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The Ultimate Guide to the Microbiome

  • 20 min read

What is Microbiome?

The human gut microbiome refers to the community of microorganisms that live in the gastrointestinal tract. These microorganisms, including bacteria, viruses, fungi, and protozoa, play a crucial role in maintaining the health and well-being of their host. The gut microbiome is considered to be a separate organ system within the body. It has a diverse array of functions, including breaking down complex carbohydrates and fibres, synthesizing vitamins and amino acids, modulating the immune system, and regulating the gut-brain axis.

The composition of the gut microbiome is unique to each individual. It can be influenced by various factors such as diet, genetics, age, and the use of antibiotics. A healthy gut microbiome is characterized by a diverse and balanced population of microorganisms. In contrast, an imbalanced gut microbiome (dysbiosis) is associated with health conditions such as inflammatory bowel disease, obesity, and type 2 diabetes.

Recent research has shown that the gut microbiome plays a crucial role in human health and disease. The gut microbiome can affect the host's metabolism, immune system, and overall well-being. For example, the gut microbiome can influence the host's metabolism by producing short-chain fatty acids, which can affect the host's energy balance and glucose metabolism. The gut microbiome can also influence the host's immune system by producing molecules that can modulate the host's immune response.

The gut microbiome can also affect the host's overall well-being by influencing the gut-brain axis, which is the communication system between the gut and the brain. This communication system is mediated by a variety of neural, hormonal, and immune signalling pathways that connect the gut and the brain. The gut microbiome can produce a variety of neurotransmitters and other signalling molecules that can influence brain function, and dysbiosis has been linked to several neurological and psychiatric disorders, such as depression and anxiety.

To maintain a healthy gut microbiome, it's important to have a diet with rich in natural wholefoods with a wide variety of dietary ingredient types and colours, typically recommended to be spready across vegetables, fruits, fermented foods and according to some, whole grains. Note that this is a simplified list and the gut microbiome has shown to be benefited from an even broader range of foods. . Avoiding processed foods and added sugars, as well as reducing the use of antibiotics, can also help maintain a healthy gut microbiome.

The gut microbiome is a complex and dynamic system that plays a crucial role in human health and disease. Further research in this field is ongoing and has the potential to lead to new treatments for a wide range of diseases and disorders that involve the gut. Maintaining a healthy gut microbiome is crucial for overall health and well-being.

 

Benefits from an improved gut microbiome health

An optimal gut microbiome can bring a wide range of benefits for overall health and well-being. Some of the main benefits include:

  1. Improved digestion
    A healthy gut microbiome can help break down food and extract nutrients more efficiently, leading to better digestion and nutrient absorption.

  2. Increased immunity
    The gut microbiome plays a crucial role in the immune system. A healthy gut microbiome can help strengthen the immune system and protect against infections and illnesses.

  3. Reduced inflammation
    An optimal gut microbiome can help to reduce chronic inflammation in the body, which is a risk factor for a wide range of diseases, including heart disease, diabetes, and cancer.

  4. Improved mental health
    The gut microbiome has been linked to mental health, and a healthy gut microbiome can help to reduce symptoms of anxiety, depression, and other mental health conditions.

  5. Weight management
    Studies have shown that a healthy gut microbiome can help to regulate appetite, metabolism and energy balance, which can aid in weight management.

  6. Better skin health
    A healthy gut microbiome can help to improve skin health by reducing inflammation and promoting collagen production.

  7. Better sleep
    A healthy gut microbiome can help to regulate the circadian rhythm and promote better sleep.

  8. Improved cardiovascular health
    The gut microbiome plays a crucial role in regulating cholesterol and blood pressure. A healthy gut microbiome can help reduce the risk of heart disease and stroke.

  9. Better athletic performance
    Studies have shown that a healthy gut microbiome can help to improve athletic performance and endurance and reduce muscle damage.

  10. Reduced risk of chronic diseases
    By improving overall health, a healthy gut microbiome can help to reduce the risk of chronic diseases such as obesity, diabetes, and heart disease.

Who discovered the microbiome?

The human gut microbiome has been known for centuries, but it was in the late 20th century that scientific research began to reveal the true complexity and importance of the gut microbiome.

