Functional testing for gut health

Functional testing for gut health blog image

In this blog, we’re looking at private functional gut health tests, including Gastro-intestinal (GI) Effects, Comprehensive Digestive Stool Analysis (CDSA) and small intestinal bacterial overgrowth (SIBO).  These are tests that are not available on the NHS.

It’s the first of two blogs about functional gut testing. You can read the second blog, about Small Intestinal Bacterial Overgrowth (SIBO), here.  If you suffer with IBS, I encourage you to read both functional gut testing blogs, as IBS can be misdiagnosed.  These two blogs will help you understand why you have IBS.

Why would I consider testing for gut health?

If you have been struggling with unexplained gut symptoms for months (or even years), have tried different diets including FODMAP, and different supplements, had a stool test through your GP, had an endoscopy and/or a colonoscopy, but still with no idea why you are getting your symptoms and you would like to remove the guesswork and get to the root cause of your symptoms, then functional testing is an effective way to do this.

Irritable bowel syndrome (IBS) is often diagnosed after tests to rule out other causes such as coeliac disease, inflammatory bowel disease (Crohn’s disease and ulcerative colitis and certain cancers). The symptoms include stomach pain and cramps, constipation, diarrhoea, excessive, unpleasant flatulence, bloating, mucus, feeling fatigued, acid reflux/ indigestion, skin problems and low mood.

A diagnosis of IBS can often be quite unhelpful because it does not tell you what has caused the symptoms (i.e the root cause). Without knowing the root cause it’s hard to get to the crux of the problem, so the focus becomes on masking the symptoms instead – at least from a conventional medicine viewpoint – with all manner of different drugs, antispasmodics, drugs to speed up the bowels, drugs to slow it down, anti-depressants and so on.

Can I get a functional test for gut health at my GP?

Sometimes your GP will do a simple stool test to see if there are any bacteria present which could be causing your symptoms. However, the test is not one that is routinely done and if you do manage to get one then it is very basic and can often result in false-negative results.

One of the reasons for this is that the test does not test for a very wide range of bacteria/ parasites, plus the test requires the lab technician to be able to see live parasites/ bacteria crawling under the microscope. However, parasites and bacteria can go through dormant phases, meaning they can be missed on a standard test. 

What are the benefits of paying for a private test?

When we do a private test, we uncover a lot more information that has been missed. The private functional tests use advanced PCR technology which can detect the DNA of parasites and bacteria, so they can be detected even if they are in a dormant phase.  Another reason the NHS test may produce a false negative is due to the fact that they only do a 1-day test, whereas a private test will require you to complete the test over 3 days so that nothing is missed.

There are a few private tests available but the most comprehensive one in my experience is the GI Effects test. This test is a 3-day stool test which you can complete at home and post back off to the lab for analysis. The cost of this test is around £355.

The test will provide really useful information and will give you a true picture of what’s happening in your stomach and gut, including many markers that the NHS test do not test for. These include:

  • Maldigestion markers (how well you digest food and your digestive enzyme status)
  • Inflammation markers (calprotectin, EPX & IgA, occult blood)
  • Dysbiosis (microbiome balance including commensal bacteria and beneficial bacteria strains to see if you are lacking in these)
  • Metabolite imbalances eg short-chain-fatty-acids (SCFA’s)
  • Infections, pathogenic bacteria, yeasts (candida) and parasites, including roundworms, tapeworms, flukes & protozoa, using the latest PCR technology as mentioned.

The full list of parasites that are tested for include the following (many of which the NHS test does not include):

A hook worm
A Hookworm
  • Nematodes – roundworms
  • Ancylostoma/Necator (Hookworm)
  • Ascaris lumbricoides
  • Capillaria philippinensis
  • Enterobius vermicularis
  • Strongyloides stercoralis
  • Trichuris trichiura
  • Diphyllobothrium latum
  • Cestodes – tapeworms
  • Dipylidium caninum
  • Hymenolepis diminuta
  • Hymenolepis nana
  • Taenia spp.
  • Trematodes – flukes
  • Clonorchis/Opisthorchis spp.
  • Fasciola spp./ Fasciolopsis buski
  • Heterophyes/Metagonimus
  • Paragonimus spp.
  • Schistosoma spp.
  • Balantidium coli
  • Protozoa
  • Blastocystis spp.
  • Chilomastix mesnili
  • Cryptosporidium spp.
  • Cyclospora cayetanensis
  • Dientamoeba fragilis
  • Entamoeba coli
  • Entamoeba histolytica/dispar
  • Entamoeba hartmanii
  • Entamoeba polecki
  • Endolimax nana
  • Giardia
  • Iodamoeba buetschlii
  • Cystoisospora spp.
  • Trichomonads (e.g. Pentatrichomonas)
  • If you have any pathogenic bacteria or an overgrowth of yeast present then the test provides a list of natural anti-microbials, such as oregano, garlic or berberine that the lab has tested on the specific strain that has been found in the sample, to see what it responds best to (some work better than others in killing certain strains so this means that the treatment can be targeted). 
  • The lab can also test if a particular bacteria has become resistant to antibiotics and suggest a natural antibiotic.

Other test types include the CDSA (comprehensive digestive stool analysis) with or without parasitology. This does not include as many markers as the GI Effects test, but it will still test for the pathogenic bacteria/ parasites and yeasts.  The CDSA test with parasitology is £245.

Could I really have a parasite in my gut?

Contrary to popular belief, you do not have to have travelled to exotic countries to pick up a parasite or pathogenic bacteria. You can get them from pets and others animals, the water supply, food (especially things like sushi and undercooked meats, pork in particular), soil, dirty toilets etc. These pathogens can can live in your gut for years if not treated, causing all manner of digestive and gut upsets.

In my experience, the presence of pathogens in the gut or the lack of beneficial bacteria and enzymes are at the root cause of most unexplained gut symptoms and once these have been eradicated the symptoms tend to go away.

Parasites or any other pathogen that should not be residing in our digestive systems can wreak havoc on your health. When the immune system is pre-occupied dealing with gut infestations, it can be distracted from other things that may require its attention. Not only can these pathogens affect your immune system but they can cause nutritional deficiencies, especially iron deficiency as the organism will use this in order to replicate and grow. This may leave you feeling constantly hungry and unable to gain weight. Other symptoms include constipation/ diarrhoea, bloating, flatulence, but also skin issues, teeth grinding, problems sleeping, fatigue, brain fog and depression/ anxiety.

A stool test only tests the large intestine and a separate test would be needed for testing the small intestine for small intestinal bacterial overgrowth (SIBO).  

A SIBO test is a breath test and this 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. This test is around £160.

Symptoms of SIBO are widespread and can include:

  • Bloating
  • Constipation
  • Diarrhoea
  • Stomach pain
  • Gas/ burping
  • Reflux
  • Brain fog
  • Fatigue
  • Skin problems
  • Joint pains

How do I access these tests?

If you are interested in ordering any of the aforementioned stool tests, then you will need to do so via a qualified natural health practitioner who will be able to assess which test would be the most appropriate for you.  The practitioner will interpret the results of the test and devise a protocol to deal with the findings.

If you would like more information, then contact the Tummy Team at and they will sign-post you to someone qualified to help you.