The small intestine is narrower than the large intestine, however, it is actually the longest section of your digestive tube, measuring about 22 feet (or seven metres) on average. Gut bacteria are throughout the whole digestive tract but in varied amounts. The majority of your bacteria are in the large bowel (colon) at the rate of 1,000,000,000 bacteria per millilitre of fluid, whereas the small intestine has less than (less than 10,000 bacteria per millilitre of fluid.

The reason for so few numbers of bacteria in the small intestine is that is where the majority of absorption and digestion of food occurs. It’s also where up to 80% of your immune system resides that helps fight various infections that could be bacterial, parasitic, viral or fungal in nature.

In addition to the immune component, they also produce beneficial compounds and nutrients such as short chain fatty acids (SCFA’s) that have multiple benefits both locally in the gut and systematically by the process of controlling inflammation

What Is SIBO?


Small Intestinal Bacteria Overgrowth (SIBO) is an increase in the number of bacteria that are present in the small intestine. SIBO is not caused by a single bacteria or an overgrowth of pathogenic bacteria per se, but an overgrowth of different bacteria should be normally found in the colon. Small Intestinal Bacteria Overgrowth NHS’s definition of this condition is when there is a rise of either methane or hydrogen gas above a certain number within a 3-hour time frame once you have ingested a type of sugar solution.

The effect of an increase in bacteria in the small intestine is that your digestion will be compromised leading to malabsorption of nutrients, especially fat-soluble vits (A, D, E and K) and B vitamins. Additionally, the damage to the small bowel mucosa can lead to what is called a “leaky gut ,” which can lead to a whole host of symptoms with inflammation as its core. 

SIBO Causes


There are can many causes of SIBO that functional medicine doctors and practitioners need to look at, as once you find out what caused it, you will have more of a chance to keep it from coming back. One of the issues I see with forums is that they are numerous people looking for protocols and diet advice. And, although this can be helpful, if they don’t find out what caused the SIBO in the first place, you may get short-term relief but it can keep coming back and this is where you need to work with a skilled practitioner who knows how to treat SIBO.

1) Altered bile flow 


Optimal bile flow is important for foods we eat and specifically for breaking down fats and proteins. If Bile isn’t working optimally, bacteria and fungus can ferment on undigested foods. Furthermore, when bile flow isn’t working optimally this will put more strain on the pancreas and stomach meaning there will be a whole digestive system that is weakened causing lack of digestion for carbohydrates, fats and proteins.  Bile acids additionally have antibacterial effects, helping to protect our gut against bacterial overgrowth

2) Stress


Stress has a negative impact on many aspects of our digestive process. When we get stressed, we produce fewer enzymes to break down food leading to the same mechanism as above with more bacteria able to use food as fuel 

Additionally, stress can weaken the immune system, allowing for dysbiosis, further increasing the risk of developing SIBO. The biggest impact from stress is gut motility and slowing the movement of food through our digestive system allowing pathogens to ferment on food.

3) Low stomach acid


Similar to the mechanism mentioned above, low stomach acid leaves food undigested and causes bacteria to proliferate.

When stomach acid levels are high, the acid will suppress the growth of bacteria, fungus, viruses and parasites.  A lot, of the time when you are travelling, picking up a pathogen is down to the fact that digestion is weak and stomach acids levels aren’t adequate allowing pathogens to enter the body. 

One of the effects of low acid is symptoms of high acid with acid refluxing up the oesophagus, however, this in fact is actually due to low levels of stomach acid and not high levels. And to make matters worse, the treatment is antacids which can lead to a further weakening of stomach acid levels. This is one of the major causes of SIBO we see in SIBO cases in the UK and at the clinic.

