Gut Microbiome Test UK

We offer a comprehensive stool test available which is proving to be of great benefit to IBS (irritable bowel syndrome) sufferers. 

IBS Specialists as featured in the Guardian

What is a Gut Microbiome Test?

Woman talking to her doctor


Recently there has been an explosion of new gut microbiome tests that have been offered by several laboratories. But what is a Gut Microbiome test and is it worth the expense?

A Gut Microbiome stool test is a diagnostic examination that assesses the microbial composition in your stool (faeces). It can be helpful in assessing the specific strains of gut bacteria in your large intestine.



What is the Microbiome?

The Microbiome is made up of tiny organisms, that are found  throughout the human body—on your skin, in your oral cavity, nasal passages and even in your genital areas. However, the term “microbiome” formally refers to the population residing in your large intestine.


Are Gut Microbiome Tests worth it?

Basic microbiome assessments are now offered by a vast number of laboratories and can provide information about the varieties and amounts of bacteria in your digestive tract. However, in truth their scope is limited when assessing the overall well-being of the health of your gut.

Gut Health Tests are more comprehensive

If you are looking for a test to assess the overall health of your gut, you may be better off using a more comprehensive stool test to assess underlying pathogens including yeasts, candida, parasites, viruses and inflammation such as Calprotectin.


What  are Gut Health Tests?

Called the CSA test, it stands for Comprehensive Stool Analysis test and comprehensive is exactly what it is. Patients send in 2-3 stool samples and they are examined using two methodologies,   an extremely powerful microscope and PCR to evaluate the status of beneficial bacteria, imbalanced commensal bacteria, pathogenic bacteria, parasites and yeasts including Candida. The most comprehensive tests can also screen for inflammation as well as Helicobacter Pylori and digestion and absorption.

If dysbiotic bacteria and yeast are identified, a sensitivity panel listing anti-fungals and anti-bacterials is provided on the report to so that the appropriate treatment is found.


This test is far more useful as it is able to screen for real conditions and pinpoint underlying pathogens that may be linked to symptoms of diarrhoea, constipation, wind and bloating.


What causes bad bacteria in your gut?

The human digestive tract typically harbours approximately 500-1000 diverse bacterial species, many of which contribute positively to our well-being. However, an imbalance may occur if potentially harmful bacteria proliferate.

Several factors including low stomach acid, stress, consumption of processed and sugary foods, and the use of antibiotics and medications may adversely impact gut health. While symptoms like diarrhoea, constipation, and gas are evident signs of an imbalance (resembling IBS), an unsettled gut may manifest in unexpected health issues, including:

  • Dermatological concerns affecting skin health such as acne, rosacea, psoriasis
  • Unexplained weight gain and a sluggish metabolism
  • Cognitive challenges like brain fog and memory issues.
  • Fatigue and low energy levels.
  • Depression, anxiety and fluctuations in mood
  • Frequent occurrences of colds and infections.
  • Insomnia/ Disturbances in sleep patterns.


What Methodology is used in your Gut Health tests?


GI Pathogens measured by multiplex PCR.


Gold standard microscopy of parasites, worms and yeasts.


Microscopy of red and white blood cells, muscle fibres, vegetable fibres, pollen and Charcot-Leyden Crystals.


Culturing of commensal and pathogenic bacteria

The Comprehensive Stool Analysis with Parasitology and PCR evaluates the following markers:


Digestion and Absorption including faecal elastase, fat, carbohydrate, muscle and vegetable fibres.


Inflammation – Calprotectin, lysozyme, lactoferrin, white blood cells and mucus detection.
This marker is very important as it can help to differentiate inflammation associated with inflammatory bowel disease (IBD) from that noted in irritable bowel syndrome (IBS).


Secretory IgA (sIgA) is also measured.


Short-chain fatty acids reflects overall gut health and microbiome balance.
This profile is indicated for gastrointestinal symptoms, autoimmune disease, joint pain, IBD, IBS, inflammation, food sensitivities, nutritional deficiencies and skin conditions.

In my experience with patients who have taken a gut health test, it almost always reveals at least one or two things which the NHS tests such as blood tests or  an endoscopy or sigmoidoscopy or a colonoscopy have not revealed.

Not surprising perhaps, when you think about it, because it examines stool samples, which the other tests don’t, and it takes great care to get them in a form unlike any other stool sample test. (Careful instructions are provided with the test kit sent to patients and the test can be done at home – which saves time and saves a trip to the hospital).

