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Stool Analysis – Providing a Spotlight on Gastrointestinal Health

grid-cell-24434-1407875545-3While it may be uncomfortable for many of us to discuss, stool analysis has become a very important tool to determine a wide range of gastrointestinal conditions.

Stool Analysis provides a comprehensive picture of many aspects of digestion, absorption, intestinal function and microbial flora as well as pathogenic bacteria, yeasts and parasites.

By indicating a poor digestive function and imbalanced gut flora a number of health conditions can be better understood and more tailored treatment protocols can be implemented.

It is widely agreed upon that the ability to digest and absorb selected nutrients from our food and drink forms the foundation of good health. To obtain these benefits we need to be able to digest and efficiently absorb these nutrients into the portal (liver) circulation.

Under normal circumstances, microbes, larger sized particles of fibre and undigested food stuffs should remain within the intestinal tube.

Poor digestion and malabsorption of vital nutrients is known to contribute to degenerative disease, poor immune status and deficiency states caused by inadequate mineral, vitamin, carbohydrate, fats and amino acid status.

The gastrointestinal tract (GIT) also eliminates undigestible food residues and toxins that are excreted via the bile into the intestinal tract, resulting in a friendly environment for the growth of friendly microorganisms.

There are a number of factors that can cause the impairment of the selective absorptive capacity or the barrier function of the gut (excessive intestinal permeability).

These include: low stomach acid, chronic maldigestion, food allergens impacting on the bowel absorptive surfaces, bacterial overgrowth or imbalances (dysbiosis), pathogenic bacteria, yeast or parasites (with the related toxic byproducts), irritants, use of Nonsteroidal Anti-inflammatory Drugs (NSAID’s) and antibiotics.


Conditions that Indicate Stool Analysis may be Warranted 

– Gut Disorders

  1. Functional disorders, non-ulcer dyspepsia, indigestion, gas, bloating
  2. Irritable Bowel Syndrome (IBS)
  3. Constipation/ Diarrhoea
  4. Gastro-oesophageal reflux disease (GORD)
  5. Malabsorption syndromes
  6. Abdominal pain
  7. Diarrhoea
  8. Inflammatory Bowel Disease

– Ageing and degenerative diseases

– Arthritis

– Autism Spectrum Disorders

– Autoimmune Disease

– Cancer

– Chronic diseases

– Coeliac Disease

– Depression

– Dysbiosis

– Food allergies and sensitivities

– Hormone and neuroendocrine disorders

– Infertility

– Immune disorders/ chronic inflammation

– Liver dysfunction

– Nutrient insufficiencies

– Psychiatric and neuropsychiatric disorders

– Skin conditions (eczema, dermatitis)

– Toxicity syndromes


Symptoms that Indicate Gut Function is Poor:

There are a range of symptoms that indicate a person may have poor gut function. These symptoms include: constipation, diarrhoea, flatulence, gas/ bloating, abdominal discomfort, bad breath, indigestion, carbohydrate sensitivity, blood or mucus in stool,  poor detoxification.


What Can Stool Analysis Test For?

  • Bacteriology
  • Yeasts
  • Parasites
  • Short Chain Fatty Acids



The balance of the normal bowel flora may be affected by taking broad-spectrum antibiotics. These drugs inhibit the growth of normal flora and allow bacteria resistant to the antibiotic to survive and overgrow in the digestive tract. The normal flora may also be affected by anti-cancer drugs due to a person having a weakened immune system, leading to bacterial overgrowth and symptoms such as diarrhoea and abdominal pain.

Damaging bacteria can also enter and infect the digestive tract by eating contaminated food or drinking. Examples of contaminated sources include raw or undercooked eggs, poultry or beef, unpasteurised milk and untreated water from lakes, rivers and (occasionally) from community water supplies.

Travellers commonly are infected with bacteria which can be classed as true pathogens while others are strains of gastrointestinal bacteria that are normal flora for the local inhabitants but cause gastrointestinal distress (and embarrassment) to the tourist. Travellers may become infected by eating or drinking anything that has been contaminated with the bacteria, even food or drink (including tap water), ice cubes in a drink, a fresh salad, or food from a vendor’s stall.

Common Gastrointestinal Bacterial Infections

  1. Salmonella – found in raw eggs (even intact disinfected eggs), raw poultry uncooked vegetables.  Some humans may become carriers of salmonella. It is possible for Salmonella to be transmitted person-to-person.
  2. Shigella – found in food and water contaminated with faeces, and from infected-person to person when careful sanitation is not observed. A common example is the spread of Shigella in a daycare or nursing home as even a very few organisms may cause disease.
  3. Campylobacter – This bacteria can be found in raw or undercooked poultry and is a common cause of bacterial diarrhoea. It may become especially serious if it spreads to the bloodstream, and it occasionally causes long-term complications such as arthritis and Guillain-Barré syndrome.
  4. Escherichia coli 0157:H7 and other toxin-producing E. coli (most strains of E. coli are considered normal flora and do not cause disease). It can be found in raw or undercooked hamburger/beef, spinach, or unpasteurised cider and can cause bloody diarrhoea leading to haemolytic uremic syndrome.
  5. Clostridium difficile – may be present as part of the normal flora, but use of broad-spectrum antibiotics can result in an overgrowth of these bacteria. Toxin-producing strains can cause diarrhea and other serious complications.

Mycology (Yeasts)

Stool analysis that focuses on mycology can indicate an overgrowth of various fungi such as yeasts and Candida species. These are opportunistic organisms that proliferate when there is a disturbance of the normal bowel flora. Candida species are able to attach and invade inflammed  intestinal lining and release further toxins.

