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.

Gut Functional Markers

Gut functional markers assess how well the gut is performing its key roles in digestion, absorption, and immune defence. They measure important indicators such as enzyme activity, inflammation levels, gut barrier function, and detoxification capacity. Together, these markers provide a clearer picture of overall digestive system health.

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.

• 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.

• 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.

• Zonulin

  Zonulin controls how tightly your gut cells are sealed. Elevated levels suggest your gut lining is “leaky,” letting unwanted substances into the body, which can drive inflammation and immune problems.

• 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.

• Steatocrit

  Steatocrit measures how much fat is in your stool. High levels suggest your body isn’t digesting or absorbing fats properly, which could affect energy levels, nutrient status, and gut health.

• 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.

• pH

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

Short Chain Fatty Acids

Short chain fatty acids (SCFAs) are important compounds produced by gut bacteria when they ferment fibre, helping to nourish the gut lining, regulate inflammation, and support immune function. Healthy SCFA levels are linked to better digestion, stronger gut barrier integrity, and reduced risk of chronic diseases like diabetes, obesity, and colorectal cancer.

This stool test measures:

• 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.

Microbial Diversity

Microbial diversity reflects the variety and richness of different bacterial species living in the gut. A diverse microbiome is associated with stronger immunity, better digestion, reduced inflammation, and improved resilience against disease. Supporting a wide range of beneficial microbes is key to long-term gut health.

This stool test measures:

• Shannon Diversity Index

  The Shannon Diversity Index shows how many different types of gut bacteria you have and how balanced they are. A higher score means a healthier, more diverse gut; a lower score suggests imbalance or low variety.

• Simpson Diversity Index

  A higher diversity index usually means more diverse and balanced bacteria, which is linked to better digestion, immunity, and mood. A low score might mean one type of bacteria is dominating — which could lead to inflammation, bloating, or poor nutrient absorption.

• Firmicutes: Bacteroidetes Ratio

  The Firmicutes:Bacteroidetes ratio is a key indicator of how well your gut is supporting digestion, metabolism, and overall health. A balanced ratio helps maintain a healthy weight, strong immunity, and a resilient gut environment.

• Bacteroidetes

  Bacteroidetes are a major group of gut bacteria that help break down complex carbohydrates and support digestion. A healthy level of Bacteroidetes is linked to better gut health and metabolism.

• Firmicutes

  Firmicutes are a major group of gut bacteria involved in breaking down dietary fats and supporting energy absorption. Their balance with other bacteria, like Bacteroidetes, plays an important role in digestion, metabolism, and overall gut health.

• Actinobacteria

  Actinobacteria are a group of beneficial gut bacteria that help break down complex plant fibers and support gut and immune health. They include important species like Bifidobacteria, which play a key role in maintaining a balanced microbiome.

• Proteobacteria

  Proteobacteria are a group of gut bacteria that include both normal residents and potential pathogens. Elevated levels are often linked to gut imbalance, inflammation, and digestive issues.

• Verrucomicrobia

  Verrucomicrobia are a smaller group of gut bacteria, best known for including Akkermansia muciniphila, a species linked to gut lining health and reduced inflammation. Healthy levels of Verrucomicrobia are associated with better metabolism, immune balance, and gut barrier function.

• Euryarchaeota

  Euryarchaeota are a group of microorganisms called archaea, naturally found in the human gut, that help break down food and produce gases like methane. While some are normal, an overgrowth can contribute to symptoms like bloating, constipation, or SIBO.

Functional Pathways

Functional Pathways assess the way your gut bacteria process nutrients, produce key compounds, and support overall health. These markers reflect your microbiome’s capability in energy production, detoxification, inflammation control, and metabolism. They provide insights into how your gut influences ageing, immune function, brain health, and cardiovascular risk, helping to identify imbalances that may impact your well-being.

• Ageing Factors (Oxidative Stress)

  Markers related to the production of free radicals, which are unstable molecules that can damage cells, accelerate ageing, and increase the risk of chronic diseases like heart disease, cancer, and Alzheimer’s. Managing oxidative stress can help slow ageing and support overall health.

