Faecal Macroscopy

Faecal macroscopy examines the physical appearance of the stool, including colour, form, mucus content, and hidden (occult) blood. These visible features offer valuable insights into digestion, gut lining integrity, and the presence of irritation or inflammation. Changes in stool appearance can often be early signs of underlying digestive issues.

This stool test measures:

• Stool Colour

  Stool colour can provide important clues about digestion, gut health, and how well the body is absorbing nutrients. Changes in colour may signal issues like bile flow problems, infections, or imbalances in the gut microbiome.

• Stool Form

  Stool form is an important indicator of digestive health and how efficiently the body is processing food and waste. Abnormal stool shapes can signal issues like dehydration, gut inflammation, slow or fast transit time, or imbalances in the microbiome.

• Mucous

  The presence of mucus in stool can be a sign of irritation or inflammation in the gut lining. While small amounts can be normal, larger or frequent amounts may indicate conditions like infections, irritable bowel syndrome (IBS), or inflammatory bowel disease (IBD).

• Faecal Occult Blood

  Occult blood refers to hidden blood in the stool that isn’t visible to the eye but can signal bleeding somewhere in the digestive tract. Its presence may indicate conditions like polyps, inflammatory bowel disease, ulcers, or early signs of colorectal cancer, making it an important marker for further investigation.

Digestive & Metabolic Markers

Microscopy is performed for detection of blood cells which may indicate infections or inflammation, as well as markers of maldigestion. The presence of food remnants may indicate poor digestion from too little gastric acid or reduced output from the pancreas.

This stool test measures:

• pH

  Imbalances in gut pH influence short chain fatty acid production and their effect.

• Red blood cells

  The presence of red blood cells in the stool may indicate the presence of an infection, inflammation or haemorrhage.

• White blood cells

  The presence of white blood cells in the stool may indicate the presence of an infection, inflammation or haemorrhage.

• Food remnants

  The presence of food remnants may indicate maldigestion.

• Meat fibres

  The presence of meat fibres may indicate maldigestion from too little gastric acid or reduced output from the pancreas.

• Vegetable fibres

  The presence of vegetable fibres may indicate maldigestion from gastric hypoacidity or diminished pancreatic output.

• Fat globules

  Too much fat in your faeces is called steatorrhoea which can be a sign of malabsorption. This means your body either isn’t absorbing nutrients properly or isn’t making the enzymes or bile needed to digest food effectively.

• Starch

  Magnesium supports muscle function and energy production. Deficiency is linked to cramps, fatigue, and anxiety.

Digestive and Absorption Markers

This stool test measures:

• Short Chain Fatty Acids, Putrefactive

  Putrefactive SCFAs are produced when anaerobic bacteria ferment undigested protein, indicating protein maldigestion.

• Pancreatic Elastase

  Pancreatic elastase tells us how well your pancreas is producing digestive enzymes. Low levels mean you might not be digesting food properly, leading to gut symptoms and nutrient problems.

• Long Chain Fatty Acids

  Elevated levels of LCFAs in the stool may indicate inadequate lipid absorption.

Metabolic Markers

This stool test measures:

• b-Glucuronidase

  β-Glucuronidase is a gut enzyme that can cause toxins and hormones to be recycled instead of eliminated. High levels suggest a need to support detoxification and balance gut bacteria.

• Short Chain Fatty Acids

  Short chain fatty acids (SCFAs) are produced by gut bacteria when they ferment fiber, helping to nourish the gut lining, control inflammation, and support immune health. Healthy SCFA levels are linked to better digestion, stronger gut barriers, and lower risk of chronic diseases.

• Butyrate

  Butyrate is a short-chain fatty acid produced by gut bacteria when they break down dietary fiber. It plays a crucial role in nourishing colon cells, reducing inflammation, strengthening the gut barrier, and supporting overall digestive and immune health.

