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 colonize 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 helps maintain the intestinal mucosa and a healthy gut lining. It is linked to positive metabolic and immune functions and may play a key role in gut health, weight management, and overall wellness.

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 stool can help detect intestinal protein loss and inflammation, supporting 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 used by microbes or absorbed and detoxified by the liver. Elevated fecal 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 indicate microbial imbalance and can interfere with detoxification by reactivating substances like estrogen 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 necessary for fat digestion, produced by the liver and stored in the gallbladder. While most are reabsorbed by the body, some are eliminated in the stool. Measuring bile acids in stool aids in evaluating digestive health, especially for diagnosing fat malabsorption and related disorders.

Bilophila wadsworthii is a gram-negative, anaerobic, sulfur-reducing bacterium commonly present in small quantities within the human gut. It can metabolize bile acids and reduce sulfur compounds to hydrogen sulfide (H₂S), a gas that, in excessive amounts, can be toxic to gut epithelial cells and compromise intestinal integrity. Increased levels of Bilophila wadsworthii have been linked to inflammatory conditions such as colitis and may signal a dysbiotic gut environment, particularly in response to high-fat or high-animal protein diets. This bacterium is regarded as a potential pathobiont due to its capacity to induce inflammation under certain circumstances.

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 considered 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 serves as a marker of inflammation, particularly in the gut. Measuring calprotectin levels in stool helps assess the degree of intestinal inflammation. This test is useful for diagnosing and monitoring inflammatory bowel diseases (IBD) such as Crohn’s disease and ulcerative colitis, and for distinguishing them from irritable bowel syndrome (IBS), which typically does not elevate 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 reside in the human gastrointestinal and genitourinary tracts. While typically harmless in healthy individuals, it can become opportunistic in immunocompromised hosts, potentially leading to infections. Compared to other Candida species, C. glabrata tends to be more resistant to common antifungal treatments. Its overgrowth in stool samples may indicate microbial imbalance (dysbiosis), immune suppression, or prior antibiotic use. Monitoring its levels may provide insights into overall gut health and susceptibility 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 in the human body but has been associated with 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 amounts. Its detection is important for assessing gut microbial balance and guiding further clinical investigation if needed.

Candida parapsilosis is a yeast species that can be part of the normal human microbiota, especially on the skin and in the gastrointestinal tract. While usually harmless in healthy individuals, it can become opportunistic and cause infections, particularly in hospitalized or immunocompromised patients. It is frequently linked to catheter-related infections, wound infections, and occasionally gastrointestinal issues. Elevated levels in stool may indicate gut microbiome imbalance, recent antibiotic use, or suppressed immune function. Monitoring its presence can be important for evaluating 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, especially in the gastrointestinal tract and mucosal surfaces. It has a higher pathogenic potential than some other non-albicans Candida species and is frequently linked to systemic infections in immunocompromised patients. In the gut, increased levels of C. tropicalis may indicate fungal overgrowth, dysbiosis, or a weakened immune system. Its detection in stool tests can aid in identifying imbalances in the gut mycobiome and possible 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 to traditional culture methods.

Desulfomonas pigra is a species of sulfate-reducing bacteria (SRB) found in anaerobic environments, including the human gut. It plays a role in sulfur metabolism by reducing sulfate to hydrogen sulfide (H₂S). While hydrogen sulfide 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 sulfur-reducing microbes, potentially associated with diets high in sulfur-containing foods or imbalances in gut microbiota.

Desulfovibrio piger is a common sulfate-reducing bacterium (SRB) in the human gut microbiota. It reduces sulfate and other sulfur compounds into hydrogen sulfide (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 sulfur intake through diet or a disrupted microbial balance that favors sulfur metabolism.

Diamine oxidase (DAO) is an enzyme that helps break down 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 metric used to evaluate the extent of imbalance in the gut microbiome, reflecting the presence and severity of dysbiosis. It measures variations in microbial diversity and composition relative to a healthy reference group. A higher index indicates more significant dysbiosis, which could be associated with health problems such as inflammation, digestive disorders, or metabolic conditions.

Enterotypes are classifications of the human gut microbiome based on the dominant 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 unique characteristics in how nutrients like fats, carbohydrates, and proteins are metabolised. For example, Prevotella (Type 2) is more efficient at carbohydrate utilisation, especially 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 estrogen and may offer various health benefits, including antioxidant and hormone-regulating effects. However, only certain individuals possess the specific gut bacteria capable of producing equol. Measuring equol in stool helps assess whether the gut microbiome can efficiently convert daidzein, providing insights into microbial diversity and function related to estrogen 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 crucial beneficial bacterium in the human gut, recognized for its anti-inflammatory properties. It plays a vital role in preserving 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 cannot be seen with the naked eye. The presence of FOB can serve as an important sign of internal gastrointestinal bleeding, often occurring without clear symptoms. FOB testing is a non-invasive procedure used to help identify potential underlying medical conditions affecting the digestive system.

Firmicutes is one of the major bacterial phyla in the human gut microbiome, comprising many species involved in energy extraction from food. These bacteria are efficient at breaking down complex carbohydrates and producing short-chain fatty acids, which can support gut and metabolic health. However, a disproportionately high ratio of Firmicutes to Bacteroidetes has been associated in some studies with 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 exist as part of a normal microbiome, Fusobacterium is also known for its association with inflammation and infection. High 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 altered 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.

Hippuric acid is a metabolic compound formed in the liver from the conjugation of benzoic acid with glycine. It reflects both detoxification capacity and microbial activity in the gut. Elevated levels may indicate increased microbial fermentation, exposure to certain food additives, or an active detoxification response. Low concentrations can be seen with reduced liver conjugation capacity or low microbial production of precursors.

