Gut Markers

Acinetobacter spp. are a group of Gram-negative bacteria commonly found in soil, water, and sometimes in the human gut. Although not typically dominant in a healthy microbiome, certain strains may colonise the intestines, especially following antibiotic use or in hospital environments. Some species, such as Acinetobacter baumannii, are known for their resistance to antibiotics and their role in infections, particularly in immunocompromised individuals. In stool analysis, the presence of Acinetobacter may reflect environmental exposure, microbial imbalance, or antibiotic-related shifts in gut flora.

Akkermansia muciniphila is a gut bacterium that supports the maintenance of the intestinal mucosa and a healthy gut lining. It is linked to beneficial metabolic and immune effects and may play an important role in gut health, weight management, and overall well-being.

Alpha-1 antitrypsin (AAT) is a protein primarily produced by the liver that helps protect the lungs and other organs from enzymes that cause inflammation. Measuring AAT levels in faeces can help detect intestinal protein loss and inflammation, assisting in the diagnosis of gastrointestinal conditions such as inflammatory bowel disease and protein-losing enteropathy.

Ammonia is a nitrogen-containing compound produced in the gut through the breakdown of proteins and amino acids by intestinal bacteria. In a healthy gut, most ammonia is either utilised by microbes or absorbed and detoxified by the liver. Elevated faecal ammonia levels may indicate excessive protein fermentation, gut dysbiosis, or an imbalance between beneficial and pathogenic bacteria. High levels can contribute to mucosal irritation, inflammation, and may compromise gut barrier function. Ammonia levels are a useful marker of microbial protein metabolism and intestinal health.

Beta-glucuronidase is an enzyme produced by certain gut bacteria that can break the bond between glucuronic acid and various toxins, hormones, or drugs that have been prepared for elimination by the liver. Elevated beta-glucuronidase activity in the stool may suggest microbial imbalance and can interfere with detoxification by reactivating substances such as oestrogen and xenobiotics in the colon. This reactivation may contribute to systemic toxicity or hormonal imbalances. Measuring beta-glucuronidase in stool helps assess microbial metabolism and detoxification efficiency in the gut.

Bile acids are compounds essential for digesting fats, produced in the liver and stored in the gallbladder. While most are reabsorbed into the body, a portion is excreted in faeces. Measuring bile acids in faeces helps assess digestive health, particularly in diagnosing fat malabsorption and related conditions.

Bilophila wadsworthii is a gram-negative, anaerobic, sulphur-reducing bacterium commonly found in the human gut in small amounts. It is capable of metabolising bile acids and reducing sulphur compounds to hydrogen sulphide (H₂S), a gas that in excessive amounts can be toxic to gut epithelial cells and disrupt intestinal integrity. Elevated levels of Bilophila wadsworthii have been associated with inflammatory conditions such as colitis and may indicate a dysbiotic gut environment, especially in response to high-fat or high-animal protein diets. This bacterium is considered a potential pathobiont due to its ability to promote inflammation under certain conditions.

Butyrivibrio spp. are beneficial gut bacteria known for producing butyrate, a short-chain fatty acid that plays a key role in maintaining intestinal health. Butyrate supports the integrity of the gut lining, reduces inflammation, and serves as a primary energy source for colon cells. The presence of Butyrivibrio is generally regarded as a positive indicator of a healthy microbiome. Low levels may suggest reduced butyrate production, which can be associated with intestinal inflammation or dysbiosis. These bacteria thrive on dietary fibre and are part of the Firmicutes phylum.

Calprotectin is a protein found in white blood cells that acts as a marker of inflammation, especially in the gut. Measuring calprotectin levels in stool helps evaluate the extent of intestinal inflammation. This test is valuable for diagnosing and monitoring inflammatory bowel diseases (IBD) such as Crohn’s disease and ulcerative colitis, and for differentiating them from irritable bowel syndrome (IBS), which usually does not cause elevated calprotectin levels.