• Ammonia/Urease Production

  Reflects the amount of ammonia produced by certain gut bacteria. High levels can be toxic to the brain and liver, potentially leading to brain fog, fatigue, and poor detoxification. This can also indicate protein malabsorption or gut dysbiosis.

• Branched Chain Amino Acid (BCAA) Production

  Measures the production of essential amino acids like leucine, isoleucine, and valine, which are critical for muscle growth, energy production, and tissue repair. An imbalance can impact muscle recovery, exercise performance, and energy levels.

• Carbohydrate Metabolism

  Assesses how well your gut bacteria break down carbohydrates into short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate, which are key for gut lining health, energy production, and immune regulation. Poor carbohydrate metabolism can contribute to bloating, weight gain, and energy crashes.

• Histamine Production

  Measures the amount of histamine produced by gut bacteria, which can trigger allergy-like symptoms, skin rashes, headaches, and digestive issues if levels are too high. This is often linked to histamine intolerance and leaky gut.

• Iron/Other Ion Metabolism

  Reflects how effectively your gut bacteria handle iron and other essential minerals like zinc, copper, and magnesium, which are critical for energy production, immune function, and oxygen transport. Imbalances can contribute to fatigue, hair loss, and weakened immunity.

• Indolepropionic Acid (IPA) Production

  A marker of gut bacteria that produce IPA, a potent antioxidant that protects the gut lining, supports brain health, and reduces inflammation. High levels are generally protective, while low levels may indicate gut barrier issues.

• Lipid Metabolism

  Assesses how well your gut bacteria break down fats and produce beneficial short-chain fatty acids. This process influences cholesterol levels, hormone balance, and weight management. Poor lipid metabolism can contribute to metabolic issues and cardiovascular risk.

• Lipopolysaccharides (LPS) Production

  Reflects the presence of inflammatory bacterial toxins produced by certain gut bacteria. When these toxins enter the bloodstream, they can trigger inflammation, disrupt the immune system, and contribute to chronic diseases like autoimmunity, heart disease, and metabolic syndrome.

• Protein/Other Energy Metabolism

  Measures how effectively your gut bacteria break down proteins into amino acids and energy, supporting muscle health, tissue repair, and immune function. Imbalances can lead to muscle wasting, fatigue, and poor recovery from exercise.

• Sulphate Production

  Reflects the production of sulfur-containing compounds that are critical for detoxification, collagen formation, and maintaining a healthy gut lining. However, high levels can contribute to gut inflammation and sulfur gas production, leading to bloating and discomfort.

• Trimethylamine (TMA) Production

  Measures the production of TMA by gut bacteria, which the liver converts to TMAO. High TMAO levels have been linked to heart disease, atherosclerosis, and kidney issues, making this an important marker for cardiovascular health.

Disease Risks

This section of the Microbiomix Test assesses your genetic risk for common gut-related conditions like colon cancer, Crohn’s disease, fatty liver, type 2 diabetes, and ulcerative colitis. Understanding these risk levels can help you take proactive steps to optimise gut health, reduce inflammation, and support long-term wellness.

This stool test measures:

• Colon Cancer Risk

  This marker reflects how your gut microbiome influences inflammation and toxin metabolism related to colon cancer. Certain bacteria can either promote or protect against cancerous changes in the colon lining.

• Crohns Disease Risk

  This assesses the presence of bacteria associated with chronic intestinal inflammation. An imbalanced microbiome may increase susceptibility to immune dysregulation seen in Crohn’s disease.

• Fatty Liver Risk

  This marker evaluates bacterial profiles linked to liver fat accumulation. Some microbes influence fat storage, insulin resistance, and liver inflammation.

• Type 2 Diabetes Risk

  This indicates how your gut bacteria affect blood sugar regulation and insulin sensitivity. Specific microbial imbalances are associated with increased risk of metabolic disorders.

• Ulcerative Colitis Risk

  This measures microbial patterns related to inflammation of the colon’s lining. A lack of beneficial species or excess pro-inflammatory bacteria may increase susceptibility to ulcerative colitis.

Bacterial Pathogens

Pathogenic bacteria are harmful microbes that can cause acute infections, inflammation, and disrupt the gut microbiome. Detecting these bacteria early helps prevent serious illness and supports faster recovery. Managing pathogenic infections is essential for maintaining a healthy and resilient digestive system.