• Acetate

  Acetate is the most abundant short-chain fatty acid produced by gut bacteria during the fermentation of fiber. It supports gut health, helps regulate appetite and metabolism, and acts as a building block for other beneficial compounds in the body.

• Propionate

  Propionate is a short-chain fatty acid produced by gut bacteria during the fermentation of dietary fiber. It helps regulate blood sugar levels, supports metabolism, and has anti-inflammatory effects that benefit both gut and overall health.

• Valerate

  Valerate is a lesser-known short-chain fatty acid produced in small amounts by gut bacteria during the fermentation of fiber and protein. It plays a minor role in supporting gut health and may help maintain a balanced microbial environment.

Inflammation Markers

This stool test measures:

• Faecal Calprotectin

  Faecal calprotectin is a marker of gut inflammation, helping to differentiate between inflammatory conditions like Crohn’s disease and non-inflammatory issues like IBS. Elevated levels suggest active inflammation and may warrant further investigation.

• Faecal Secretory IgA

  Faecal Secretory IgA measures how strong your gut’s immune defense is — acting like a “security system” for your digestive tract. Too low or too high can signal imbalance or stress in the gut.

• a-Transglutaminase IgA

  α-Transglutaminase IgA helps detect if your gut immune system is reacting to gluten. High levels suggest gluten sensitivity or possible coeliac-related gut damage, even if blood tests are normal.

Tumour/ Ulcer Markers

This stool test measures:

• M2 Pyruvate Kinase

  M2-PK is the key regulator of tumour metabolism and its measurement in faeces may assist in identifying gastrointestinal tumours, even in the absence of gastrointestinal bleeding.

• H.Pylori antigen

  A positive test result indicates the presence of a current infection and is not affected by the presence of other organisms, antacids, barium sulphate, blood or fat.

Beneficial Bacteria

Significant numbers of bacteria are normally present in the healthy gut. Lactobacilli and Bifidobacteria in particular, are essential for gut health because they help to inhibit gut pathogens and carcinogens, control pH, reduce cholesterol and synthesise vitamins.

This stool test measures:

• Bifidobacteria longum

  Bifidobacteria are considered “friendly” bacteria that are found in fermented foods like yogurt and cheese, and are used in probiotics. The gut needs these bacteria to perform several jobs, including breaking down foods, taking in nutrients, and preventing overgrowth of “bad” pathogenic bacteria.

• Bifidobacteria bifidum

  Bifidobacteria are considered “friendly” bacteria that are found in fermented foods like yogurt and cheese, and are used in probiotics. The gut needs these bacteria to perform several jobs, including breaking down foods, taking in nutrients, and preventing overgrowth of “bad” pathogenic bacteria.

• Bifidobacteria animalis

  Bifidobacteria are considered “friendly” bacteria that are found in fermented foods like yogurt and cheese, and are used in probiotics. The gut needs these bacteria to perform several jobs, including breaking down foods, taking in nutrients, and preventing overgrowth of “bad” pathogenic bacteria.

• Bifidobacteria pseudocaten

  Bifidobacteria are considered “friendly” bacteria that are found in fermented foods like yogurt and cheese, and are used in probiotics. The gut needs these bacteria to perform several jobs, including breaking down foods, taking in nutrients, and preventing overgrowth of “bad” pathogenic bacteria.

• Bifidobacteria breve

  Bifidobacteria are considered “friendly” bacteria that are found in fermented foods like yogurt and cheese, and are used in probiotics. The gut needs these bacteria to perform several jobs, including breaking down foods, taking in nutrients, and preventing overgrowth of “bad” pathogenic bacteria.

• Eschericia coli

  Most E. coli strains are harmless and play an essential role in keeping the digestive system healthy, helping to digest food and producing Vitamin K. However, some E. coli bacteria are pathogenic and can cause disease.