Changes are caused by prolonged or overuse of anti- biotic, steroids, antacids, oral contraceptive pills (OCP), acid/alkaline imbalance, high sugar diet and alcohol consumption, hormonal imbalance and depleted immune function.

It is important to note that episodes of yeast infection after anti-biotic use has been identified in patients with both gastrointestinal and vaginal symptoms.


Symptoms of the presence of parasites include acute watery diarrhoea, nausea, abdominal pain and cramps, fatigue and weight loss.

The parasites Blastocystis hominis, Dientamoeba fragilis, Giardia lamblia, Endomilax nana and Entamoeba histolytica are the most common culprits when it comes to parasitic infections.

Stool analysis requires testing over 3 consecutive days as this increases the likelihood of detection rates to 95%.

This is due to parasites not shedding and their eggs do not appear on stool specimens on a regular basis. One days sample may appear negative while the following days sample may appear positive.

Short Chain Fatty Acids (SCFA)

SCFA are the end product of the bacterial fermentation process of fermentable dietary fibre (prebiotics) and probiotics. This gives an indication of the individuals fibre intake as well as potential dysbiosis indicating the health of the intestines.

SCFAs decrease the pH of the intestines, making the environment unsuitable for pathogens including bacteria and yeast.

SCFA role include providing nutrients for the colonic epithelium, modulators of pH and cell volume.

Stool needs to be collected for 3 days in a row if the sample is being tested for quantitative fats. Collection of stool begins on the morning of the first day. The samples are placed in a large container and then refrigerated.


Common Biochemical Markers Stool Analysis Examines

  1. pH (bowel) – Where a neutral pH is 7, an elevated pH (alkaline) could indicate a lack of SCFA, ammonia production, slow bowel transit time or hypochlorohydria. A decreased (acidic) pH may indicate excess SCFA/ bacterial overgrowth, carbohydrate maldigestion or rapid transit time/ diarrhoea.
  2. n-Butyrate – the main SCFA and the preferred fuel for the colonic epithelium. Low levels is associated with an increased risk of ulcerative colitis, colon cancer and constipation. High levels are associated with carbohydrate intolerance and diarrhoea.
  3. Valerate/ iso-butyrate – This is a branched chain fatty acid that is produced by amino acid fermentation and indicates the efficiency of protein digestion. The fats and oils are mostly consumed as triglycerides and an elevated level in the stool indicates reduced fat breakdown by pancreatic lipase; suggesting pancreatic insufficiency.
  4. Pancreatic Elastase (PE1) – Indicates efficiency of pancreatic exocrine function. It is closely correlated with protein digestion in the stomach, duodenum and small intestine. A decreased production of this enzyme may be associated with chronic pancreatitis, gallstones, diabetes mellitus.
  5. Gut Ecology (bacteriology, parasitology and mycology) – Maintaining the delicate balance of intestinal microbial flora is critical to prevent dysbiosis and the proliferation of harmful bacteria, parasites and yeasts.
  6. Sensitivities – particularly to bacteria/ yeasts.
  7. Muscle Fibres – A detection of muscle fibres in the stool is indicative of protein digestion and a reduction (hypochlorhydria) or absence (achlorhydria) of hydrochloric acid secretion within the stomach and / or insufficient output of pancreatic enzymes or even excessive meat consumption.
  8. Vegetable Fibres – Excessive amount of vegetable fibres in the stool indicate some kind of maldigestion. If the vegetable can be identified this may possibly indicate inadequate chewing or fast eating.



Emed provides CDSA test kits. Click here to order your test kit today. If you are unsure of which level to purchase, contact one of our Emed Practitioners on 1300 00 3633.

Depending on the specimen requirements one or a number of stool collections may be required. Most stool testing is suitable for children.

Samples from babies and young children may be collected from nappies (as long as the stool is not contaminated with urine).



Follow the usual diet prior to collecting a stool specimen. The stool specimen should be collected in the morning where possible. Do not do the test if you have your period as this will contaminate the sample (for women).



A typical protocol for collecting the stool could resemble the following:

  • Urinate before collecting the stool so that no urine gets in the stool sample.
  • Put on gloves before handling stool. Stool can contain germs that spread infection. Wash hands after gloves are removed.
  • Pass stool (but no urine) into a dry container. A plastic basin that can be placed under the toilet seat to catch the stool may be provided.
    • Either solid or liquid stool can be collected.
    • If you have diarrhoea, a large plastic bag taped to the toilet seat may make the collection process easier; the bag is then placed in a plastic container.
    • If you are constipated, you may be given a small enema.
    • Do not collect the sample from the toilet bowl.
    • Do not mix toilet paper, water, or soap with the sample.
  • Place the lid on the container and label it with your name, your practitioner’s name, and the date the stool was collected. Use one container for each day’s collection, and collect a sample only once a day unless your practitioner gives you other directions. On days where consecutive stools are required, store the collections in the fridge.


Other Medicines

Many medicines can change the results of a stool test. Certain medicines will need to be avoided depending on which kind of stool analysis is to be done.

Common culprits include: antacids, antidiarrhoeal medicines, antiparasite medicines, antibiotics, laxatives, or nonsteroidal anti-inflammatory drugs (NSAIDs) for 1 to 2 weeks before you have the test.

Be sure to tell your practitioner about all the nonprescription and prescription medicines you take to ensure the results from the stool analysis are not corrupted.


Further Investigations

The Intestinal Permeability test is a useful addition to a stool sample. A leaky gut may contribute to or be caused by poor digestive function.

For more information on Stool Analysis or if you think you might benefit from a stool analysis, contact our practitioners at Emed.


Further Reading


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