This stool test measures:

• Aeromonas hydrophila

  Aeromonas hydrophila is a bacterium commonly found in freshwater and sometimes in the human gut, where it can cause gastrointestinal infections. It is typically associated with symptoms like diarrhoea, stomach cramps, and, in some cases, more severe infections in vulnerable individuals.

• Campylobacter species

  Campylobacter species are bacteria commonly found in contaminated food, particularly poultry, and can cause foodborne infections. Infections typically lead to symptoms like diarrhoea, abdominal cramps, and fever, and can be more severe in people with weakened immune systems.

• Clostridium difficile Toxin A

  Clostridium difficile Toxin A is a toxin produced by Clostridium difficile bacteria, which is a major cause of healthcare-associated gastrointestinal infections. The toxin causes inflammation in the intestines, leading to symptoms like diarrhoea, abdominal pain, and in severe cases, colitis or toxic megacolon.

• Clostridium difficile Toxin B

  Clostridium difficile Toxin B is a potent toxin produced by Clostridium difficile, contributing to severe gastrointestinal infections. It causes significant damage to the intestinal lining, leading to symptoms like diarrhoea, abdominal pain, and potentially life-threatening conditions such as colitis.

• Enteroaggregative E. coli

  Enteroaggregative E. coli (EAEC) is a type of pathogenic E. coli that can cause chronic diarrhea, particularly in young children and immunocompromised individuals. It is characterised by its ability to adhere to the intestinal lining in a characteristic pattern, leading to inflammation and digestive symptoms.

• Enteropathogenic E. coli

  Enteropathogenic E. coli (EPEC) is a strain of E. coli that causes severe diarrhoea, especially in infants and young children. It infects the intestinal lining, leading to inflammation, dehydration, and symptoms such as stomach cramps and vomiting.

• E. coli O157

  E. coli O157 is a dangerous strain of E. coli that can cause severe gastrointestinal illness, including bloody diarrhoea, abdominal cramps, and vomiting. In some cases, it can lead to complications like haemolytic uraemic syndrome (HUS), which affects the kidneys and can be life-threatening.

• Hypervirulent Clostridium difficile

  Hypervirulent Clostridium difficile is a more aggressive strain of the bacteria that produces toxins, leading to severe gastrointestinal infections, including antibiotic-associated colitis. This strain is associated with higher rates of recurrence, increased severity, and complications like toxic megacolon and perforated bowel.

• Enteroinvasive E. coli/Shigella

  Enteroinvasive E. coli (EIEC) and Shigella are bacteria that can invade the intestinal lining, causing severe dysentery-like symptoms, including bloody diarrhoea, abdominal cramps, and fever. Both pathogens are transmitted through contaminated food or water and can cause significant intestinal inflammation.

• Enterotoxigenic E. coli LT/ST

  Enterotoxigenic E. coli (ETEC) produces toxins known as LT (heat-labile) and ST (heat-stable), which cause travelers’ diarrhea by disrupting the gut’s normal function. These toxins lead to watery diarrhoea, abdominal cramping, and nausea, often resulting from contaminated food or water.

• Salmonella species

  Salmonella species are bacteria that can cause foodborne illnesses, leading to symptoms such as diarrhoea, fever, and abdominal cramps. They are typically transmitted through contaminated food, especially raw meat, eggs, or unpasteurised dairy products.

• Shiga-like Toxin E. coli

  Shiga-like Toxin E. coli (STEC) produces toxins that damage the intestinal lining, causing symptoms such as bloody diarrhea, abdominal pain, and vomiting. In severe cases, it can lead to complications like haemolytic uraemic syndrome (HUS), which can affect the kidneys and be life-threatening.

• Vibrio species

  Vibrio species are bacteria commonly found in marine environments and can cause foodborne infections, particularly through the consumption of undercooked seafood. Infections may lead to symptoms such as diarrhoea, vomiting, and abdominal cramps, with some species causing more severe conditions like cholera.

