clinic, I find that SIBO exists on a spectrum. It is not something that you have or don't have. It is rather something on a continuum, causing symptoms in some people if these harmful bacteria overgrow at certain times, and then, according to your diet, small intestinal bacterial overgrowth improves at other times. Even when we treat someone, they won't be cured for life, as these bacteria can overgrow at a later stage again.


The key in taking control of your own health, is to start noticing when you have certain symptoms, and trace it back to when it started for you. Reflect on your day, your diet and lifestyle to figure out what makes it worse, and what makes it better. Your Health Practitioner can help you figure this out by taking a thorough medical history.




2. Symptoms of SIBO

SIBO symptoms affect the gut. Bloating is one of the most common symptoms of SIBO. Abdominal pain is often described as a dull ache that may be worse after eating. Some people experience cramps, some diarrhea, and some constipation.

Patients often experience indigestion, and then commonly get prescribed an antacid such as a proton pump inhibitor which lowers stomach acid in the upper gut where we normally have a higher content of stomach acid. Even though proton pump inhibitors decrease the level of stomach acid, it does not treat the root cause of intestinal bacterial overgrowth (SIBO) and is actually another risk factor for developing intestinal bacterial overgrowth (SIBO). Some people complain about a regular feeling of fullness. Some people experience abdominal pain due to gas. Some people experience unexpected weight loss.

Nutrient deficiencies are another common symptom of SIBO. This is because harmful bacterial overgrowth takes the place of good bacterial overgrowth (the way it would be in the small intestinal environment of healthy controls)

3. Causes of SIBO

There are many potential causes of intestinal bacterial overgrowth (SIBO), but the most common is a diet high in sugar and processed foods. This allows the bad bacteria to grow and overpopulate the gut. This small intestinal overgrowth of bacteria that shouldn't be there produces toxins we can easily pickup with breath testing (glucose breath testing discussed in next paragraph) Other potential causes include a weakened immune system, certain medications, and surgery.

The most common cause is an underlying condition that slows down the movement of food through the small intestine. These conditions include: Crohn's Disease, Diabetes, Systemic Sclerosis, HIV, Parkinson's Disease, Hypothyroidism, medications which slow down the gut (some pain meds) and leaky gut syndrome.

In the hospital, I commonly see this after gastric surgery in a condition called 'blind loop syndrome'. I also see it in patients with connective tissue disorders, short bowel syndrome, people with a deficiency in bile salts due to liver disease, people with pancreatic insufficiency, abnormal bile acids, anatomical abnormalities and motility disorder of the small intestinal tract.

For patients in my Clinic (outside of the hospital), the causes of small intestinal bacterial overgrowth (SIBO) are diverse.

Intestinal bacterial overgrowth (SIBO) is often associated with viral gastroenteritis (a stomach bug/ stomach flu). Celiac disease, Chron’s disease, hypochlorhydria (low stomach acid caused by different factors, including taking antacids/ proton pump inhibitors.)

Gastroparesis (decreased gastrointestinal motility) is a big cause of small intestinal bacterial overgrowth. Yet again, there are many different causes for gastrointestinal motility disorders, one of the risk factors is diabetes, another risk factor is central nervous system diseases causing a slower intestinal transit time.




4. Testing and diagnosis for SIBO

Breath tests

If you are experiencing any of the symptoms of SIBO, your doctor may recommend a lactulose breath test or glucose breath test to diagnose intestinal bacterial overgrowth. Lactulose breath testing test involves drinking a solution of lactulose and then measuring the amount of hydrogen and methane gas in your breath over time. Breath testing can be done at a Laboratory that offers breath testing, or in some countries you can order a breath test online.

There are two main types of SIBO: methane-predominant and hydrogen-predominant. This depends on the type of intestinal bacterial overgrowth. Methane-predominant is more common and is associated with constipation. Hydrogen-predominant is less common and is associated with diarrhea. Both are as a result of small bowel bacterial overgrowth.

Blood tests / Cultures

If SIBO treatments are not working, we sometimes need to test fluid from the small bowel to test the bacterial population (intestinal bacteria), in hospital we call this a small bowel culture.

Some doctors may order blood tests. These doctors order blood tests to test for fat soluble vitamins, as vitamin and mineral deficiencies give us an indication of your body's ability to absorb nutrients. The ability to absorb nutrients is directly related to intestinal permeability which relies on gut bacteria (or intestinal bacteria) to absorb nutrients.

IBS patients, patients with scar tissue in their gut from previous surgery, patients who have been on antibiotic treatment for another illness often have a disrupted gut microbiome (this means the normal balance of gut flora or gut bacteria is disrupted). This is very often the cause of persistent symptoms in IBS subjects in studies.