In the early 1900s, scientists began to study the microorganisms that lived in the human gut, but it was not until the invention of new techniques, such as culture-independent methods and next-generation sequencing, that the true diversity and complexity of the gut microbiome became apparent.

In the early 2000s, researchers began to use these new techniques to study the gut microbiome. They discovered that the gut microbiome is a diverse and complex ecosystem that plays a crucial role in human health and disease. For example, the Human Microbiome Project (HMP) was initiated in 2007 by the National Institutes of Health (NIH). It was the first large-scale, comprehensive effort to understand the human microbiome. The HMP was completed in 2012 and provided a wealth of information about the human gut microbiome and its role in human health.

Another study, published in Nature in 2012, was the first to use metagenomic sequencing to characterize the gut microbiome of healthy adults. This study established the concept of a "core" gut microbiome.

Overall, the discovery of the human gut microbiome is an ongoing process that began in the early 1900s and continues to this day, with new studies and technologies revealing more about the gut microbiome and its role in human health.

 

What microorganisms live in the microbiome?

The human gut microbiome is a complex ecosystem comprising a diverse array of microorganisms, including bacteria, viruses, fungi, and protozoa. The key elements of the human gut microbiome include:

  1. Bacteria
    The gut microbiome is primarily composed of bacteria, with the majority belonging to the phyla Firmicutes and Bacteroidetes. These bacteria play a crucial role in breaking down complex carbohydrates and fibres, synthesizing vitamins and amino acids, and modulating the immune system.

  2. Viruses
    Viruses, also known as bacteriophages, play a role in shaping the bacterial community. They can also help to control the growth of harmful bacteria.

  3. Fungi
    Fungi, also known as yeasts, are present in the gut microbiome. They are a smaller component of the gut microbiome, but they can play a role in regulating the immune system and modulating gut function.

  4. Protozoa
    Protozoa are single-celled organisms that are also present in the gut microbiome. They play a role in the breakdown of complex carbohydrates and can also influence the composition of the bacterial community.

  5. Metabolites
    The gut microbiome produces a wide range of metabolites, including short-chain fatty acids, vitamins, and amino acids, which play a crucial role in maintaining the health and well-being of the host.

  6. Genetics
    The gut microbiome is unique to each individual and can be influenced by various factors such as diet, genetics, age, and the use of antibiotics.

  7. Interactions
    The gut microbiome is a complex ecosystem shaped by interactions between the different microorganisms and the host. These interactions can have a major impact on the overall health and well-being of the host.

The gut microbiome is a complex and dynamic system that is still being studied to understand fully. The knowledge about the gut microbiome is continually evolving and new research is shedding light on the role of the gut microbiome in human health.

 

What are the key dietary elements for a healthy gut microbiome?

Here are some key dietary elements that are important for a healthy gut microbiome:

  1. Dietary Fibre
    Fibre is a crucial dietary element for maintaining a healthy gut microbiome. It serves as a food source for beneficial gut bacteria, promoting the growth of healthy gut bacteria and helping to keep harmful bacteria in check.

    RNA provides 30g of dietary fibre per 2,000kcal.

  2. Prebiotics
    Prebiotics are non-digestible carbohydrates that are fermented by gut bacteria, promoting the growth of beneficial bacteria. They can be found in foods such as fruits, vegetables and grains.

    RNA provides 20g of prebiotics per 2,000kcal.

  3. Probiotics
    Probiotics are live microorganisms that are similar to beneficial microorganisms found in the gut. They can be consumed through fermented foods such as yogurt, kefir, sauerkraut, kimchi, and miso.

  4. Plant-based foods
    Plant-based foods, such as fruits, vegetables, nuts, and seeds, are rich in fibre, prebiotics, and antioxidants that promote the growth of beneficial gut bacteria and support gut health.

    RNA provides 8 servings of vegetables and fruit per 2,000kcal.

  5. Healthy fats
    Healthy fats, such as those found in olive oil, avocado, and fatty fish, are essential for maintaining the gut barrier, which helps to protect the gut microbiome from harmful substances.

    RNA provides health fats from natural wholefood sources.