Candida dubliniensis is a yeast species closely related to Candida albicans and can be part of the normal microbial flora in the gastrointestinal tract. Under certain conditions, such as weakened immunity, dysbiosis, or high sugar intake, it can overgrow and contribute to fungal imbalance and gastrointestinal symptoms. It is less common than C. albicans but shares many similar characteristics, including its ability to form biofilms and cause mucosal infections. Measuring its levels in stool helps assess fungal overgrowth and the balance of the gut mycobiome.

Candida glabrata is a species of yeast that can naturally inhabit the human gastrointestinal and genitourinary tracts. While usually harmless in healthy individuals, it can become opportunistic in immunocompromised patients, potentially causing infections. Compared to other Candida species, C. glabrata is generally more resistant to common antifungal treatments. Its overgrowth in stool samples may indicate a microbial imbalance (dysbiosis), immune suppression, or previous antibiotic use. Monitoring its levels may offer insights into overall gut health and vulnerability to fungal overgrowth.

Candida krusei is a species of yeast that can be part of the gut mycobiome but is generally present in low numbers. It is known for its natural resistance to certain antifungal treatments, particularly fluconazole, making its identification clinically relevant. An overgrowth of C. krusei may occur in individuals with compromised gut flora, immune suppression, or high sugar intake. Elevated levels in stool may reflect a disruption in microbial balance or a yeast overgrowth condition that could contribute to digestive discomfort and systemic symptoms.

Candida lusitaniae is a less common yeast species that can be part of the normal flora of the human body but has been linked to opportunistic infections, particularly in individuals with weakened immune systems. It is notable for its potential resistance to certain antifungal treatments, especially amphotericin B. In stool analysis, the presence of C. lusitaniae may indicate fungal overgrowth or dysbiosis, particularly when found in elevated quantities. Its detection is important for assessing gut microbial balance and guiding further clinical investigation if necessary.

Candida parapsilosis is a yeast species that can be part of the normal human microbiota, particularly on the skin and in the gastrointestinal tract. While often harmless in healthy individuals, it can become opportunistic and cause infections, especially in hospitalised or immunocompromised patients. It is commonly associated with catheter-related infections, wound infections, and sometimes gastrointestinal disturbances. Elevated levels in stool may indicate an imbalance in the gut microbiome, recent antibiotic use, or suppressed immune function. Monitoring its presence can be relevant in assessing fungal overgrowth or gut dysbiosis.

Candida spp is a group of yeast-like fungi that can affect various parts of the body, including the gut and vagina. These fungi often cause symptoms such as itching, discomfort, and discharge, typically resulting from an imbalance in the body’s natural flora. In the gut, Candida spp can interfere with digestion, leading to bloating and changes in bowel habits. Factors such as diet, overall health, and antibiotic use can contribute to their overgrowth, and addressing these factors is important to restore balance and relieve symptoms.

Candida tropicalis is a yeast species that can be part of the normal human microbiota, particularly in the gastrointestinal tract and on mucosal surfaces. It has a higher pathogenic potential compared to some other non-albicans Candida species and is commonly linked to systemic infections in immunocompromised individuals. In the gut, elevated levels of C. tropicalis may indicate fungal overgrowth, dysbiosis, or a weakened immune system. Its presence in stool tests can help detect imbalances in the gut mycobiome and potential sources of inflammation or infection.

Citrobacter spp. are a group of gram-negative bacteria belonging to the Enterobacteriaceae family. They are commonly found in soil, water, and the intestinal tract of humans and animals. While some species are part of the normal gut flora in small amounts, elevated levels may indicate dysbiosis or an overgrowth. Certain species, like Citrobacter freundii, have been linked to gastrointestinal disturbances, urinary tract infections, and hospital-acquired infections in vulnerable individuals. In stool testing, the presence of Citrobacter may reflect microbial imbalance, immune stress, or past antibiotic use.