5. Treatment for SIBO

Treatment differs depending on the underlying cause of the SIBO. The goal of treatment is to correct your gut flora, also known as your gut microbiome. When we obtain normal balance by restoring the intestinal microbiome of your small intestinal, your symptoms should resolve. This is the best indication of cure. You don't need a breath test to tell you that your intestinal bacterial environment is back in balance. If the use of antibiotics is the cause, then treatment will involve taking probiotics and prebiotics for a period of time. If there is an underlying health condition causing the SIBO, that will need to be treated first. For most people avoiding sugar and flour products (bread, pizza, muffins) helps significantly.

Low FODMAP diet

A low FODMAP diet may also be recommended. This is a diet that avoids foods that are high in fermentable carbohydrates like wheat, garlic, and onion. Treatment can also involve the use of herbal antibiotics like oregano oil or berberine. These natural treatments are thought to be just as effective as traditional antibiotics but have far fewer side effects. Oregano oil has a very strong bitter taste, so most of my patients prefer to take this in a capsule/ pill form.

Antibiotics and Herbicides

For some patients antibiotics might be necessary. Patients who are dehydrated and malnourished might need treatment in hospital to replace fluids . According to the latest ACG clinical guideline , the antibiotics we typically use in hospital are Ciprofloxacin, Metronidazole or Rifaximin. I generally don't prescribe antibiotics for patients as an outpatient, because, even though they decrease the number of bacteria in the small intestine, they will not address the underlying issue, the root cause, that caused the problem in the first place. I often find that these patients' SIBO symptoms return again after a couple of months when the underlying cause wasn't addressed. However, now they have a disrupted microbiome in the rest of their gut, especially their large intestine, which might cause even worse gastrointestinal symptoms.

Herbs that kill SIBO:

  • Philodendron

  • Oregon grape root

  • Godenseal

  • Barberry

  • Coptis chinensis


6. Diet and nutrition for people with SIBO

There are many different treatment protocols for treating SIBO. SIBO treatment will depend on the cause. For most people, the following does improve their symptoms:

  • Avoid sugar and processed foods.

  • Eat plenty of fiber, especially soluble fiber like oats, barley and psyllium husk. This aids with healthy bacterial growth.

  • Include medium chain triglycerides in your diet. These fats are absorbed directly without the need for digestive enzymes. Organic coconut oil is a great example.

  • You can take digestive enzymes if your root cause is liver disease / pancreatic insufficiency.

  • Drink plenty of fluids, especially water. Apart from improving SIBO symptoms, it also improves large intestine symptoms (e.g. irritable bowel syndrome.)

  • Take probiotics supplements. Especially if your doctor has prescribed antibiotic therapy, it is critical to replace all the small intestinal bacteria again. Lactobacillus plantarum / Lactobacillus G are probiotics we typically use, they will also be of benefit in your large intestine.



Many people find that following a low-FODMAP diet helps to reduce abdominal pain and bloating. FODMAPs are a type of carbohydrate that some people have trouble digesting. There is some evidence that following a low-FODMAP diet can help to reduce symptoms in people with SIBO. A low-FODMAP diet is an extensive topic, so I will write another blog on this next month.

Some patients with persistent symptoms of small intestinal bacterial overgrowth, who are having a hard time correcting their gut microbiome, people with excessive weight loss caused by SIBO symptoms, people with poor calcium absorption due to bacterial overgrowth and disrupted intestinal permeability of their digestive tract or people who has an impaired quality of life due to their gastrointestinal symptoms might choose to go on to an elemental diet.

An elemental diet is usually the last resort in my Clinic. We only use for patients with abnormal short chain fatty acids, where bacterial overgrowth has been confirmed on breath tests. These patients often have other conditions as well such as irritable bowel syndrome, inflammatory bowel disease, small bowel diverticulosis or Crohn's disease. These patients often feel their SIBO symptoms or IBS symptoms causes significant abdominal pain that impairs their quality of life significantly.

The elemental diet is a liquid meal replacement diet that offers a complete nutritional profile broken down into its most “elemental” form. Proteins, fats and carbohydrates are broken down into amino acids, short-chain triglycerides and short-chain maltodextrins, combined with vitamins, minerals and electrolytes.

These dietary “building blocks” are easily absorbed in the upper digestive tract, allowing the rest of your digestive system to rest and recover from illness or injury. They come in a liquid or powder form designed to be mixed with water. Some people order this online. In hospital we often give this to patients while they are recovering from surgery, for people with significant vitamin and mineral deficiencies. These patients often do not secrete normal bile salts needed to help to break down and absorb food.


If you are suffering from SIBO, don’t despair. There is hope. You can take control of your own health and heal yourself by making a few simple changes to your diet. Cut out sugar and bread and eat more raw vegetables and other healthy foods with pre- and probiotics.

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