Every gut microbiome is unique and there is no one-size-fits-all diet for a healthy gut microbiome. A diet rich in whole foods, including a variety of fruits, vegetables, whole grains, and lean proteins, and low in processed foods is a good starting point for promoting a healthy gut microbiome.

 

    What are the types of dietary fibres?

    There are two main types of dietary fibres: soluble and insoluble fibres:

    Soluble fibres
    Soluble fibre is known to have a number of beneficial effects on digestion. When consumed, it absorbs water and forms a gel-like substance in the gut. This gel-like substance can help slow down food movement through the digestive system, which can help promote feelings of fullness and regulate bowel movements.

    Soluble fibre can also help to regulate blood sugar levels by slowing down the absorption of carbohydrates. This can help to prevent rapid spikes in blood sugar, which can be beneficial for people with diabetes or other conditions that affect blood sugar regulation.

    In addition, the fermentable nature of soluble fibres can promote the growth of beneficial bacteria in the gut; this process is called fermentation. This fermentation process produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut health by increasing the gut barrier, producing SCFAs, and modulating the immune system.

    Another benefit of soluble fibre is that it can help lower cholesterol levels by binding bile acids in the gut and removing them from the body. This can help to lower the levels of LDL (bad) cholesterol in the blood, which can reduce the risk of heart disease.

    Overall, the effects of soluble fibre on digestion are to promote feelings of fullness and regulate bowel movements, regulate blood sugar levels, improve gut health and lower cholesterol levels. It is important to consume a variety of soluble and insoluble fibres in order to get the maximum benefits for your health.

    Insoluble fibres
    Insoluble fibre is known to have a number of beneficial effects on digestion. When consumed, it does not dissolve in water and instead passes through the digestive system relatively unchanged. This can help to promote regular bowel movements and prevent constipation.

    Insoluble fibre can also help keep the digestive system healthy by promoting food movement through the gut and preventing the build up of toxins and waste products.

    Insoluble fibre can also help to promote a healthy gut microbiome. The undigested nature of insoluble fibre makes it a good food source for the beneficial bacteria that live in the colon, thus helping to promote the growth of these bacteria, which are important for maintaining a healthy gut.

    Insoluble fibre can also help lower the risk of some types of cancer, such as colon cancer, by promoting regular bowel movements and removing toxins and waste products from the colon before they can cause damage.

    Overall, insoluble fibre's effects on digestion promote regular bowel movements, prevent constipation, maintain a healthy gut and lower the risk of some types of cancer. It is important to consume a variety of soluble and insoluble fibres to get the maximum benefits for your health.

     

    What are prebiotics?

    Prebiotics are non-digestible carbohydrates that are fermented by the beneficial bacteria in the gut. They promote the growth and activity of these beneficial bacteria, known as probiotics, which can help to improve gut health.

    Prebiotics can be found in various foods such as fruits, vegetables, whole grains and legumes. Some examples include inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS).

    When consumed, prebiotics are not digested in the small intestine and reach the colon, where they are fermented by bacteria in the gut. This fermentation process produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which can help to improve gut health. SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

    Prebiotics have also been shown to promote the growth of beneficial bacteria in the gut, such as Bifidobacterium and Lactobacillus. These bacteria play an important role in maintaining a healthy gut by producing SCFAs, improving gut barrier function, and modulating the immune system.

    A diet rich in prebiotics can help to promote a healthy gut microbiome, which may lower the risk of chronic diseases such as obesity, type 2 diabetes, and inflammatory bowel disease. They can also improve digestion and bowel regularity, as well as boost the immune system.

    It is important to note that prebiotics should not be confused with probiotics, which are live microorganisms consumed for their beneficial effects on health. While prebiotics act as food for probiotics, probiotics are not the same as prebiotics. Both prebiotics and probiotics are important for a healthy gut microbiome and may provide optimal benefits when consumed together.

     

    Which prebiotics does Radix RNA include in its Microbiome Complex’s?

    Radix Nutrition Architecture (RNA) focuses on including a wide range of prebiotics that have been scientifically shown to benefit microbiome health. Radix continuously improves RNA to take in to account a wider range of prebiotics for an even greater positive effect on the gut health the microbiome.