• Lactobacilli plantarum

  Lactobacilli and Bifidobacteria are essential for gut health because they prevent overgrowth of gut pathogens, and contribute to managing intestinal pH, cholesterol, and synthesis of vitamins and disaccharidase enzymes.

• Lactobacilli rhamnosus

  Lactobacilli and Bifidobacteria are essential for gut health because they prevent overgrowth of gut pathogens, and contribute to managing intestinal pH, cholesterol, and synthesis of vitamins and disaccharidase enzymes.

• Lactobacilli paracasei

  Lactobacilli and Bifidobacteria are essential for gut health because they prevent overgrowth of gut pathogens, and contribute to managing intestinal pH, cholesterol, and synthesis of vitamins and disaccharidase enzymes.

• Lactobacilli casei

  Lactobacilli and Bifidobacteria are essential for gut health because they prevent overgrowth of gut pathogens, and contribute to managing intestinal pH, cholesterol, and synthesis of vitamins and disaccharidase enzymes.

• Lactobacilli acidophilus

  Lactobacilli and Bifidobacteria are essential for gut health because they prevent overgrowth of gut pathogens, and contribute to managing intestinal pH, cholesterol, and synthesis of vitamins and disaccharidase enzymes.

• Enterococci

  Together with other healthy bacteria and fungi, enterococci work to keep unhealthy (pathogenic) bacteria from flourishing and helps to restore the balance of the microbiome.

Pathogenic Bacteria

These bacteria are pathogenic and are those that have the potential to cause disease in the gut.

This stool test measures:

• Aeromonas

  Aeromonas are bacteria that can cause an acute diarrhoeal illness that normally clears without treatment. It is a fairly common cause of gastroenteritis, which occurs most often throughout the warm summer months in most countries.

• Campylobacter

  Campylobacter infection (campylobacteriosis) is a bacterial infection which most commonly causes gastroenteritis (also known as ‘gastro’) but may also cause illness affecting the entire body.

• Salmonella

  Salmonella infection usually results from ingestion of the bacteria from contaminated food, water or hands. Eggs, milk, meat or poultry are particularly high risk foods.

• Shigella

  Shigella infection (shigellosis) is a type of gastroenteritis caused by Shigella bacteria. The symptoms of Shigella infection include fever, diarrhoea, (sometimes with blood and mucous), vomiting and stomach cramps.

• Yersinia

  This infectious bacteria can cause gastroenteritis and symptoms beyond the gut. Symptoms include diarrhoea, nausea, vomiting, fever and abdominal pain. It can mimic appendicitis or Crohn’s disease.

Opportunistic Bacteria

Our gut bacteria can be divided into ‘bad’ and ‘good’. The good ones for the most part benefit us, whreas the bad ‘pathogenic’ ones can cause disease. Pathogens are usually present in small quantities in the microbiome, however in excessive amounts they can have adverse effects on the body. The beneficial bacteria of the microbiome have a protective function against colonisation by pathogenic bacteria.

This stool test measures:

• Pseudomonas

  Pseudomonas is found in water and soil as well as fruits and vegetables, and is considered an opportunistic pathogen.

• Streptococcus mitis

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus sanguinis

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus anginosus

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus parasanguinis

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus dysgalactiae

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus salivarius

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Streptococcus mutans

  Streptococcus is common in the gut flora. With the exception of very rare cases, streptococcus species are not implicated in gastric disease.

• Enterococcus faecalis

  Enterococcus species are part of normal flora in the human gut, but can however be implicated in a variety of infections of which urinary tract infections are the most common.

• Enterococcus faecium

  Enterococcus species are part of normal flora in the human gut, but can however be implicated in a variety of infections of which urinary tract infections are the most common.

• Enterococcus casseliflavus

  Enterococcus species are part of normal flora in the human gut, but can however be implicated in a variety of infections of which urinary tract infections are the most common.

• Enterococcus durans

  Enterococcus species are part of normal flora in the human gut, but can however be implicated in a variety of infections of which urinary tract infections are the most common.