Coprococcus spp. are beneficial bacteria in the human gut microbiome, belonging to the Firmicutes phylum. These microbes are known for their ability to produce butyrate, a short-chain fatty acid that supports gut barrier integrity, modulates inflammation, and promotes overall digestive health. Higher levels of Coprococcus are often associated with a well-balanced microbiome and improved mental well-being, as butyrate can also influence brain health via the gut-brain axis. Low levels may reflect poor fibre fermentation, gut dysbiosis, or inflammation. Their presence is generally considered a marker of a healthy, fibre-rich diet.

D-arabinitol is a sugar alcohol used as a biomarker in the body to help detect Candida infections. Elevated levels of D-arabinitol often indicate an overgrowth of Candida, especially in immunocompromised individuals. Measuring D-arabinitol provides a faster and less invasive way to diagnose systemic candidiasis compared with traditional culture methods.

Desulfomonas pigra is a species of sulphate-reducing bacteria (SRB) found in anaerobic environments, including the human gut. It plays a role in sulphur metabolism by reducing sulphate to hydrogen sulphide (H₂S). While hydrogen sulphide is a naturally occurring compound in the colon, elevated levels produced by SRBs like D. pigra can disrupt intestinal barrier function and contribute to gastrointestinal inflammation or discomfort. Increased abundance of Desulfomonas pigra may indicate an overgrowth of sulphur-reducing microbes, potentially associated with diets high in sulphur-containing foods or imbalances in gut microbiota.

Desulfovibrio piger is a common sulphate-reducing bacterium (SRB) in the human gut microbiota. It reduces sulphate and other sulphur compounds into hydrogen sulphide (H₂S), a gas that in small amounts plays physiological roles but in excess can be toxic to intestinal cells. Elevated levels of D. piger have been associated with gastrointestinal disorders such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Its abundance may reflect increased sulphur intake through diet or a disrupted microbial balance that favours sulphur metabolism.

Diamine oxidase (DAO) is an enzyme that aids in the breakdown of histamine, a compound involved in immune function, digestion, and nervous system activity. Maintaining healthy DAO levels is essential for regulating histamine balance and reducing the risk of histamine intolerance.

Diversity refers to the variety of bacterial species present in the gut microbiome. A higher microbial diversity is generally associated with better digestive health, immune function, and resilience against pathogens. Low diversity, on the other hand, may be linked to inflammation, poor nutrient absorption, and various chronic health conditions.

The Dysbiosis Index is a measure used to evaluate the extent of imbalance in the gut microbiome, indicating the presence and severity of dysbiosis. It quantifies variations in microbial diversity and composition compared to a healthy reference population. A higher index indicates greater dysbiosis, which may be associated with health issues such as inflammation, digestive disorders, or metabolic conditions.

Enterotypes are classifications of the human gut microbiome based on the predominant bacterial groups and their metabolic functions. There are three main enterotypes: Bacteroides-dominant (Type 1), Prevotella-dominant (Type 2), and Ruminococcus-dominant (Type 3). Each type has distinct characteristics in how nutrients such as fats, carbohydrates, and proteins are metabolised. For instance, Prevotella (Type 2) is more efficient at carbohydrate utilisation, particularly in fibre-rich diets, but less capable of synthesising certain vitamins. Your enterotype may influence nutrient absorption, gut health, and how your body responds to different types of diets.

Equol is a compound produced by gut bacteria during the metabolism of the soy isoflavone daidzein. It functions as a non-steroidal oestrogen and may offer various health benefits, including antioxidant and hormone-balancing effects. However, only some individuals harbour the specific gut bacteria capable of producing equol. Measuring equol in stool helps determine whether the gut microbiome can convert daidzein efficiently, providing insight into microbial diversity and function related to oestrogen metabolism.

Eubacterium spp. are a diverse group of anaerobic bacteria found in the human gut, classified within the Firmicutes phylum. Many species within this genus play a beneficial role in maintaining gut health by producing short-chain fatty acids (SCFAs), particularly butyrate. These compounds help nourish colon cells, support immune function, and reduce inflammation. Some species may also be involved in bile acid metabolism and vitamin synthesis. An imbalance in Eubacterium populations may be associated with dysbiosis or chronic gastrointestinal conditions.