• Yersinia species

  Yersinia species are bacteria that can cause gastrointestinal infections, leading to symptoms like fever, abdominal pain, and diarrhoea. Yersinia enterocolitica, in particular, is commonly transmitted through contaminated food, especially undercooked pork, and can cause more severe illness in vulnerable individuals.

Helicobacter Pylori

Helicobacter pylori is a common stomach bacterium associated with ulcers, digestive discomfort, and inflammation. Testing for H. pylori helps determine if treatment is needed to restore stomach health and prevent complications like gastritis or more serious conditions. Managing H. pylori can greatly improve overall digestive wellbeing.

This stool test measures:

• H.pylori Virulence Factor, babA

  BabA is a virulence factor that enables H. pylori to bind to the stomach lining, promoting infection and increasing the risk of ulcers and gastric cancer.

• H.pylori Virulence Factor, oipA

  OipA is a virulence factor that helps H. pylori adhere to the stomach lining, contributing to inflammation and increasing the risk of ulcers and gastric cancer.

• H.pylori Virulence Factor, virB

  VirB is a virulence factor that helps H. pylori inject harmful proteins into host cells, contributing to inflammation and enhancing its ability to cause stomach ulcers and cancer.

• H.pylori Virulence Factor, cagA

  CagA is a virulence factor in H. pylori that disrupts stomach cell signaling, leading to inflammation, ulcers, and an increased risk of gastric cancer.

• H.pylori Virulence Factor, iceA

  IceA is a virulence factor in H. pylori that contributes to inflammation and enhances the bacterium’s ability to persist in the stomach, potentially leading to ulcers and gastric cancer.

• H.pylori Virulence Factor, vacA

  VacA is a virulence factor in H. pylori that disrupts the stomach lining by inducing cell death and inflammation, contributing to the development of ulcers and gastric cancer.

• H.pylori Virulence Factor, virD

  VirD is a virulence factor in H. pylori that plays a role in the bacterium’s ability to transfer DNA to host cells, enhancing its capacity to cause infection and contribute to gastric diseases.

• Resistance gene A2142C

• Resistance gene A2142G

• Resistance gene A2143G

Fungi & Yeast

Yeast and fungi naturally exist in small amounts within the gut but can cause health problems if they grow unchecked. Overgrowth may lead to digestive discomfort, skin issues, fatigue, and weakened immunity. Assessing fungal balance helps identify hidden drivers of gut symptoms and supports targeted recovery.

This stool test measures:

• Candida albicans

  Candida albicans is a common yeast naturally found in the gut, mouth, and other mucosal surfaces, where it usually lives harmlessly in balance with other microbes. However, overgrowth can cause infections like thrush, yeast infections, or contribute to gut imbalances and digestive symptoms.

• Candida dubliniensis

  Candida dubliniensis is a yeast that can live in the mouth, gut, and other mucosal surfaces, usually without causing problems in healthy individuals. However, overgrowth may lead to infections, particularly in people with weakened immune systems or imbalanced gut flora.

• Candida famata

  Candida famata is a yeast that can be found in the gut and other mucosal surfaces, typically without causing harm. However, in cases of immune weakness or gut imbalance, it may overgrow and contribute to infections or digestive disturbances.

• Candida glabrata

  Candida glabrata is a type of yeast that normally lives in small amounts on mucosal surfaces like the gut and mouth. However, overgrowth can lead to infections, particularly in individuals with weakened immune systems or disrupted gut microbiomes.

• Candida guilliermondii

• Candida intermedia

  Candida intermedia is a less common yeast species that can be found in the human gut and mucosal surfaces. While typically harmless, overgrowth may contribute to gut imbalance and can cause infections, especially in those with weakened immunity.

• Candida keyfr

  Candida kefyr is a yeast that normally lives in the gut and on mucosal surfaces, typically without causing problems. However, when gut balance is disrupted, Candida kefyr can overgrow and may contribute to digestive symptoms or infections, particularly in people with weakened immune systems.

• Candida krusei

  Candida krusei is a yeast that can naturally exist in the human gut and mucous membranes but is known for its resistance to common antifungal treatments. Overgrowth of Candida krusei may lead to digestive disturbances or systemic infections, particularly in individuals with weakened immune systems.

