The advancement of new scientific innovations, such as next generation sequencing, enables the thorough examination of microbial composition. Over three million microbial genes and a population of approximately 1000-1500 distinct microbes fill the gastrointestinal system.

The gut microbiome’s primary roles can be divided into three main categories: structural, protective, and metabolic. The production of vitamins, neurotransmitters, amino acids, and enzymes—all crucial for organ and body function—is aided by the gut microbiota. It is crucial for the synthesis of short-chain fatty acids (SCFAs) and the absorption of minerals and nutrients. Acetate, propionate, and butyrate are SCFAs that are essential for gut health and are produced by intestinal microbial fermentation. They improve the integrity of the epithelial barrier and offer immunomodulation to ward against infections.

Health depends on a balanced microbial community, whereas dysbiosis is an imbalance or change in this community. Reduced diversity and quantity of commensal bacteria can be a consequence of intestinal dysbiosis. There is mounting evidence that gut microbiome dysbiosis contributes significantly to a number of disorders, including illnesses of the heart, metabolism, nervous system, autoimmune system, gastrointestinal tract, inflammatory bowel disease, obesity, and cancer. Additionally, organ health, emotions, and cognitive processes can all be impacted by dysbiosis. On the other hand, a variety of factors, including early life infant delivery and feeding practices, continuous environmental exposures, medication usage, food, and stress, can influence the growth and modification of the gut microbiome.

Gut functional markers

Butyrate

Butyrate is one of the most important short chain fatty acids (SCFAs), as it serves as the primary energy source for colonocytes (the cells lining the colon) and has anti-inflammatory properties.

Potential Causes of low SCFAs: Low fibre intake (especially resistant starch and other fermentable fibres), dysbiosis, or a lack of butyrate-producing bacteria (eg. Faecalibacterium prausnitzii, Roseburia).
Clinical Implications: Low butyrate is associated with an increased risk of inflammatory bowel diseases (IBD) like ulcerative colitis, irritable bowel syndrome (IBS), metabolic disorders, colorectal cancer, and general gut inflammation.

Acetate

Acetate is the most abundant SCFA in the gut and serves as a precursor to produce butyrate and propionate. It also has roles in lipid
metabolism and cholesterol regulation.

Potential Causes of low acetate: Low fibre intake, reduced fermentation capacity, or a lack of acetate-producing bacteria (e.g., ). Bifidobacterium
Clinical Implications: Low acetate can indicate poor microbial diversity and compromised fermentation activity, which may lead to metabolic issues and a weakened intestinal barrier.

Propionate

Propionate plays a role in glucose and lipid metabolism and has anti-inflammatory effects. It is produced by certain gut bacteria and absorbed by the liver, where it influences metabolic processes.

Potential Causes of low propionate: Low fibre intake, reduced diversity of propionate producing bacteria (e.g., Bacteroides, Prevotella), or
compromised fermentation activity.

Clinical Implications: Low propionate levels can be associated with poor gut health, metabolic dysfunction, and an increased risk of insulin resistance or type 2 diabetes.

Calprotectin

Calprotectin is a protein found in neutrophils (a type of white blood cell) that is released during inflammation. Measuring calprotectin
levels in the stool is a common diagnostic tool for detecting intestinal inflammation, particularly to differentiate between inflammatory bowel
disease (IBD) and irritable bowel syndrome (IBS). It serves as a noninvasive marker for conditions that cause inflammation in the intestines.

High calprotectin levels indicate significant inflammation in the gut. This is commonly associated with inflammatory bowel diseases such as Crohn’s disease or ulcerative colitis, or in response to an infection or other inflammatory conditions.

Clinical implications of high calprotectin: IBD diagnosis. Further investigation is warranted if calprotectin is elevated, further diagnostic testing such as endoscopy, colonoscopy, or imaging may be required to confirm the underlying cause of inflammation.
Monitoring inflammation: Persistent high levels of calprotectin may indicate ongoing inflammation, suggesting that treatment for IBD or
infections may need adjustment. Differentiation from IBS: Elevated calprotectin helps distinguish IBD from IBS, as IBS does not cause gut
inflammation.