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 crucial role in inflammation. Elevated stool histamine levels may suggest conditions such as food allergies, inflammatory bowel disease (IBD), or mast cell activation, assisting 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 a necessary signaling molecule, excess production in the gut can contribute to symptoms resembling allergies, such as rashes, headaches, or digestive discomfort. These bacteria may flourish 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 like Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance. Elevated hydrogen levels suggest that undigested carbohydrates are being fermented by gut bacteria, which can cause symptoms such as bloating, diarrhoea, and abdominal discomfort.

Indole-3-acetic acid is a tryptophan-derived metabolite produced by intestinal bacteria. It contributes to gut–liver communication and can affect oxidative stress and intestinal permeability. Elevated levels of IAA may indicate dysbiosis, increased bacterial tryptophan metabolism, or altered liver detoxification pathways. Normal concentrations suggest a balanced gut microbiota activity and efficient metabolic clearance.

Indolpropionic acid (IPA) is a microbial metabolite derived from the amino acid tryptophan. It is known for its antioxidant properties and plays a protective role in gut barrier integrity and glucose metabolism. Higher levels are generally associated with a balanced gut microbiota and healthy intestinal environment. Low concentrations may indicate reduced microbial diversity, altered tryptophan metabolism, or increased oxidative stress.

Indoxyl sulfate is a uremic 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 technique that measures the quantity of methane gas produced by intestinal bacteria. Methane is formed by specific gut microbes during the fermentation of certain carbohydrates. Raised methane levels in breath tests are associated with conditions like Small Intestinal Bacterial Overgrowth (SIBO), fructose intolerance, and sorbitol intolerance, which can lead to symptoms such as bloating, constipation, abdominal pain, and changes in bowel movements.

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

p-Cresol sulfate is a metabolite produced by intestinal bacteria through the breakdown of the amino acid tyrosine. It is primarily detoxified in the liver and excreted by the kidneys. Higher levels may reflect increased bacterial protein fermentation, impaired detoxification, or reduced renal clearance. Balanced levels indicate efficient gut microbial metabolism and normal liver–kidney function.

Pancreatic elastase is an enzyme produced by the pancreas that plays a crucial role in protein digestion. Measuring its levels in stool can offer valuable insights into pancreatic function. Since the enzyme remains stable in fecal matter, it serves as a reliable marker for evaluating 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 that gut bacteria produce during the fermentation of certain amino acids, especially tyrosine. Some phenols, like p-cresol, can be toxic at high levels and are linked to dysbiosis or imbalances in gut microbiota. Increased phenol levels in stool indicate microbial activity that may strain the liver’s detoxification functions. Tracking phenols helps evaluate how effectively the gut is handling protein breakdown and microbial fermentation.

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 that belong to the Enterobacteriaceae family. They are not typically dominant members of the gut microbiome but can be found in small amounts. Some species, such as Providencia stuartii and Providencia rettgeri, are considered opportunistic pathogens and have been associated with urinary tract infections and gastrointestinal disturbances. Elevated levels in a stool sample may indicate microbial imbalance (dysbiosis) or an overrepresentation of potentially pathogenic strains. Providencia species are also known for their ability to produce urease and contribute to ammonia formation.

Putrescine is a biogenic amine produced by the bacterial and cellular breakdown of the amino acid ornithine. It contributes to cell growth, tissue regeneration, and the regulation of intestinal function. Elevated levels of putrescine may result from increased microbial fermentation, protein degradation, or intestinal dysbiosis. Balanced levels signify normal gut metabolic activity and effective detoxification processes.

The stool fat test is a diagnostic tool that measures the quantity of fat excreted in stool samples. It is used to evaluate fat absorption and identify malabsorption syndromes. Raised fat levels in stool, termed steatorrhea, may suggest digestive or absorption problems in the gastrointestinal tract. This test helps diagnose conditions like pancreatic insufficiency, cystic fibrosis, celiac 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 feces, to assess protein digestion and absorption. This test is crucial for evaluating nutritional status, especially in clinical settings where protein-energy malnutrition or imbalances might be a concern. It provides valuable insights into metabolic functions linked to protein turnover and helps diagnose conditions affecting protein metabolism, including kidney disease, malabsorption syndromes, and certain metabolic disorders.

The quantitative stool sugar test is a diagnostic method used to measure the levels of specific sugars in stool samples to evaluate carbohydrate malabsorption. It helps in diagnosing conditions such as lactose intolerance, fructose intolerance, and other disorders that impair sugar digestion and absorption. By identifying 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 including bloating, gas, diarrhea, and abdominal pain.

The stool water content analysis is a test that measures the amount of water present in feces. 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.

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 like 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 fiber-degrading abilities. Altered levels of Ruminococcus have been associated with digestive issues, irritable bowel syndrome (IBS), and metabolic disorders.

Secondary bile acids are formed in the colon through bacterial transformation of primary bile acids originally synthesized in the liver. While they play roles in digestion and microbial regulation, elevated levels may indicate dysbiosis, excessive fat consumption, or altered bile acid metabolism. Some 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 elevated. Measuring them in stool helps evaluate gut microbial activity and bile detoxification status.

The secretory IgA (sIgA) level indicates the quantity of an essential immune protein called Immunoglobulin A, primarily located in mucosal areas such as the intestines, respiratory tract, and saliva. Secretory IgA plays a crucial role in the body’s first line of defense 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. When present in normal amounts, it is harmless and part of a healthy microbiome. However, an imbalance can cause overgrowth, potentially leading 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 impact gut permeability, potentially contributing to various health concerns.