• Candida lambica

  Candida lambica is a yeast species sometimes found in the gut and mucosal surfaces, typically in small, harmless amounts. However, overgrowth can contribute to gut imbalance and may cause infections, especially in individuals with compromised immune systems.

• Candida lipolytica

  Candida lipolytica is a yeast that can naturally exist in the environment and occasionally in the human gut. While generally harmless, it can overgrow in individuals with weakened immunity or disrupted gut balance, potentially leading to digestive or systemic infections.

• Candida lusitaniae

  Candida lusitaniae is a yeast that can live on mucosal surfaces like the gut and is usually harmless in healthy individuals. However, it can cause infections if it overgrows, particularly in people with weakened immune systems or underlying health conditions.

• Candida parapsilosis

  Candida parapsilosis is a yeast commonly found on the skin and in the gut that is usually harmless in small amounts. However, overgrowth can lead to infections, particularly in individuals with weakened immune systems or disrupted gut balance.

• Candida tropicalis

• Geotrichum species

  Geotrichum species are fungi commonly found in the environment and sometimes in the human gut and mouth, usually without causing harm. However, overgrowth can contribute to gut imbalance or infections, particularly in people with weakened immune systems.

• Rhodotorula species

  Rhodotorula species are pigmented yeasts that are commonly found in the environment and can occasionally colonise the human gut or mucosal surfaces. While usually harmless, they can cause infections if they overgrow, particularly in people with weakened immune systems.

• Saccharomyces cerevisiae

  Saccharomyces cerevisiae, often known as baker’s or brewer’s yeast, is commonly found in the human gut and is usually considered beneficial. It can support digestion and gut health, but in some cases, overgrowth may contribute to digestive symptoms or inflammation.

Potential Autoimmune Triggers

Some gut bacteria have been associated with triggering autoimmune responses when present in high levels. Identifying these microbes can offer early insights into autoimmune risk and guide personalised strategies to reduce inflammation and protect immune system balance. Keeping these bacteria in check is important for long-term health resilience.

This stool test measures:

• Bacteroides fragilis

  Bacteroides fragilis is a common gut bacterium that plays an important role in breaking down complex molecules and supporting immune system development. In healthy amounts, it helps maintain gut balance, but overgrowth can sometimes contribute to inflammation or infection.

• Bilophila wadsworthia

• Enterococcus gallinarum

• Escherichia coli

  E. coli is commonly found in the intestines. However if E. coli migrates to the vaginal area, it can cause an infection known as E. coli vaginitis. Symptoms can include abnormal vaginal discharge, odor, itching, and pain during sex or urination.

• Fusobacterium nucleatum

• Klebsiella pneumoniae

  Klebsiella pneumoniae is a bacterium that can live harmlessly in the gut but is known for its ability to cause infections, particularly in the lungs, urinary tract, and bloodstream. In the gut, overgrowth may contribute to inflammation, dysbiosis, and digestive symptoms.

• Mycoplasma hominis

  Mycoplasma hominis is a bacteria that naturally colonises the human genital and urinary tracts. However in individuals with weakened immune systems or those who are more susceptible to infections, Mycoplasma hominis can cause infections.

• Streptococcus pyogenes

  Streptococcus pyogenes is not typically a dominant resident and may indicate transient colonisation or infection. Its presence can reflect dysbiosis or potential pathogenic activity, especially if gut immunity is compromised.

Opportunistic Bacteria

Opportunistic bacteria are strains that are normally harmless in small amounts but can cause problems if they overgrow. Elevated levels may contribute to digestive symptoms, inflammation, or disruptions in the gut microbiome balance. Monitoring these bacteria helps protect gut health and prevent chronic issues.

This stool test measures:

• Abiotrophia defectiva

• Acinetobacter baumannii

• Acinetobacter haemolyticus

• Acinetobacter junii

• Bacteroides caccae

• Bacteroides vulgatus

• Citrobacter freundii

  Citrobacter is considered an opportunistic pathogen and therefore can be found in the gut as normal flora. It is occasionally implicated in diarrhoeal disease, particularly C. freundii, C. diversus and C. koseri.

