SIBO – Small Intestinal Bacteria Overgrowth

SIBO stands for Small Intestine Bacterial Overgrowth. SIBO is a condition that affects the gut and seems to be ever more prevalent. It can cause a great deal of digestive discomfort and can also trigger symptoms outside of the gastrointestinal tract. SIBO is now considered to be a common underlying cause of IBS.

We all have some bacteria in the small intestine, but these normally occur at a much lower level than in the large intestine. The bacteria involved in SIBO are not normally pathogenic, as you might encounter in a bout of food poisoning, but are likely to be commensal or opportunistic bacteria – almost like the right bacteria that are just in the wrong place.

One of the roles of bacteria in the large intestine is to break down foods that we aren’t able to digest by our own enzymes, further up the GI tract. This break down process by bacteria is called fermentation. When this fermentation process happens in the small intestines it can cause a lot of gas and bloating. Most of our food is digested and absorbed in the small intestine by our own range of digestive enzymes, but when excess bacteria are present they interfere with this process and get the opportunity to digest the food before we do with their fermentation activity, depriving us of the nutrients we would normally extract.

Bacteria produce methane and hydrogen gases that are responsible for some of the symptoms of SIBO; for example, gas, bloating, constipation or diarrhoea. Bacteria can also produce chemicals that damage the lining of your small intestine, further inhibiting your ability to absorb nutrients. Once the gut lining has been damaged toxins can leak through and cause problems elsewhere in the body, sometimes leading to Leaky Gut Syndrome, where the intestinal wall is letting large molecules of undigested food matter through into the bloodstream and causing immune system reactions.

Other signs and symptoms of SIBO include: belching; GERD (Gastro-Esophageal Reflux Disorder – commonly known as heartburn); nausea; food sensitivities; nutrient malabsorption; leaky gut; fatigue; brain fog; anxiety; muscle or joint pains.

There are a variety of factors that increase the risk of a bacterial overgrowth including: low digestive secretions (stomach acid, pancreatic enzymes, bile); sometimes also caused by the use of stomach-acid suppressing drugs called PPIs – Proton Pump Inhibitors, like omeprazole (e.g. Prilosec and Losec) and similar drugs used for GERD; obstruction/dysfunction in the GI tract; food poisoning; stress; antibiotic use; long term use of PPIs; hypothyroidism; and Ehlers Danlos syndrome.

SIBO is most commonly assessed via a breath test which measures levels of methane and hydrogen gases and can be easily carried out in your own home. Many people consider the lactulose breath test to be the gold standard test, but a glucose breath test can also be used. This is thought to be less reliable. The other way of testing for SIBO is via a bacterial culture taken during an endoscopy. This is an invasive method and risks giving a negative result if the sample is taking from a different area to where the overgrowth is actually occurring.

Treatment for SIBO often requires a multipronged attack combining antimicrobial agents, prokinetics, and diet and lifestyle changes. The antibiotic Rifaximin has been found to be extremely useful as it has a large, oily molecule which is not absorbed by the epithelial layer of the digestive tract, keeping the antibiotic inside the lumen of the small intestine where it can work on the pathogenic microbes. Additionally, it has a very short half-life which means that by the time it makes its way down to the large intestine, it is largely spent, thus sparing the gut flora within the bowel. For this reason, it is a useful treatment both before or after FMT (Fecal Microbiota Transplant).

A low FODMAP diet is often used to manage symptoms, but other diets have also been found to be beneficial: the Fast Track Diet; Specific Carbohydrate Diet (SCD); Gut and Psychology Syndrome (GAPS); Bi-Phasic Diet; and Allison Siebecker’s SIBO Specific Food Guide, which combines the SCD and Low FODMAP diets.

It is important to find an experienced practitioner to work with when trying to treat SIBO. Diet alone is rarely successful in eradicating a bacterial overgrowth, so advice and support regarding other treatment options is essential.

At Taymount we are often asked whether FMT is a suitable treatment for SIBO, but as yet there isn’t any research on the efficacy of FMT for this condition. Some of our patients have reported that FMT has been helpful with some of their SIBO symptoms, but we advise people to reduce their bacterial overgrowth as much as possible before coming to the clinic. However, a thriving, diverse set of bacteria in the large intestine generally has positive effects on the GI tract as a whole, and improving gut function overall would no doubt be beneficial.

Nina Mansell
FMT Nutritional Therapist


  1. Ghoshal, UC. Shukla, R. Ghoshal, U. (2017) Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy. Gut Liver. Mar 15;11(2), pp.196-208.
  2. Bures, J. (2010) Small intestinal bacterial overgrowth syndrome. World J Gastroenterology. Jun 28;16(24), pp.2978–2990.
  3. Siebecker, A. Sandberg-Lewis, S. (2013). Small Intestine Bacterial Overgrowth: Often-Ignored Cause of Irritable Bowel Syndrome. Townsend Letter, the Examiner of Alternative Medicine, Online Alternative Medicine Magazine. Feb/Mar.
  4. Bohm, M. Siwiec, RM. Wo, JM. (2013) Diagnosis and management of small intestinal bacterial overgrowth. Nutrition in Clinical Practice. Jun;28(3), pp.289-99.
  5. Triantafyllou, K. Chang, C. Pimentel, M. (2014). Methanogens, Methane and Gastrointestinal Motility. Journal of Neurogastroenterology and Motility. 20(1), pp.31-40.
  6. Halmos, E, Power, V, Shepherd, S., Gibson, P. and Muir, J. (2014). A Diet Low in FODMAPs Reduces Symptoms of Irritable Bowel Syndrome. Gastroenterology. 146(1), pp.67-75.e5.