Pancreatic Elastase

Pancreatic elastase is an enzyme produced by the pancreas that helps digest proteins. Measuring the levels of pancreatic elastase in the stool provides information about pancreatic function. Low PE levels suggest exocrine pancreatic insufficiency (EPI), meaning the pancreas is not producing sufficient enzymes to support proper digestion, particularly of fats and proteins.
Clinical implications: Fat malabsorption: Low pancreatic elastase levels lead to fat malabsorption, resulting in symptoms like steatorrhea (fatty, oily stools), weight loss and nutrient deficiencies (Vitamins A, D, E, and K).
Protein malabsorption: Poor protein digestion can occur potentially causing weakness or muscle wasting.

Gastrointestinal symptoms: Symptoms of exocrine pancreatic insufficiency include diarrhoea, bloating, and discomfort after meals

Dietary modifications: A low-fat diet or medium-chain triglyceride (MCT) supplements may help reduce symptoms of fat malabsorption.

Secretory IgA

Secretory IgA (sIgA) is the predominant antibody in the gut’s mucosal surfaces and plays a critical role in immune defence by neutralizing pathogens and maintaining the balance of the gut microbiota. sIgA binds to microbes and antigens, preventing them from crossing the intestinal barrier, and helps maintain immune homeostasis.

Leaky gut (intestinal permeability): With reduced immune protection, the gut lining may become compromised, allowing antigens and toxins to pass into the bloodstream, potentially leading to systemic inflammation.
Low sIgA level in the gut suggests a weakened mucosal immune defence. This can make the gut lining more susceptible to infections, toxins, and antigens, allowing them to penetrate the gut barrier and potentially trigger immune reactions or inflammation.
Clinical Implications: Increased susceptibility to infections: Low sIgA may lead to frequent gut infections, yeast overgrowth, or other microbial imbalances. Probiotics that specifically boost sIgA production, such as Lactobacillus rhamnosus and Bifidobacterium strains.

Food sensitivities: Low sIgA can increase the likelihood of food sensitivities or intolerances because the immune system may struggle to neutralize antigens in the gut. Supplementation with nutrients that support immune health (e.g. vitamin A, vitamin D, zinc).

Zonulin

Zonulin is a protein that regulates the permeability of tight junctions between cells in the gut lining, essentially controlling the “leakiness” of the gut barrier. Increased levels of zonulin are associated with greater intestinal permeability (commonly referred to as “leaky gut”), which
can allow harmful substances like bacteria, toxins, and undigested food particles to pass into the bloodstream, potentially triggering systemic inflammation and immune responses.

High Zonulin levels suggest increased intestinal permeability, meaning the tight junctions in the gut lining are loosened, allowing substances that are normally restricted (e.g., toxins, antigens, bacteria) to pass through the gut barrier into the bloodstream. This is often referred to as
“leaky gut syndrome.” Increased risk of chronic diseases: Leaky gut can contribute to systemic inflammation, immune activation, and potentially lead to conditions like rheumatoid arthritis, lupus, and multiple sclerosis, among others. Manage stress: Reducing stress through
lifestyle changes (e.g. mindfulness, exercise, adequate sleep) can help lower gut permeability.

Clinical Implications: Leaky gut syndrome: High zonulin levels are a key marker of intestinal hyperpermeability (leaky gut), which has been linked to various systemic conditions, including autoimmune diseases, chronic inflammation, allergies, and metabolic disorders.

Digestive discomfort: High zonulin is often associated with digestive issues like bloating, gas, food sensitivities, or irritable bowel syndrome (IBS). Reduce inflammation: Anti-inflammatory diets (rich in omega-3s, fibre, and polyphenols) and nutrients like zinc, vitamin D, and glutamine can help repair the gut lining and reduce zonulin levels. Intervention: Identify and remove triggers. If elevated zonulin is associated with gluten sensitivity or food intolerances, eliminating gluten and other problematic foods can help reduce zonulin levels.