    So far Radix includes the following sources of prebiotics:

     

    Proanthocyanidins (PAC)

     

    Proanthocyanidins (PAC)
    PACs are a type of flavonoid compound that have been found to have prebiotic properties. These compounds are found in many fruits, vegetables, nuts, and seeds. PACs are particularly abundant in certain fruits such as cranberries, grapes, and blueberries, as well as in nuts and seeds such as hazelnuts and pecans. They are also found in tea and chocolate.

    PACs are considered prebiotics because they can promote the growth of beneficial bacteria in the gut, such as Bifidobacterium and Lactobacillus, which play an important role in maintaining a healthy gut. PACs are fermented by gut bacteria which produce short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Resistant Starch (RS)


    Resistant Starch (RS)
    Resistant starch is a type of dietary fibre that is resistant to digestion in the small intestine and, instead, reaches the colon, where gut bacteria ferment it. Resistant starch is considered a prebiotic because it selectively stimulates the growth of beneficial bacteria within the gut, promoting a healthy gut microbiome. Resistant starch is found in unripe bananas, cooked and cooled potatoes, legumes, whole grains and various other foods.

    When resistant starch reaches the large intestine, it is fermented by gut bacteria, which produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Pectin (PEC)


    Pectin (PEC)
    Pectin is a complex carbohydrate made up of chains of sugar molecules. It is considered a prebiotic because it selectively stimulates the growth of beneficial bacteria in the gut. Pectin is a dietary fibre found in many fruits, especially citrus fruits like oranges, lemons, apples and berries.

    Pectin is not digested in the small intestine and reaches the colon, where it is fermented by gut bacteria. The fermentation process produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Arabinoxylan (AX)


    Arabinoxylan (AX)
    Arabinoxylan is a complex carbohydrate made up of a xylan backbone that is substituted with arabinose residues. Arabinoxylan is considered a prebiotic because it selectively stimulates the growth of beneficial bacteria in the gut. Arabinoxylan is a dietary fibre found in cereal grains, rice, flaxseed, bamboo shoots, and other foods.

    Arabinoxylan is not digested in the small intestine and reaches the colon, where it is fermented by gut bacteria. The fermentation process produces short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, which have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Galactooligosaccharides (GOS)


    Galactooligosaccharides (GOS)
    Galactooligosaccharides are a type of prebiotic carbohydrate that is made up of chains of simple sugars called galactose. GOS are considered prebiotics because they selectively stimulate the growth of beneficial bacteria in the gut, promoting a healthy gut microbiome. These compounds are found in beetroots, black beans, pumpkin, chickpeas, green peas and many other foods.

    When GOS reach the large intestine, they are fermented by gut bacteria, which leads to the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Inulin


    Inulin
    Inulin is a complex carbohydrate made up of chains of fructose molecules. Inulin is considered a prebiotic because it selectively stimulates the growth of beneficial bacteria in the gut, promoting a healthy gut microbiome. Inulin can be found in various plants, including chicory root, agave, bananas, onions, and asparagus.

    When inulin reaches the large intestine, it is fermented by gut bacteria, which leads to the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

    Fructooligosaccharides (FOS)


    Fructooligosaccharides (FOS)
    Fructooligosaccharides are a type of prebiotic carbohydrate that is made up of chains of simple sugars called fructose. FOS are considered prebiotics because they selectively stimulate the growth of beneficial bacteria in the gut, promoting a healthy gut microbiome. They are found naturally in small amounts in some fruits and vegetables, such as bananas, onions, and garlic, and can also be produced through the enzymatic conversion of sucrose.

    When FOS reach the large intestine, they are fermented by gut bacteria, which leads to the production of short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate. These SCFAs have been shown to improve gut barrier function, modulate the immune system, and lower inflammation.

     

     

    Polyunsaturated fatty acids (PUFA)


    Polyunsaturated fatty acids (PUFA)
    PUFAs are a type of fat that is not considered a prebiotic. Prebiotics are non-digestible carbohydrates that provide food for the beneficial bacteria in the gut microbiome, whereas PUFAs are types of fats that are not digested by the human body and are not considered prebiotics.