What is so remarkable about the Comprehensive Stool Analysis Test CSA?

The answer is the examining a vast range of bacteria, parasites, yeast and intestinal ecology. All are helpful because getting one’s intestinal ecology right is an important step for everyone. For IBS sufferers the major areas are as follows:


These have been a cause of IBS symptoms in 31% of all patients who have taken the test via us. They are particularly likely to be a cause where diarrhoea or loose stools are the major symptoms and parasites are particularly likely to be present if the patient’s symptoms can be traced back to a stomach bug experienced on foreign travel. Even if this stomach bug was treated with antibiotics at the time, often parasites will not have been completely eradicated and could still be causing symptoms several years later. This is particularly true if the patient was ill on a trip to India, Nepal, Egypt, South America or a similar exotic location. Even if the patient has been tested for parasites on the NHS it is very possible the CSA, because of its more sophisticated techniques, will find something the NHS test did not. Dientamoeba fragilis and Blastocystis hominis, for example, are parasites that cause IBS symptoms and are not looked for by the NHS test.

Friendly Gut Flora

Otherwise known as probiotics, are very important to a healthy gut. The test measures on a scale of one to four the presence or absence of Lactobacillus acidophilus and Bifidobacterium, two of the most important friendly bacteria which are found in natural, organic yoghurt. These are very beneficial to intestinal health and are why, just in the last few years, commercial yoghurt makers such as Yakult and Benecol have entered the market to try and persuade us all to eat yoghurt with these friendly bacteria added. Unfortunately, all these yoghurt drinks contain added sugar and so are not the best way to re-populate the gut with friendly bacteria.


Just as is the case with parasites, bacteria such as Klebsiella or Citrobacter freundii or Pseudomonas Aeruginosa can be the hidden cause of IBS. It is nearly impossible to tell from clinical symptoms if they are a cause so here the CSA is invaluable. Not only does the test reveal which bacteria are the problem, it provides a list of which drugs and/or natural remedies have been found to be the most effective at eradicating the offending bacteria.

Candida Albicans and Other Species of Yeast Overgrowth

Such as Geotrichum can be a contributory cause of IBS and the test identifies the presence of any of these yeasts (all of which can contribute to gut fermentation) and, again, provides a list of the most effective remedies.

The CSA also tests for occult blood in the stool, which can be due to haemorrhoids or an anal fissure, but which can also indicate the possibility of more serious pathology, such as cancer. It measures the presence of meat and vegetable fibres in the stool which are an indicator of how well the patient is digesting protein and carbohydrate and how well they are digesting fat.

My background is that of a nutritionist who specialises in food intolerances. I used to look at IBS mostly in terms of food intolerances and, believe me, they are a very important cause of IBS symptoms. But when the Comprehensive Parasitology and the CSA test became available to a small number of private nutritionists (different from dieticians, who work in hospitals), I was intrigued. Since then we have used it with every IBS patient (and those with Ulcerative Colitis and Crohn’s) who does not respond to the food intolerance approach or wants to take the test immediately. In the case of those with a history of one or more stomach upsets in the course of foreign travel we recommend it at once.

To be honest, it helps almost everyone with IBS because, even if their symptoms have improved considerably from the food intolerance approach, it shows whether something is still basically wrong. We should all have one or two perfectly formed bowel movements every day. Anyone who differs from that norm should try and understand what factors may be preventing them from enjoying  better gut health with the aid of the test.

Man talking to his doctor

Case History: John Taylor

John Taylor was a dynamic executive in his late forties who had everything else in his life very much under control. In fact his life was probably perfect in every respect, bar one: he had had very distressing IBS symptoms for at least ten years.

John came to the IBS and Gut Disorder Centre because he’d taken a food intolerance test and he wanted our help with formulating a diet for him which avoided milk and oats, which were the two foods his particular test had shown him to be intolerant of. (NB: This does not apply to all IBS sufferers; it simply applied to John Taylor.)

In many cases very accurate identification of one’s food intolerances will relieve symptoms of IBS considerably but, as I have stated in the accompanying article, there are some people who just do not respond to elimination of allergenic foods. John Taylor was one of them. So I suggested he do the CSA test and its revelations were startling. He had parasites, unusual bacteria and a very high degree of Candida Albicans. So he had not just one cause of his IBS but three major ones and, in addition, a finding of a complete absence of the friendly bacteria Lactobacillus acidophilus. After appropriate treatment he has improved enormously.