• Citrobacter koseri

• Citrobacter youngae

• Corynebacterium urealyticum

• Desulfovibrio piger

  Desulfovibrio piger is a sulfate-reducing bacterium found in the gut that produces hydrogen sulfide gas during digestion. In small amounts, it can be part of a normal microbiome, but overgrowth may contribute to gut inflammation, bloating, and digestive discomfort.

• Enterobacter cloacae

• 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 Faecalis

  Enterococcus faecalis is a type of bacteria naturally found in the human gut that helps with digestion and maintaining microbial balance. However, if it overgrows or spreads outside the gut, it can cause infections, particularly in the urinary tract or bloodstream.

• Enterococcus Faecium

  Enterococcus faecium is a gut bacterium that normally supports digestion and microbial balance but can become harmful if it overgrows. It is also known for its ability to cause infections outside the gut, particularly in hospital settings where antibiotic resistance can be a concern.

• Fusobacterium ulcerans

• Klebsiella oxytoca

• Methanobrevibacter smithii

  Methanobrevibacter smithii is a type of archaea commonly found in the human gut that helps break down complex carbohydrates by producing methane gas. While it plays a role in digestion, high levels have been associated with conditions like constipation and small intestinal bacterial overgrowth (SIBO).

• Morganella morganii

• Prevotella amnii

• Prevotella bivia

• Prevotella melaninogenica

• Proteus mirabilis

• Pseudoflavonifractor capillosus

• Pseudomonas aeruginosa

  Pseudomonas aeruginosa is an opportunistic pathogen that can cause infections in the gut, lungs, and other parts of the body, especially in people with weakened immune systems. In the gut, its overgrowth may contribute to inflammation, digestive issues, and microbial imbalance.

• 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.

• Streptococcus agalactiae

  Group B Streptococcus (GBS)is a frequent cause of bacterial infections in newborns which they can acquire from their mothers during delivery.In pregnant women, GBS can sometimes cause an infection in the vagina, leading to symptoms such as abnormal vaginal discharge, odour, itching, and pain during sex or urination.

• Streptococcus anginosus

  Streptococcus anginosus is a type of bacteria normally found in the mouth, gut, and respiratory tract, often without causing harm. However, if it overgrows or moves to other areas, it can contribute to infections such as abscesses or inflammatory conditions.

• 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 mutans

  Streptococcus mutans is a bacterium commonly found in the mouth and is best known for its role in tooth decay by producing acid that damages tooth enamel. Although primarily linked to oral health, it can occasionally be detected in the gut and may contribute to microbial imbalance if present in high amounts.

• Streptococcus salivarius

  Streptococcus salivarius is a beneficial bacterium found in the mouth and upper respiratory tract that supports oral and throat health. It helps maintain microbial balance and can protect against harmful bacteria by producing natural antimicrobial substances.

• Streptococcus suis

• Veillonella parvula

Normal Bacterial Gut Flora

A healthy gut microbiome is rich in beneficial bacteria that aid digestion, produce important nutrients, and support immune function. Measuring the levels and balance of these bacteria helps assess the resilience and health of the gut ecosystem. Strong levels of beneficial flora are linked to better digestion, mood balance, and disease prevention.

This stool test measures:

• Akkermansia muciniphila

  Akkermansia muciniphila is a beneficial gut bacterium that plays a key role in maintaining the gut lining and supporting a healthy immune response. Higher levels of Akkermansia are associated with better metabolism, reduced inflammation, and improved gut barrier function.

• Bacteroides thetaiotaomicron

• Bacteroides uniformis

• Bifidobacterium adolescentis

  Bifidobacterium adolescentis is a beneficial gut bacterium that helps break down complex carbohydrates and produce important short-chain fatty acids. It supports digestive health, immune balance, and may help reduce inflammation in the gut.

• Bifidobacterium animalis

• Bifidobacterium bifidum

  Bifidobacterium bifidum is a beneficial gut bacterium that supports digestion, strengthens the gut barrier, and helps regulate the immune system. It is one of the first bacteria to colonise the gut after birth and plays a key role in maintaining overall gut and immune health throughout life.

• Bifidobacterium breve

  Bifidobacterium breve is a beneficial gut bacterium known for helping digest complex carbohydrates and producing nutrients like short-chain fatty acids. It supports a healthy gut environment, boosts immune function, and may help protect against harmful bacteria and inflammation.

