Intstinal Dysbiosis in Irritable Bowel Syndrome

Intestinal dysbiosis is a term to describe an imbalance in the gut commensal (normally resident) microbiome. When the balance of the bacteria in the bowel is upset, usually by a diet too high in sugars and refined carbohydrates, the gut contents becomes more acidic. This encourages Streptococcus overgrowth and e-Coli undergrowth. The clinic staff in conjunction with Bioscreen Medical Laboratory has been investigating gastrointestinal changes reflected in abnormal faecal tests of IBS patients, as well as those with ASD and anxiety. The results of these tests and investigations are helping us to formulate effective treatment protocols, which have resulted in significant improvements if not normalisation in gut function and amelioration of IBS symptoms.


A healthy gastrointestinal tract is one that has a particular set of bacteria living within it. Normally it is difficult to change the number and type of these healthy bacteria and they are remarkably stable over many different populations around the world, even though we live in different environments and eat different diets. It is becoming widely recognised that alterations in these bacteria population and count can adversely influence our health. This is because bacteria in our digestive tract produce many vitamins, micronutrients and chemicals that maintain the health of our bodies. When these bacteria are not normally distributed, chemicals that are detrimental to our health might be produced in larger amounts and can cause dysfunction. That is why so many bacterial supplements (probiotics) have become available. For example probiotics containing Lactobacillus acidophillus and Bifidobacterium are common and their health benefits are greatly touted.  Unfortunately it is not as simple as talking probiotics. Often these common bacteria are overgrown in the gut resulting in increased amine production, which in turn causes cognitive and attention deficits, depression and tiredness.


There are two main classes of bacteria in our large intestines: aerobic bacteria, which need some oxygen to survive, and anaerobic bacteria, which will die in the presence of oxygen. The most common aerobic bacteria, or aerobe, found in healthy individuals is Escherichia coli (E.coli) and it accounts for 90-95% of all the aerobic bacteria. The second most common aerobe is Enterococcus, although it is a lot less common than E.coli at an average of 5% in the Gut.

In our experience, the E.coli count is often quite low in IBS, at approximately 50% compared to the normal 90-95%. In about 80% of IBS patients that we have tested, the percentage of E.coli was actually less than 10% of the aerobes and is associated with depression and fatigue. In another 20% streptococcus is overgrown replacing E.coli, a condition also associated with similar symptoms.

Changes to the anaerobes, or bacteria which don’t like oxygen, are also commonly evident. Normally, Bacteroides are the most abundant anaerobic bacteria in our large bowel. We consistently find a significant decrease in Bacteroides, and an increase in the number of Bifidobacteria in the faeces of IBS patients compared to healthy control subjects


Analysis of the urinary amino acids of IBS patients also show reductions in key neurotransmitter precursor amino acids and other amino and organic acids involved in energy production and muscle metabolism. Tryptophan is of particular importance as it is a precursor of serotonin which is an important brain neurotransmitter and is essential in the maintenance of gastrointestinal motility and function. Interestingly E.Coli and bacteroides both make tryptophan by breaking down proteins.


We use Pathlab urine tests and the Bioscreen faecal tests to identify alterations in body biochemistry, microbiology and digestive capacity. The nature of these tests results can provide avenues for the identification of treatment protocols that may involve:

  • normalisation of the gastrointestinal bacteria through use of specific antibiotics, that target overgrown bacteria; replacement of undergrown bacteria (e.g. very specific probiotics and prebiotics) and specific nutritional supplementation;
  • supplementation with individualised amino-acid supplements based on the profile of deficiencies of amino acids found in the urine test, and
  • supplementation with digestive enzymes, electrolytes, and essential nutritional minerals to help impaired digestion and metabolism.
  • Nutritional supplements to improve gut cell wall integrity and function.