3) Nerve dysfunction


The digestive tract requires peristalsis to move food down all of the digestive tract. There are many conditions that can affect this including medications such as anticholinergics. Structural changes in the digestive tract can also inhibit the movement of bacteria from the small intestine to the large intestine, or allow the migration of bacteria upwards from the large intestine. Ileocecal valve impairments can also interfere with the normal bacterial flow

4) Immune system dysregulation


Immune system irregularities can happen from birth with C sections and bottle feeding causing a greater risk of imbalances and a higher incidence of dysbiosis. We also know that the higher prevalence of autoimmune can predispose someone to SIBO

6) Antibiotics


The way we have given antibiotics routinely for conditions that don’t need them or for the treatment of the common cold can lead to an imbalance in the bacterial ecosystem. With SIBO, even though the imbalance shows up in the small intestine, the root cause which is what we are always concerned about as a functional medicine practitioner comes from the large bowel.  There is a place for them but we need to be very selective in our use of them.

7) Food poisoning


Food poisoning makes you produce certain antibodies to fight the foodborne illness.These antibodies attack Vinculin which is an important protein for nerves and the resulting motility in the small intestine is affected and this can lead to the development of SIBO.

8) Additional Potential Causes and Risk Factors

  • Irritable bowel syndrome
  • Celiac disease (long-standing)
  • Crohn’s disease
  • Prior bowel surgery
  • Diabetes mellitus (type I and type II)
  • Organ system dysfunction, such as liver cirrhosis


A SIBO breath test is a simple and non-invasive test that can be done at home. The 2 different types of SIBO tests are the lactulose breath test and glucose breath test.  Before ingesting either a lactulose and glucose solution you will provide an initial breath sample by blowing into a test tube which will give us your baseline reading.

Then, you will drink the sugar substrate solution containing either glucose or lactulose.

Breath samples will then be taken every 15 minutes for just over two hours in order to measure hydrogen and methane, post-ingestion. The test will be completed in 3 hours. 

UK SIBO Tests can be ordered via your specialist and not your GP or your functional medicine practitioner. At the clinic, this is one of the most common tests we order for clients not just in the UK but globally by our partner lab. 



There are no exact figures for people suffering from SIBO and this is more to the fact that it’s heavily undiagnosed with many doctors and GI specialists still failing to recognize this condition. Up to 80% of IBS have SIBO which is a general complaint for 10 to 15% of the population, and so the definitive figures could be quite high.

Besides this, the accuracy of breath testing has quite a high number of false negatives depending on what method of testing you use (lactulose, glucose or fructose).

The most common symptoms of SIBO include:

  • Abdominal pain
  • Bloating and abdominal distention
  • Diarrhoea
  • Constipation
  • Gas
  • GERD
  • Nutrient Deficiency
  • Anxiety/Depression

The difficulties in treating SIBO


The most common way to treat SIBO conventionally is with antibiotics with rifaximin being the most commonly prescribed antibiotic. Even as naturopathic and functional medicine practitioners, this is an antibiotic we encourage as its non-absorbed which makes it one of the most unique antibiotics as it doesn’t have the negative effects standard antibiotics do.

However, studies show that over 50% of recurrence develops within a year. Reoccurrence rates for a natural botanical approach showed slightly improved figures but still not much improved below 50%

This is where functional medicine doctors and practitioners should be the preferred route as their ability to understand any predisposing factors should see a much high clearance rate. Some of the predisposing factors have been listed above and it may be that slow transit time is the issue which means using a prokinetic to increase the migrating motor complex or improving the mucosal layer of the large intestine which could have a number of infections such as Candida.

As more research into SIBO continues, we are starting to gain more insight into the many complexities of this disease and how a holistic approach is a more favoured approach in dealing with SIBO. SIBO NHS treatments can be helpful, however, more often than not, they may miss many of the predisposing factors which is where functional medicine can really help understand what caused SIBO in the first place. One of the other main issues is getting a diagnosis as NHS SIBO symptoms can be a multitude of gut issues that overlap which means getting the relevant testing can be a long process. The other issue with NHS SIBO treatments is they won’t test on the large bowel (colon) and this is where the dysfunction probably started. Functional Medicine doctors and practitioners are generally well versed with these symptoms and are more prone to test for this condition and can get a much quicker diagnosis.

If you need support in dealing with SIBO, consider working with the London Centre for Functional Medicine. We work with SIBO cases on a daily basis and help make the changes necessary to reclaim their digestive health. Feel free to contact us and book a free discovery call

Recent Articles