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 beneficial gut bacterium, known for its role in maintaining intestinal mucosa and promoting a healthy gut lining. It's linked to positive metabolic and immune responses, playing a crucial part in gut health, weight management, and overall well-being....

Alpha-1 antitrypsin (AAT) is a protein primarily produced by the liver, playing a key role in protecting the lungs and other organs from enzymes that can cause inflammation. In feces, measuring alpha-1 antitrypsin can help assess intestinal protein loss and inflammation, indicating gastrointestinal disorders like inflammatory bowel disease or 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, essential for digesting fats, are produced in the liver and stored in the gallbladder. Normally, they are reabsorbed into the body, but a portion ends up in stool. Analyzing bile acids in stool can help understand digestive health, especially in diagnosing malabsorption issues....

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, a protein in white blood cells, indicates inflammation, especially in the gut. Testing calprotectin in feces shows how inflamed the intestines are. This helps diagnose and track inflammatory bowel diseases like Crohn's and ulcerative colitis. It also helps distinguish these from irritable bowel syndrome (IBS), which usually doesn't raise 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 includes various yeast-like fungi affecting body parts like the gut and vagina. These infections often cause itching, discomfort, and discharge. They result from flora imbalance. In the gut, Candida spp can disrupt digestion. This leads to bloating and changes in bowel habits. Diet, health, and antibiotics are contributing factors. Addressing these is crucial 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 for diagnosing and monitoring Candida infections, particularly in immunocompromised patients. Elevated levels of D-arabinitol can indicate an overgrowth of Candida, often associated with systemic candidiasis. Its measurement can provide a quicker and non-invasive diagnostic alternative compared to 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 breaks down histamine, a compound involved in immune responses, gut health, and neurological functions. Adequate DAO levels are crucial for managing histamine levels in the body, preventing histamine intolerance and related symptoms....

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 is a key beneficial bacterium in the human gut, known for its anti-inflammatory properties. It plays a crucial role in maintaining gut health, contributing to a balanced gut microbiome and supporting the intestinal barrier....

Fecal occult blood (FOB) is blood present in the feces that is not visible to the naked eye. This condition can be a crucial indicator of internal gastrointestinal bleeding, which may not produce any visible symptoms. FOB testing is a non-invasive method used to detect hidden blood in the stool, which can be a sign of various medical conditions....

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 type of fungus often found in soil, water, air, and some food products. In the human body, it's commonly present in the gut and on the skin. While typically harmless, Geotrichum candidum can cause issues in immunocompromised individuals....

The measurement of histamine in stool is a diagnostic test used primarily to detect and evaluate allergic reactions and inflammatory conditions in the gastrointestinal tract. Histamine, a biogenic amine, is released by immune cells in response to allergens and plays a key role in inflammatory processes. High levels of histamine in the stool can indicate gastrointestinal disorders such as food allergies, inflammatory bowel disease (IBD), and mast cell activation syndromes. This test helps in identifying the presence of excessive immune response and aids in the diagnosis and management of conditions related to increased histamine activity....

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 method used to detect abnormal levels of hydrogen in the breath, which are produced by bacterial fermentation in the intestines. This test is particularly useful for diagnosing Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance. Elevated hydrogen levels can indicate that undigested carbohydrates are being fermented by bacteria in the gut, leading to symptoms like bloating, diarrhea, and abdominal pain....

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 testing through breath analysis is a diagnostic tool used to detect excessive methane production by intestinal bacteria. Methane is a gas produced by specific microbes within the gut, particularly in response to the fermentation of certain carbohydrates. Elevated methane levels in breath tests are associated with conditions like Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance. These conditions can lead to symptoms such as bloating, constipation, abdominal pain, and altered 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, crucial for digesting proteins. Measuring its levels in feces provides valuable information about pancreatic function. This enzyme remains stable in fecal matter, making it a reliable indicator for evaluating the exocrine function of the pancreas, particularly in diagnosing conditions like pancreatic insufficiency....

The pH value of the stool can indicate if there are any conditions of excess decay or fermentation in the intestine. A too low pH value often occurs in combination with a dysfunctional intestinal flora, as complex sugars are metabolized to fatty acids, which can contribute to an acidified stool. A too high pH value can be due to excessive amounts of protein, which can stimulate certain intestinal bacteria to produce ammonia and other metabolic products, thus raising the pH value of the stool....

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 quantitative determination of fat in stool samples, often referred to under the umbrella of digestive residues, is a diagnostic test used to evaluate fat absorption and to identify malabsorption syndromes. This test, measures the amount of fat that is excreted in the stool. Excessive fat in the stool, a condition known as steatorrhea, can indicate problems with digestion or absorption of fat in the gastrointestinal tract. The results of this test help in diagnosing conditions such as pancreatic insufficiency, cystic fibrosis, celiac disease, and Crohn's disease....

The quantitative determination of nitrogen is a laboratory test primarily used to assess protein digestion and absorption by measuring nitrogen levels in bodily excretions, usually urine or feces. This test is instrumental in evaluating nutritional status, particularly in clinical settings where protein-energy malnutrition or imbalances might be a concern. It serves as a key indicator of metabolic functions related to protein turnover. The test can help diagnose conditions that affect protein metabolism, such as kidney disease, malabsorption syndromes, and certain metabolic disorders...

The quantitative determination of sugar in stool is a diagnostic test used primarily to detect carbohydrate malabsorption. This type of test is valuable for diagnosing conditions such as lactose intolerance, fructose intolerance, and other disorders where the digestion and absorption of sugars are impaired. By measuring the levels of sugars such as lactose, fructose, or sorbitol in the stool, healthcare providers can identify the specific sugars that a patient's digestive system cannot process effectively. The presence of undigested sugars in the stool often leads to symptoms such as bloating, gas, diarrhea, and abdominal pain....

The quantitative determination of water in stool, commonly referred to as stool water content analysis, is a diagnostic test used to evaluate the water content in feces. This test is crucial for diagnosing conditions associated with abnormal water absorption or secretion in the gastrointestinal tract, such as various forms of diarrhea. Diarrhea can result from infections, inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), or malabsorption syndromes, where there is either excessive secretion or inadequate absorption of water 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.

Secretory IgA (Immunoglobulin A) is a critical component of the immune system, primarily found in mucosal areas like the intestines, respiratory tract, and saliva. It plays a key role in the body's first line of defense, protecting mucosal surfaces by binding to pathogens and preventing their entry into the body. Secretory IgA is essential for maintaining gut health and overall immune function....

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, a type of fungus, is commonly found in the human body, especially in the gut and on the skin. In small amounts, it's harmless. However, imbalances can lead to overgrowth, causing various health issues. Factors like diet, antibiotics, and overall health influence yeast levels....

Zonulin is a protein that regulates the permeability of tight junctions between cells in the digestive tract. It plays a crucial role in the intestinal barrier, controlling the passage of substances, including nutrients and antigens, between the gut and the bloodstream. Imbalances in zonulin levels can affect gut permeability, potentially leading to various health issues....