Small intestinal bacterial overgrowth (SIBO)

This blog is the second of two blogs about functional gut testing. You can read the first blog about GI Effects testing and comprehensive digestive stool analysis (CDSA) with parasitology here. If you suffer with IBS, I encourage you to read both blogs, as IBS is often misdiagnosed, and both these functional gut testing blogs will help you understand why you may have developed IBS.

What is SIBO?

The name stands for Small Intestinal Bacterial Overgrowth or SIBO for short.

As the name suggests, this bacterial overgrowth is present in the small intestine where bacteria should not reside. There should be bacteria present in the large intestine, but the small intestine should be sterile. The small intestine is 20 feet long and it is where our food is absorbed via our villi. However, if there is an excess of bacteria in this area, the food cannot be properly absorbed, and the bacteria feed off this stagnant food, fermenting it and create toxic gases. The gases that can be produced are hydrogen, hydrogen sulphide and methane.

This gas build up causes bloating and discomfort in the abdomen, and an increase in intra-abdominal pressure. This excess pressure can cause the contents of the stomach to be forced up which can result in reflux, nausea and heartburn, not to mention increasing the risk of a hiatus hernia and shortness of breath due to the bloated, expanded intestines pushing up into the chest cavity and ‘crushing’ the ribcage and lungs.

This situation in the small intestine can cause problems in the large intestine too, resulting in constipation or diarrhoea, and inconsistent bowel movements. SIBO can result in gut inflammation and damage to the mucosal membranes which can lead to ‘leaky gut’ which has been linked to the onset of food intolerances and autoimmune diseases.

Usually, the small intestine is kept sterile from the Migrating Motor Complex’s (MMC) sweeping action every 4 hours that ‘cleans’ any bacteria or debris in there, but if the bacteria are hiding in pockets, scar tissue or adhesions, they can escape this cleaning action. Similarly, if the MMC is not working correctly then it cannot perform this job correctly.

Sometimes, if you take certain strains of probiotics, your symptoms can worsen if you have SIBO as this is like adding fuel to the fire where there is already too much bacteria present. This is because the bacteria present in SIBO are not always pathogenic, it can be an overgrowth of good strains of bacteria like the ones in probiotics that are growing in the wrong place.

Symptoms of SIBO

There are plenty of gastro-intestinal (GI) symptoms associated with SIBO including constipation/ diarrhoea, flatulence (often quite smelly), burping, bloating, abdominal pain, acid reflux, bad breath, vomiting. However, the symptoms extend beyond the GI tract and also include brain fog, fatigue, skin issues (rashes, eczema, acne), joint pains, anxiety, depression, hormonal imbalances, malnourishment, issues with histamine break down, bile acid malabsorption (BAM) and rosacea.

Risk factors for developing SIBO:

  • Low stomach acid – allows bacteria to survive past the stomach
  • Use of antibiotics, lowers immune defences
  • Use of the contraceptive pill disrupts the microbiome
  • Use of certain medications can affect transmit times
  • Long term constipation can affect the ileocecal valve allowing bacteria to travel up from the large intestine to the small.
  • Stress can cause the Lower Oesophageal Sphincter to become impaired. Stress can also cause low stomach acid
  • Adhesions from surgeries including laparoscopy, appendectomy, caesarean etc can affect the MMC.

Food poisoning – bacteria from food poisoning can secrete a toxin called Cytolethal Distending Toxin B (a neurotoxin). This can damage the nerve cells in the small intestine which help the Migrating Motor Complex (MMC) to work properly in ‘cleaning’ the small intestine of bacteria and debris. If this is not working properly then you get a build-up of bacteria in the small intestine. MMC is different to peristalsis, the involuntary contraction and relaxation of the gastro-intestinal (GI) tract, pushing food down from the mouth to the anus. MMC is an electrical wave that occurs only between meals in a fasted state, essentially ‘cleaning’ the small intestine of debris. It is mainly limited to the small intestine, not the whole GI tract.

  • Endometriosis and diverticular disease can allow for blind loops where bacteria can hide and multiply
  • Diabetic neuropathy to the Autonomic Nervous System (ANS), particularly in the gastrointestinal tract (GIT) can cause hypomotility and SIBO.
  • Autoimmune attack on the ileocecal valve
  • Altered collagen levels (Ehler’s Danlos Syndrome)
  • Impaired gut-brain axis function
  • Hypothryoidism can affect transmit time and pre-dispose to SIBO
  • Heavy metal toxicity

Testing options:

A SIBO test is a breath test and it measures hydrogen and methane gases from the small intestine. These gases are produced by bacteria residing in the small intestine. High levels indicate the presence of bacteria in the small intestine where they should not be.

The test is a home testing kit which you can easily complete following a prep diet and an overnight fast. You then post the test kit back off to the lab and wait 10 days for the results.

There is the option of 2 substrates for the test including lactulose and glucose. Generally speaking it is best to use lactulose as this measures a larger proportion of the small intestine whereas the glucose substrate only tests the top end, so it can produce a false negative result as it misses half of the picture.

A SIBO test is not available from your GP.  Most GP’s may not understand SIBO well. If you can get a referral to a gastroenterologist that understands SIBO, then you may be able to eventually get a test for this on the NHS, but you may be waiting months to get an initial appointment and even longer for the test. Also, the test that they use only uses the glucose substrate which only tests the top end of the small intestine as mentioned above. Also, their test only measures hydrogen gas, not the methane gas, so you only get half of the picture and there are many cases that are missed due to these false negative results. A private SIBO test will cost you around £160.


The treatment for SIBO may include the use of SIBO specific antibiotics like Rifaximin, which are quite hard to get prescribed.  However, the reoccurrence rates for those who use antibiotics to treat their SIBO is very high. This is because the antibiotics kill off any good bacteria which are needed as part of the immune system in fighting off bacteria. Also if there is a fungal element to your overgrowth (SIFO) then the antibiotics will not work against this, and may actually encourage the growth of fungus in the small intestine. The bacteria may also be resistant to the antibiotics that are used.

Because of all of the above, especially the high reoccurrence rate after using antibiotics and the damage that antibiotics can have on your gut microbiome, I recommend taking a natural approach using natural anti-microbials and other specific nutrients that are specific to your type of SIBO.

It is advised that you work alongside a nutritional therapy practitioner who is experienced in SIBO. The treatment will depend on the type of SIBO that you have and how severe the overgrowth is. Your therapist will prescribe the best and most suitable supplements for your individual makeup, checking them for any drug-nutrient interactions. They will also advise on the different dietary protocols that are available for treating SIBO, again they will discuss the best diet for you based on your individual needs and symptoms.