    PUFAs are essential for human health and play an important role in maintaining overall health. They are important for cell membrane structure, regulation of inflammation and blood clotting, and are also important for the proper functioning of the immune system. They are found in foods such as fatty fish, nuts and seeds, and vegetable oils.

    While PUFAs are not considered a prebiotic, they may indirectly affect the gut microbiome. Some studies suggest that consuming a diet high in PUFAs may promote the growth of certain beneficial bacteria in the gut, which can help maintain a healthy gut microbiome.

    It's important to note that the effects of PUFAs can vary depending on the specific type and the individual's health status. Therefore, it is always best to consult a healthcare professional before making any significant changes to your diet and before taking any supplement of PUFAs.

     

    What are probiotics?

    Probiotics are live microorganisms, such as bacteria and yeasts, that are similar to the beneficial microorganisms found in the human gut. They are often referred to as "good" or "helpful" bacteria because they help maintain the gut microbiome's balance and support overall health.

    Probiotics can be found in a variety of forms, including supplements, foods, and fermented products like yogurt, kefir, and sauerkraut. They are typically consumed to increase the number of beneficial microorganisms in the gut, which can help to improve digestion, boost the immune system, and prevent the growth of harmful bacteria.

    Probiotics are particularly beneficial for people who have experienced disruptions in their gut microbiome, such as those who have taken antibiotics, experienced stress, or have a condition that affects the gut, such as irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD).

    There are many different strains of probiotics, each with their unique properties and health benefits. Lactobacillus and Bifidobacterium are two of the most widely studied probiotic strains. Lactobacillus is often found in fermented dairy products like yogurt and kefir and has been shown to improve digestion and boost the immune system. Bifidobacterium is often found in supplements and has been shown to improve gut health, reduce inflammation, and enhance the immune system.

    Probiotics can also be found in fermented foods like sauerkraut, kimchi, and kombucha, which can be a great way to introduce probiotics into your diet. However, it's worth noting that the effects of probiotics can vary depending on the specific strain of probiotics and the individual's gut microbiome.

    Probiotics have been found to be effective in treating a number of gastrointestinal disorders, including IBS, IBD, and infectious diarrhoea. They have also been found to be effective in treating a number of other conditions, including eczema, allergies, and even obesity.

    Probiotics have been found to have a positive impact on mental health as well by influencing the gut-brain axis. Studies have found that probiotics can help to reduce anxiety and depression symptoms, improve cognitive function, and even alter brain activity.

     

    What are postbiotics and metabolites?

    Postbiotics are the metabolites or by-products produced by probiotics or the gut microbiome. They include short-chain fatty acids (SCFAs), vitamins, antioxidants, and enzymes. These by-products play a key role in maintaining a healthy gut microbiome and overall health.

    Short-chain fatty acids (SCFAs) such as butyrate, acetate and propionate are the most well-known postbiotics. They are produced when probiotics ferment fibre and are a primary energy source for colonic epithelial cells. They also have anti-inflammatory properties and have been shown to improve gut barrier function, which can help to prevent the leakage of harmful substances into the bloodstream.

    Vitamins, such as Vitamin K and B12, are also postbiotics. They are produced by the gut microbiome and can be absorbed by the body. Vitamin K is essential for blood clotting, and Vitamin B12 is essential for the formation of red blood cells and the proper functioning of the nervous system.

    Antioxidants and enzymes are also considered postbiotics. These by-products have been shown to positively impact overall health, including reducing inflammation, improving gut health, and reducing the risk of certain diseases.

    Postbiotics are still a relatively new field of research, and more studies are needed to understand their mechanisms of action and health benefits fully. However, postbiotics are thought to play a crucial role in maintaining a healthy gut microbiome and supporting overall health.

    It's worth noting that the effects of postbiotics can vary depending on the specific strain of probiotics and the individual's gut microbiome.

     Some examples of gut microbiome metabolites include:

    1. Short-chain fatty acids (SCFAs)
      These are produced when probiotics ferment fibre and are a primary energy source for colonic epithelial cells. They also have anti-inflammatory properties and have been shown to improve gut barrier function.

