SIBO – Small Intestine Bacterial Overgrowth

What is SIBO?

The human intestine is actually two different organs. The small intestine and the large intestine, which is also called the colon. Trillions of bacteria should colonise the large intestine, and in comparison, the small intestine should have very few. SIBO means there are too many bacteria in the small intestine.

It’s not that the type of bacteria are bad. The bacteria are normal inhabitants of the human body and do not normally cause any problems. They are what is called commensal bacteria, meaning neither good or bad. The problem in SIBO is that they are colonising a part of the body that is not their usual habitat, and which is not designed to house them.

Where do the bacteria come from?

The small intestine is not meant to be sterile. There is a constant flow of bacteria moving through from the stomach to the small intestine. So, bacteria can enter the small intestine from the stomach or they can move backwards from the large intestine into the small intestine.

Does SIBO damage the gut?

Bacteria ferment certain foods and create gas, which can be felt as a sensation of bloating and may be seen as actual distension of the abdomen.

The gas itself may damage the structure of the lining of the intestines which acts as a barrier between the inside of the intestines and the rest of the body. So, a compromised barrier can lead to problems such as leaky gut.

Damage to the gut lining can also affect its role in the process of digestion and absorption.

What gases do the gut bacteria produce?

The main gas that bacteria produce is hydrogen. But, some micro-organisms use the hydrogen to form other gases. So, as well as hydrogen, methane and hydrogen sulphide are sometimes produced in the small intestine as well.

What impact does methane have in SIBO?

Methane is a gas that is produced by Archaea, a different type of micro-organism that can live in the gut. Archaea are sometimes called methanogens, or methanogenic bacteria, though strictly speaking, they are not bacteria.

Methane production in the small intestine can be a problem because it directly affects the nervous system that controls the movement of the gut, slowing it down. This means that the gut contents hang around a lot longer than they should.

A slower moving gut means more bloating and increases the risk of constipation. In fact, the more methane produced the worse the constipation is.

What are the symptoms of SIBO?

The symptoms of bacterial overgrowth are very similar to those of IBS, and in many cases, SIBO can be a cause of IBS.

The main symptoms of SIBO are gas and bloating, with diarrhoea, constipation, or a mixture of constipation and diarrhoea. Some people might also have pain and cramping in the abdomen.

Since the intestinal lining is altered and doesn’t function properly it is also common to have food intolerances, malabsorption, or malnutrition. These can lead to other problems such as weight loss, anaemia and loss of bone density.

Is there a test for SIBO?

There is breath testing for SIBO that detects hydrogen and methane gases in the small intestine. More gas means more micro-organisms, so this can be used as a simple test to diagnose the presence of bacterial overgrowth.

Is testing necessary to diagnose SIBO?

SIBO can not be diagnosed without testing.

But, lab testing can be expensive, so many practitioners will try simple treatments first and then if the results are not satisfactory then testing might be recommended.

How is SIBO treated?

A low FODMAP diet is sometimes used to manage symptoms of bacterial overgrowth. This diet reduces the amount of fermentable carbohydrates and therefore there is less fermentation and so less gas and less symptoms.

There are also other diets that can be tried, such as the GAPS diet or Specific Carbohydrate diet, and sometimes a bit of experimentation might help to find the most appropriate one for the individual person.

However, dietary changes like these, without other treatment are usually not enough to eradicate SIBO.

Since SIBO is caused by microbial overgrowth then the treatment is aimed at ridding the small intestine of bacteria. A doctor might prescribe antibiotics. A medical herbalist would suggest herbal antimicrobial remedies.

Research has shown that herbal antimicrobials are just as effective at eliminating the micro-organisms as antibiotics, but the natural remedy must be taken for a longer period of time.

Does SIBO treatment work?

SIBO treatments do kill bacteria and archaea but sometimes the treatments need to be repeated, whether that is antibiotic treatment or herbal antimicrobials. This can sometimes occur because there were more bacteria than was possible to kill with one round of treatment. Or there could have been successful eradication but then a relapse occurred.

Relapses occur because eradicating the micro-organisms alone is often not enough. It is usually necessary to discover what is the underlying cause. Why did the bacteria colonise the small intestine in the first place?

Effectively treating SIBO is not just about fixing the symptoms but finding and addressing the underlying cause. And, because there are many possible underlying causes this demands some detective work.

What are the underlying causes of SIBO?

There are many, many possible underlying causes of SIBO, from structural problems of the digestive tract, such as partial obstructions, to weak digestive function caused by a lack of stomach acid.

The most common but often an unrecognised cause of SIBO is food poisoning. People don’t realise that food poisoning caused their symptoms because in many cases the SIBO doesn’t develop until months later.

Toxins produced during an episode of food poisoning result in damage to the intestinal cells which slows down the migrating motor complex, which increases the risk for SIBO.

What is the migrating motor complex?

The migrating motor complex is the name given to the cleaning process that occurs in the intestines between meals. This clearing away, sometimes likened to a scrubbing clean of the intestines is our major protection against bacteria stagnating in the small intestine.

With a well functioning migrating motor complex bacteria are moved out of the small intestine and into the large intestine where they have a beneficial role creating substances that we need. Without a well functioning migrating motor complex, gut bacteria can flourish and multiply in the small intestine causing the symptoms of SIBO.

The most common cause of disruption to the migrating motor complex is food poisoning and many people develop SIBO after a case of food poisoning. In many cases people don’t even realise that the food poisoning and the SIBO are linked because the SIBO may take several months to develop.

The migrating motor complex is triggered by the nervous system. So, another risk factor is damage to the nerves or muscles of the digestive tract. This might occur in diseases like hypothyroidism, diabetes or Parkinson’s disease, demonstrating the gut-brain connection. Similarly, when we are under stress, our digestion can be affected, so stress is another cause of disruption to the migrating motor complex.

Not forgetting another very common cause of a slowing down of the gut, in the form of prescribed medications such as antibiotics and opioids.


Similar to SIBO, SIFO is Small Intestinal Fungal Overgrowth. SIFO can occur at the same time as bacterial overgrowth.

How is SIFO treated?

Antibiotics for bacterial overgrowth are not designed to be effective against SIFO. However, many herbal anti-microbials offer the advantage of being effective against both bacteria and fungal species.

Help to identify what is causing SIBO

The key takeaways are that for two-thirds of people with SIBO it is along-term condition. It is important to understand the underlying causes. And it is usually necessary to have more than one round of treatment to fully eradicate SIBO.

I have mentioned some of the most common reasons underlying SIBO, but of course there are more.

In my role as a practitioner, I help people to identify the underlying causes of SIBO, or other chronic problems. If you would like to hear more about how I can help, you can book a free, no-obligation hello call with me to have a chat about your health concerns.

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