Faecalibacterium prausnitzii (F. prausnitzii) is a key beneficial bacterium in the human gut, recognised for its anti-inflammatory properties. It plays an important role in maintaining gut health by supporting a balanced microbiome and reinforcing the intestinal barrier.

Fecal occult blood (FOB) is a test that detects hidden blood in the stool, which is not visible to the naked eye. The presence of FOB can be an important indicator of internal gastrointestinal bleeding, often occurring without obvious symptoms. FOB testing is a non-invasive method used to help identify potential underlying medical conditions affecting the digestive tract.

Firmicutes is one of the major bacterial phyla in the human gut microbiome, comprising many species involved in energy extraction from food. These bacteria efficiently break down complex carbohydrates and produce short-chain fatty acids, which can support gut and metabolic health. However, a disproportionately high ratio of Firmicutes to Bacteroidetes has been linked in some studies to obesity and metabolic disturbances. The balance of Firmicutes is therefore an important marker for assessing microbial diversity and potential metabolic tendencies. Individual health effects depend on overall composition and host factors.

Fusobacterium is a genus of anaerobic, gram-negative bacteria naturally found in the human oral cavity, gastrointestinal tract, and sometimes in the vaginal flora. While some species may be part of a normal microbiome, Fusobacterium is also recognised for its association with inflammation and infection. Elevated levels in the gut have been linked to conditions such as inflammatory bowel disease (IBD) and colorectal cancer. Its presence is often considered a marker of microbial imbalance or pathogenic overgrowth, especially when found alongside symptoms like bloating or changes in bowel habits.

Geotrichum candidum is a fungus commonly found in the environment, including soil, water, air, and certain foods. It is also a natural part of the human microbiota, typically residing in the gut and on the skin. While usually harmless, it can become opportunistic and cause infections in individuals with weakened immune systems.

Histamine (Stool) is a diagnostic marker used to evaluate allergic and inflammatory activity within the gastrointestinal tract. Histamine is a biogenic amine released by immune cells in response to allergens and plays a central role in inflammation. Elevated histamine levels in stool may indicate conditions such as food allergies, inflammatory bowel disease (IBD), or mast cell activation, aiding in the diagnosis and management of related immune responses.

Histamine-producing bacteria are gut microbes capable of converting the amino acid histidine into histamine, a biogenic amine that plays a central role in immune responses and allergic reactions. While histamine is an essential signalling molecule, excess production in the gut can contribute to symptoms resembling allergies, such as rashes, headaches, or digestive discomfort. These bacteria may thrive in the presence of chronic stress, poor gut barrier function, or diets rich in histidine-containing foods. Elevated levels are associated with conditions like histamine intolerance or pseudoallergies. Maintaining a balanced microbiome and proper gut barrier integrity may help reduce histamine load from microbial sources.

Hydrogen breath testing is a diagnostic tool that measures the amount of hydrogen in the breath, which is produced by bacterial fermentation in the intestines. This test is commonly used to identify conditions such as Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance. Elevated hydrogen levels indicate that undigested carbohydrates are being fermented by gut bacteria, which can cause symptoms including bloating, diarrhoea, and abdominal discomfort.

Indoxyl sulfate is a uraemic toxin formed when gut bacteria metabolise the amino acid tryptophan into indole, which is then absorbed and converted into indoxyl sulfate in the liver. While small amounts are normally excreted via the kidneys, elevated levels may indicate impaired detoxification, dysbiosis, or renal stress. Indoxyl sulfate has been linked to oxidative stress, systemic inflammation, and vascular dysfunction—especially in individuals with compromised kidney function. It serves as a marker of both microbial activity and the body’s ability to process and eliminate metabolic waste.

Methane breath testing is a diagnostic method that measures the amount of methane gas produced by intestinal bacteria. Methane is produced by specific gut microbes during the fermentation of certain carbohydrates. Elevated methane levels in breath tests are associated with conditions such as Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance, which can cause symptoms including bloating, constipation, abdominal pain, and changes in bowel habits.