    2. Methane and hydrogen
      These gases are produced by certain microorganisms in the gut and can be used to identify certain gut disorders, such as small intestinal bacterial overgrowth (SIBO).

    3. Indoles
      These compounds are produced by gut bacteria and have been shown to have anti-inflammatory and antioxidant properties.

    4. Phenolic compounds
      These compounds are produced by gut bacteria and have been shown to have anti-inflammatory, antioxidant and anti-cancer properties.

    5. Amino acids
      These compounds are produced by gut bacteria and are essential for the body's growth and repair.

    6. Bile acids
      These compounds are produced by the liver and are important for the digestion of fats.

    7. Tryptophan metabolites
      These compounds are produced by gut bacteria from the amino acid tryptophan and have been linked to mental health and behaviour.

    Gut microbiome metabolites play a role in maintaining the balance of the gut microbiome and support overall health. However, it is important to note that the gut microbiome is a complex system, and the production of these compounds depends on several factors, including diet, lifestyle and the presence of specific microorganisms in the gut.

    What are metabolites are considered beneficial and which are harmful?

    The human gut microbiome is one of the most fascinating areas of science in the pursuit of metabolic health. As this exciting field develops, science is increasing the understanding of how the microbiome functions and the community that calls it home. The gut microbiome is also one of the first areas being addressed with personalised nutrition.

    Below are a lists of metabolites thought to be beneficial to good health and those that are considered to be a sign of suboptimal health.

    Beneficial Metabolites:

    1. Butyrate
      Butyrate is a short-chain fatty acid (SCFA) and a by-product of fermentation in the gut microbiome. It is produced by gut bacteria when they ferment dietary fibres and is a primary energy source for colonic epithelial cells. It has anti-inflammatory properties and has been shown to improve gut barrier function, which can help to prevent the leakage of harmful substances into the bloodstream.

    2. Gamma-Aminobutyric acid (GABA)
      GABA is a neurotransmitter produced by the gut microbiome. It acts as an inhibitory neurotransmitter, reducing the activity of neurons it binds to and slowing down their firing rate. It also plays a role in regulating muscle tone, as well as promoting relaxation and sleep. It helps to balance the activity of the gut microbiome, and it may help to prevent the over-excitement of neurons. It can be found in some fermented foods and supplements, but it still needs to be determined if it directly affects gut microbiome health.

    3. Lactate
      Lactate is a by-product of fermentation in the gut microbiome, produced by gut bacteria during the breakdown of sugars. Lactate is a source of energy for the gut microbiome, and it can be used as a substrate for the production of other compounds, such as butyrate. High levels of lactate in the gut have been associated with gut disorders such as inflammatory bowel disease, but more research is needed to understand the exact relationship between lactate and the gut microbiome. Consuming lactate in fermented food like yogurt, kefir, or kimchi could be beneficial.

    4. Indole Propionic Acid (IPA)
      Indole Propionic Acid is a short-chain fatty acid (SCFA) produced by gut bacteria when they ferment dietary fibres. IPA is an important antioxidant, and it is known to have anti-inflammatory properties. It has been shown to have a protective effect on the gut lining, helping to prevent the leakage of harmful substances into the bloodstream. IPA also plays a key role in maintaining a healthy gut microbiome by promoting beneficial bacteria growth and reducing harmful bacteria growth. Therefore, IPA is an essential nutrient for the gut microbiome.

    5. Acetate
      Acetate is a short-chain fatty acid (SCFA) produced by gut bacteria during the fermentation of dietary fibres. Acetate is the most abundant SCFA found in the colon and is a primary energy source for colonic epithelial cells. It also helps to regulate the pH of the gut and may help to prevent the overgrowth of harmful bacteria. Acetate also regulates appetite and energy metabolism by interacting with the brain through the gut-brain axis. Therefore, it is an essential nutrient for the gut microbiome and overall health.

    6. Oxalate
      Oxalate is a naturally occurring compound found in certain foods, and it is also produced by gut bacteria during the metabolism of specific amino acids. Some research suggests that the gut microbiome may play a role in the metabolism of oxalate, and an imbalanced gut microbiome may contribute to the formation of kidney stones. But more research is needed to understand the exact relationship between oxalate and the gut microbiome.