• Bifidobacterium longum

  Bifidobacterium longum is a beneficial gut bacterium that helps break down dietary fiber, produce important nutrients, and support immune health. It also plays a role in reducing inflammation and protecting the gut lining, contributing to overall digestive wellbeing.

• Bifidobacterium pseudolongum

• Clostridium butyricum

• Faecalibacterium prausnitzii

  Faecalibacterium prausnitzii is one of the most important beneficial bacteria in the gut, known for producing butyrate, a short-chain fatty acid that nourishes the gut lining and reduces inflammation. High levels of this bacterium are associated with better gut health, stronger immunity, and protection against chronic diseases.

• Lactobacillus acidophilus

  Lactobacillus acidophilus is a beneficial probiotic bacterium that helps maintain a healthy balance of gut bacteria, supports digestion, and boosts immune function. It also produces lactic acid, which helps protect the gut from harmful microbes and promotes overall digestive health.

• Lactobacillus casei paracasei

• Lactobacillus crispatus

• Lactobacillus delbrueckii

  Lactobacillus delbrueckii is a beneficial bacterium commonly found in fermented foods and the gut, where it helps support digestion and maintain a healthy balance of gut bacteria. It produces lactic acid, which protects the gut environment and promotes overall digestive health.

• Lactobacillus fermentum

• Lactobacillus gasseri

• Lactobacillus helveticus

• Lactobacillus johnsonii

• Lactobacillus plantarum

  Lactobacillus plantarum is a beneficial probiotic bacterium that supports digestion, strengthens the gut barrier, and helps reduce inflammation. It also plays a role in protecting the gut against harmful microbes and promoting overall gut and immune health.

• Lactobacillus reuteri

• Lactobacillus rhamnosus

  Lactobacillus rhamnosus is a well-studied probiotic bacterium known for supporting digestive health, boosting immune function, and helping protect against harmful bacteria. It is also commonly used to help manage symptoms like diarrhea, gut inflammation, and food sensitivities.

• Lactobacillus salivarius

  Lactobacillus salivarius is a beneficial probiotic bacterium that helps maintain a healthy balance of gut and oral microbiota. It supports digestion, strengthens the immune system, and produces compounds that help protect against harmful bacteria.

• Lactococcus lactis

• Oxalobacter formigenes

  Oxalobacter formigenes is a beneficial gut bacterium that helps break down oxalates, compounds found in many plant foods. By reducing oxalate levels, it may help lower the risk of kidney stone formation and support overall urinary and gut health.

• Pediococcus acidilactici

• Pediococcus pentosaceus

• Roseburia hominis

• Roseburia intestinalis

• Roseburia inulinivorans

• Streptococcus thermophilus

Parasites

Parasites can disrupt digestion, nutrient absorption, and gut lining integrity, sometimes without obvious symptoms. Detecting parasitic infections early allows for prompt treatment to restore gut function and prevent further health complications. Regular screening is important, especially for those with chronic digestive or immune symptoms.

This stool test measures:

• Cryptosporidium

  Cryptosporidium is a microscopic parasite that can infect the intestines and cause watery diarrhoea, stomach cramps, and dehydration. It spreads through contaminated water, food, or surfaces and is a common cause of gastrointestinal illness worldwide.

• Entamoeba histolytica

  Entamoeba histolytica is a parasitic amoeba that can infect the intestines and cause symptoms like diarrhoea, abdominal pain, and, in severe cases, liver abscesses. It is typically spread through contaminated food or water, particularly in areas with poor sanitation.

• Giardia intestinalis

  Giardia intestinalis is a parasite that infects the small intestine and can cause diarrhea, bloating, stomach cramps, and fatigue. It is commonly transmitted through contaminated water, food, or contact with infected surfaces.

• Blastocystis hominis

  Blastocystis hominis is a common intestinal parasite that can live harmlessly in the gut but may cause symptoms like diarrhoea, bloating, and abdominal discomfort in some people. Its role in gut health is still being studied, as it can be found in both healthy individuals and those with digestive issues.