Methanobrevibacter species are archaea—microorganisms distinct from bacteria—that primarily inhabit the human gut. These microbes are known for producing methane gas as a by-product of fermentation, especially from hydrogen and carbon dioxide. Elevated levels of Methanobrevibacter spp. have been linked to slowed intestinal transit and symptoms such as constipation and bloating. Unlike many bacteria, archaea are not affected by standard antibiotics, making their overgrowth more difficult to manage. Their presence offers insight into the balance of microbial communities and gas production within the gut.

Morganella spp., most notably Morganella morganii, are gram-negative bacteria belonging to the Enterobacteriaceae family. They are considered opportunistic pathogens and are occasionally found in the human intestinal tract as part of the normal flora. However, elevated levels in stool may indicate dysbiosis or potential infection risk, especially in immunocompromised individuals. Morganella is also known for its production of biogenic amines, such as putrescine and cadaverine, which can contribute to gut and systemic symptoms. In clinical settings, Morganella morganii has been associated with urinary tract infections and other hospital-acquired infections.

Pancreatic elastase is an enzyme produced by the pancreas that plays a vital role in protein digestion. Measuring its levels in stool can provide valuable insights into pancreatic function. As the enzyme remains stable in faecal matter, it serves as a reliable marker for assessing the exocrine function of the pancreas, particularly in diagnosing pancreatic insufficiency.

The stool pH value is a measure that indicates the acidity or alkalinity in the intestines. It reflects the balance of metabolic processes such as fermentation and protein breakdown. A low stool pH often suggests increased fermentation of complex sugars by intestinal bacteria, which can acidify the stool. Conversely, a high stool pH may result from excessive protein metabolism, leading to the production of ammonia and other compounds that raise the stool’s pH level.

Phenols are organic compounds produced by gut bacteria during the fermentation of certain amino acids, particularly tyrosine. Some phenols, such as p-cresol, can be toxic at high concentrations and are linked to dysbiosis or imbalances in the gut microbiota. Elevated phenol levels in stool may indicate microbial activity that places stress on the liver’s detoxification systems. Monitoring phenols helps evaluate how effectively the gut is managing protein breakdown and microbial fermentation processes.

Proteobacteria is a large phylum of Gram-negative bacteria that includes both harmless commensals and potential pathogens. In the gut, a small amount of Proteobacteria can be normal, but elevated levels are often considered a marker of dysbiosis and inflammation. This group includes species such as Escherichia, Salmonella, Helicobacter, and Klebsiella, some of which are linked to gastrointestinal disorders, infections, and metabolic imbalances. An increased abundance of Proteobacteria may reflect microbial instability or a pro-inflammatory gut environment.

Providencia spp. are gram-negative, facultatively anaerobic bacteria belonging to the Enterobacteriaceae family. They are not usually predominant members of the gut microbiome but can be found in small amounts. Certain species, such as Providencia stuartii and Providencia rettgeri, are regarded as opportunistic pathogens and have been linked to urinary tract infections and gastrointestinal disturbances. Elevated levels in a stool sample may indicate microbial imbalance (dysbiosis) or an overgrowth of potentially pathogenic strains. Providencia species are also noted for their ability to produce urease and contribute to ammonia formation.

The stool fat test is a diagnostic procedure that measures the amount of fat present in stool samples. It is employed to evaluate fat absorption and identify malabsorption syndromes. Raised fat levels in stool, referred to as steatorrhoea, can signal digestive or absorption problems within the gastrointestinal tract. This test supports the diagnosis of conditions such as pancreatic insufficiency, cystic fibrosis, coeliac disease, and Crohn’s disease.

The quantitative determination of nitrogen (N) is a laboratory test that measures nitrogen levels in bodily excretions, typically urine or faeces, to assess protein digestion and absorption. This test is essential for evaluating nutritional status, especially in clinical settings where protein-energy malnutrition or imbalances may be a concern. It provides key insights into metabolic functions related to protein turnover and can help diagnose conditions affecting protein metabolism, including kidney disease, malabsorption syndromes, and certain metabolic disorders.