• Mucoid Eschericia Coli

  Most E. coli strains are harmless and play an essential role in keeping the digestive system healthy, helping to digest food and producing Vitamin K. However, some E. coli bacteria are pathogenic and can cause disease.

• Enterobacter asburiae

  There are 14 species in the genus, although only E. cloacae has been associated with gastrointestinal infection.

• Enterobacter kobei

  There are 14 species in the genus, although only E. cloacae has been associated with gastrointestinal infection.

• Staphylococcus species

  Unlike Staphylococcus aureus, Staphylococcus species refers to various staphylococcus bacteria commonly found in the gut, which are typically commensal (non-harmful) or opportunistic pathogens.

• Staphylococcus aureus

  Staphylococcus aureus is an opportunistic bacterium. While not usually harmful in small amounts, elevated levels may indicate gut imbalance or weakened immunity, and can contribute to symptoms if the microbiome is disrupted.

• Bacillus species

  Bacillus species are associated with food-borne diarrhoeal illness and meat dishes are a common source of infection.

Yeasts

This test looks for evidence of candida or other yeast overgrowth. Whilst yeasts are a normal inhabitant of the gastrointestinal tract, they may become an opportunistic pathogen after disruption of the mucosal barrier, imbalance of the normal intestinal flora or impaired immunity. This can be caused by things like antibiotics, antacids and stress.

This stool test measures:

• Candida albicans

  Candida albicans is the main type of yeast which colonises the human body. It normally lives in the gastrointestinal tract and other areas of the body without causing problems, but imbalance in the microbiome can lead to overgrowth.

• Candida parapsilosis

  Candida parapsilosis is an emerging major human pathogen that has dramatically increased in significance and prevalence over the past 2 decades, such that C. parapsilosis is now one of the leading causes of invasive candidal disease.

• Candida glabrata

  Candida glabrata is an opportunistic yeast pathogen that has adapted to colonise all segments of the human gastrointestinal tract.

• Geotrichum

  Geotrichum yeasts can be found in soil, dairy products and in human skin and mucosae, and are usually only considered an opportunistic pathogen in immune-compromised hosts. Geotrichum may play a role in IBS.

• Rhodotorula

  A common environmental yeast which is not considered pathogenic in nature. These yeasts are ubiquitous in the environment and can be found on fruits, vegetables and other plant materials.

• Other yeasts

  Whilst yeasts are a normal inhabitant of the gut, they may become an opportunistic pathogen after disruption of the mucosal barrier, imbalance of the normal intestinal flora or impaired immunity. This can be caused by things like antibiotics, antacids and stress.

Parasites

Some gut problems can be a consequence of an undetected gut infection. A significant number of IBS (irritable bowel syndrome) cases could actually be due to undiagnosed gut parasites such as Blastocystis hominis and Dientamoeba fragilis.

This stool test measures:

• Cryptosporidium

  Cryptosporidium is a microscopic parasite that causes the diarrhoeal disease cryptosporidiosis. Both the parasite and the disease are commonly known as “Crypto.”

• Giardia lamblia

  Symptoms of Giardia infection can occur with 3 to 25 days and may include diarrhoea, nausea, vomiting, pale greasy foul-smelling stools, stomach cramps, passing excess gas, bloating, weight loss and fatigue.

• Entamoeba histolytica

  Amoebiasis is a parasitic disease (also known as amoebic dysentery) caused by infection with Entamoeba histolytica or another amoeba (for example, E. dispar). The disease may not cause symptoms in most individuals.

• Blastocystis hominis

  Some research suggests that people with IBS may be more likely to have Blastocystis hominis organisms in their stool.

• Dientamoeba fragilis

  The bacteria can be present in the gut for months or year and misdiagnosed as IBS. Infection can cause diarrhoea, abdominal pain and cramping, anal itching, nausea, loss of appetite, headache, dizziness, depression, weight loss and fatigue.