B-Glucuronidase

Beta-glucuronidase is an enzyme produced by certain bacteria in the gut and is involved in the breakdown of complex carbohydrates and the
deconjugation of metabolites, such as hormones, drugs, and toxins. It plays an important role in the detoxification process in the body. However, elevated levels of beta-glucuronidase can disrupt this process and have been linked to various health issues, particularly with hormone reabsorption and cancer risk.

High beta-glucuronidase levels indicate increased enzyme activity, which can lead to the reabsorption of deconjugated compounds, such as hormones (especially oestrogen), toxins, and bile acids, rather than their elimination. This can contribute to various health concerns, particularly in the context of hormonal imbalances and toxicity. Detoxification impairment: High betaglucuronidase levels can lead to the reactivation of detoxified toxins (such as carcinogens) in the gut, increasing the risk of toxicity and cancer. Clinical Implications: Hormone-related issues: High beta-glucuronidase can lead to oestrogen reabsorption from the gut, contributing to oestrogen dominance, which is linked to conditions like PMS, fibroids, endometriosis, and hormonedependent cancers (eg., breast, uterine, prostate).

Chronic disease risk: Elevated levels are associated with an increased risk of colon cancer due to the deconjugation and reabsorption of carcinogens. Gut inflammation: High levels may also indicate gut dysbiosis or inflammation, leading to impaired detoxification and toxin reabsorption.

Intervention: Increase fibre intake: A high-fibre diet, particularly soluble fibre (e.g., from fruits, vegetables, legumes), can help bind and excrete toxins and reduce beta-glucuronidase activity.Probiotic support: Certain probiotics, particularly Lactobacillus Bifidobacterium and strains, may help lower beta-glucuronidase production by promoting healthier gut flora. Calcium-D-glucarate supplementation: This
supplement can inhibit beta-glucuronidase activity and support the proper elimination of hormones like oestrogen and toxins. It is often recommended for individuals with elevated beta-glucuronidase and oestrogen dominance. Promote regular bowel movements: Supporting
healthy digestion and regular bowel movements can help reduce beta-glucuronidase activity by promoting proper elimination.

Steatocrit

Steatocrit is a measure of the fat content in stool and is used to evaluate fat malabsorption (steatorrhea). The test helps assess how well the digestive system, particularly the pancreas and small intestine, is processing and absorbing dietary fats. High steatocrit levels indicate fat
malabsorption, meaning that a significant amount of dietary fat is not being absorbed and is being excreted in the stool.

Nutrient deficiencies: Fat malabsorption can lead to deficiencies in fat-soluble vitamins (A, D, E, and K), potentially causing a range of health issues, from poor bone health to immune dysfunction.

Anti-transglutaminase

IgA Anti-tTG IgA is an autoantibody commonly used in the diagnosis of celiac disease. It targets the enzyme tissue transglutaminase (tTG),
which is involved in the immune response triggered by gluten in genetically susceptible individuals.

Elevated anti-tTG IgA levels indicate an active immune response against the enzyme tTG, which is a hallmark of celiac
disease. This suggests the person is likely to have gluten-induced damage to the small intestine. Active celiac disease: High anti-tTG IgA levels are used as a diagnostic marker for celiac disease. They often correlate with the intestinal damage (villous atrophy) seen.

Faecal pH

Faecal pH measures the acidity or alkalinity of the stool, which can provide insights into the digestive processes and microbial activity
in the gut.

Low pH (acidic stool) generally indicates increased fermentation of carbohydrates by gut bacteria, producing short-chain fatty acids (SCFAs) like lactic acid and acetic acid. Clinical Implications: Digestive issues: Low faecal pH is often associated with symptoms like
bloating, gas, diarrhoea, and discomfort due to carbohydrate malabsorption.

High pH (alkaline stool) suggests protein putrefaction or insufficient carbohydrate fermentation by gut bacteria, often linked with a high fat or high-protein diet. Clinical Implications: Poor digestion: High faecal pH is associated with protein malabsorption and putrefaction, which can lead to symptoms like bloating, foul-smelling stools, and discomfort.

 

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