    7. Propionate
      Propionate is a short-chain fatty acid (SCFA) produced by gut bacteria during the fermentation of dietary fibres. It is a primary energy source for colonic epithelial cells. Propionate has been shown to have anti-inflammatory properties and helps to regulate appetite and energy metabolism by interacting with the brain through the gut-brain axis. It also helps to regulate the pH of the gut and may help to prevent the overgrowth of harmful bacteria. It is an essential nutrient for the gut microbiome and overall health. Additionally, it can play a role in blood glucose and lipid metabolism and has been associated with a lower risk of obesity and type 2 diabetes.

    Detrimental Metabolites:

    1. Succinate
      Succinate is a metabolic intermediate produced during the breakdown of glucose by gut bacteria. Succinate is also produced as a by-product of the citric acid cycle in the mitochondria of cells. It plays a role in regulating the gut microbiome by influencing the growth and metabolism of certain bacteria. Studies have shown that succinate can regulate the immune system and modulate the production of inflammatory molecules. It has also been linked to the development of certain diseases, such as cancer, metabolic and neurological disorders. Therefore, the role of succinate in the gut microbiome is complex and more research is needed to understand its effects on gut health fully.

    2. Histamine
      Histamine is a biogenic amine primarily produced by gut bacteria during the fermentation of certain foods, such as fermented foods and aged cheese. Histamine is also a neurotransmitter that is involved in the immune response, regulating gut motility and playing a role in the regulation of stomach acid. High levels of histamine in the gut can cause histamine intolerance symptoms such as headaches, hives, and digestive issues. Studies suggest that gut bacteria play a role in histamine metabolism, and an imbalanced gut microbiome may contribute to histamine intolerance.

    3. Trimethylamine (TMA)
      Trimethylamine is a molecule produced by gut bacteria during the metabolism of certain foods, particularly choline-rich foods such as red meat, egg yolks and high-fat dairy products. TMA is then converted to trimethylamine-N-oxide (TMAO) by the liver, and high levels of TMAO have been linked to an increased risk of cardiovascular disease. Studies have shown that the gut microbiome plays a key role in the metabolism of TMAO, and an imbalanced gut microbiome may contribute to high levels of TMAO.

    4. Hexa-acylated Lipopolysaccharides (Hexa-LPS)
      Hexa-acylated Lipopolysaccharides are a type of bacterial cell wall component of gram-negative bacteria. It is known for its immune-stimulating properties and is found in large amounts in the gut microbiome. Hexa-LPS is recognized by toll-like receptor 4 (TLR4), which is expressed in many immune cells and is responsible for activating the innate immune system. Studies have shown that Hexa-LPS can also play a role in the development of chronic disease. The gut microbiome plays an important role in the metabolism of Hexa-LPS, and an imbalanced gut microbiome may contribute to high levels of Hexa-LPS.

    5. Gamma-Aminobutyric Acid (GABA)
      Gamma-Aminobutyric Acid is a neurotransmitter involved in the regulation of the nervous system. It is produced by gut bacteria during the fermentation of specific fibres. Low levels of GABA in the gut have been associated with anxiety, depression, and other mental health disorders. An imbalanced gut microbiome can contribute to decreased production of GABA. Therefore, maintaining a healthy gut microbiome is important to support optimal GABA levels and may promote overall mental health.

    6. Ammonia
      Ammonia is a toxic by product of protein metabolism produced by gut bacteria. High ammonia levels in the gut can cause damage to the gut lining and are associated with chronic conditions such as liver disease, kidney disease, and gut disorders. An imbalanced gut microbiome can contribute to the increased production of ammonia.

    7. Hydrogen Sulfide (H2S)
      Hydrogen Sulfide is a gas produced by gut bacteria and is known for its toxic properties. High levels of H2S in the gut have been associated with chronic inflammation and is linked to several chronic diseases such as obesity, type 2 diabetes, and cardiovascular disease. An imbalanced gut microbiome can contribute to the increased production of H2S. Therefore, maintaining a healthy gut microbiome is important to regulate H2S levels and promote overall health.