• Dientamoeba fragilis

  Dientamoeba fragilis is a microscopic parasite that can infect the large intestine and may cause symptoms like diarrhoea, abdominal pain, bloating, and fatigue. It is often transmitted through close contact or contaminated food and water, though some people can carry it without symptoms.

Worms

Intestinal worms can cause a range of digestive and immune issues, particularly if left undetected. Identifying and addressing worm infections helps restore proper nutrient absorption and gut balance. Screening for worms is an important step in protecting overall digestive health.

This stool test measures:

• Roundworm - Ancylostoma duodenale

  Ancylostoma duodenale (hookworm) infects the intestines, causing abdominal pain, diarrhea, and anemia, typically through contact with contaminated soil.

• Roundworm - Ascaris lumbricoides

  Ascaris lumbricoides, a large roundworm, causes abdominal pain, bloating, and nutrient malabsorption, spreading through contaminated food, water, or soil.

• Whipworm - Trichuris trichiura

  Trichuris trichiura (whipworm) infects the large intestine, causing diarrhoea, abdominal pain, and anemia, typically from contaminated food or soil.

• Enterocytozoon

  Enterocytozoon species (microsporidia) are parasites that infect the intestines, causing diarrhoea and digestive upset, especially in those with weakened immune systems.

• Roundworm - Strongyloides

  Strongyloides species are roundworms causing chronic infections with abdominal pain, diarrhoea, and skin rashes, typically spread through contaminated soil.

• Hookworm - Necator americanus

  Necator americanus, a hookworm, infects the intestines, causing abdominal pain, diarrhoea, and anemia, typically from skin contact with contaminated soil.

• Pinworm - Enterobius vermicularis

  Enterobius vermicularis (pinworm) causes itching around the anus, spreading through contaminated hands, surfaces, and bedding, especially in children.

• Tapeworm - Hymenolepis

  Hymenolepis species are small tapeworms causing abdominal pain, diarrhea, and weight loss, typically from contaminated food, water, or surfaces.

• Tapeworm - Taenia

  Taenia species are tapeworms from undercooked beef or pork, causing digestive symptoms and, in rare cases, serious complications if larvae spread.

Viral Pathogens

Certain viruses can infect the gastrointestinal tract and contribute to inflammation, digestive symptoms, and immune system strain. Identifying viral infections supports a clearer understanding of gut health and helps guide appropriate immune support strategies. Early detection can help minimise long-term effects on gut function.

This stool test measures:

• Adenovirus 40/41

  Adenovirus 40/41 are viruses that can infect the gastrointestinal tract and cause diarrhea, especially in young children. They are typically associated with viral gastroenteritis and can contribute to digestive symptoms like cramping and dehydration.

• Norovirus GI/II

  Norovirus GI/II are common viruses that cause gastroenteritis, leading to symptoms like diarrhoea, vomiting, and stomach pain. They are highly contagious and a frequent cause of outbreaks of stomach flu.

• Rotavirus A

  Rotavirus A is a virus that primarily causes severe diarrhoea and vomiting, especially in infants and young children. It is a leading cause of viral gastroenteritis worldwide and can lead to dehydration if not managed properly.

• Sapovirus (I,II,IV,V)

  Sapovirus is a virus that can cause gastroenteritis, leading to symptoms like diarrhoea, vomiting, and stomach cramps. It is most common in children but can affect people of all ages, especially in group settings like schools and care facilities.

• Astrovirus

  Astrovirus is a virus that causes mild to moderate gastroenteritis, particularly in young children, the elderly, and those with weakened immune systems. It typically leads to symptoms like diarrhoea, nausea, and stomach pain.

Disclaimer for Shotgun Microbiome Sequencing

The results from this shotgun microbiome sequencing analysis are for informational and research purposes only. They do not diagnose, treat, or predict any disease or health condition. While certain bacterial compositions may be associated with an increased or decreased risk of specific health outcomes, having a higher risk does not mean you will develop the disease, nor does a lower risk guarantee protection. The microbiome is a complex and dynamic ecosystem influenced by various factors, including diet, lifestyle, genetics, and environment. These results should be interpreted in conjunction with other clinical assessments and professional medical advice.