The quantitative stool sugar test is a diagnostic tool that measures the amount of specific sugars in stool to assess carbohydrate malabsorption. It helps identify conditions such as lactose intolerance, fructose intolerance, and other disorders affecting sugar digestion and absorption. By detecting undigested sugars like lactose, fructose, or sorbitol in the stool, this test assists healthcare professionals in determining which sugars the digestive system has difficulty processing, often associated with symptoms such as bloating, gas, diarrhoea, and abdominal pain.

The stool water content analysis is a test that measures the amount of water present in faeces. This assessment is important for diagnosing conditions related to abnormal water absorption or secretion in the gastrointestinal tract. It helps identify causes of diarrhoea, which may result from infections, inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), or malabsorption syndromes, where there is either excessive water secretion or insufficient absorption in the intestines.

Roseburia spp. are beneficial, anaerobic bacteria belonging to the Firmicutes phylum and are common residents of the healthy human gut. These bacteria are recognised for their ability to produce butyrate, a short-chain fatty acid that serves as a vital energy source for colonocytes and helps to reduce inflammation in the gut. A well-balanced level of Roseburia is often associated with better metabolic health, improved gut barrier function, and a lower risk of inflammatory disorders. Decreased levels have been linked to conditions such as obesity, type 2 diabetes, and inflammatory bowel disease.

Ruminococcus spp. are a group of anaerobic bacteria within the Firmicutes phylum, commonly found in the human gut microbiota. They play a significant role in the fermentation of complex carbohydrates and the production of short-chain fatty acids such as acetate and butyrate, which support gut health and energy metabolism. Ruminococcus species are considered important for maintaining a balanced gut environment, particularly due to their fibre-degrading capabilities. Altered levels of Ruminococcus have been linked to digestive issues, irritable bowel syndrome (IBS), and metabolic disorders.

Secondary bile acids are produced in the colon through the bacterial conversion of primary bile acids, which are originally synthesised in the liver. While they contribute to digestion and regulation of the microbiota, elevated levels may indicate dysbiosis, excessive fat consumption, or altered bile acid metabolism. Certain secondary bile acids, such as deoxycholic acid (DCA) and lithocholic acid (LCA), have been linked to mucosal irritation, inflammation, and a higher risk of colorectal disorders when persistently raised. Measuring them in stool samples aids in evaluating gut microbial activity and the status of bile detoxification.

The secretory IgA (sIgA) level indicates the quantity of a key immune protein called Immunoglobulin A, predominantly found in mucosal areas such as the intestines, respiratory tract, and saliva. Secretory IgA plays a crucial role in the body’s primary defence by attaching to pathogens and blocking their entry, thereby helping to protect mucosal surfaces and support overall immune and gut health.

Trimethylamine (TMA) is a metabolite produced by gut bacteria during the breakdown of choline, carnitine, and lecithin—nutrients commonly found in meat, eggs, and dairy. In the liver, TMA is converted into Trimethylamine N-oxide (TMAO), a compound that has been linked to cardiovascular risk in several studies. Elevated TMA/TMAO levels may reflect high microbial conversion activity in the gut, imbalanced microbiota, or a diet rich in animal-based products. While research is ongoing, high TMAO has been associated with inflammation and impaired cholesterol metabolism. Balanced gut flora and plant-forward diets may help maintain healthy TMAO levels.

Yeast is a type of fungus naturally found in the human body, especially in the gut and on the skin. In normal quantities, it is harmless and part of the healthy microbiome. However, an imbalance can cause overgrowth, which may lead to various health issues. Factors such as diet, antibiotic use, and overall health can influence yeast levels.

Zonulin is a protein that regulates the permeability of tight junctions between cells in the digestive tract. It plays a key role in maintaining the intestinal barrier by controlling the passage of substances, such as nutrients and antigens, from the gut into the bloodstream. Imbalances in zonulin levels can affect gut permeability, potentially contributing to various health issues.