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Gut index

We have explained everything you need to know about the intestine.


The microbiome is the totality of all microorganisms (bacteria, archaea, fungi, viruses) that colonise a macroorganism (human, animal, plant).

The intestine is a muscular tube that extends from the stomach to the anus and forms the longest digestive organ. In addition to digestion and the ingested food, the intestine is also essential for our immune system and for our psychological well-being.

Is the penetration of a substance into a cell or tissue through a boundary layer.

Glucose is a carbohydrate and the most abundant simple sugar in nature. In the body, it is serves as fuel for many metabolic processes and provides the body with energy. However, too much glucose consumption can promote insulin resistance and obesity.

Fructose (also known as fruit sugar) is a naturally occurring carbohydrate and a simple sugar. Fructose provides energy to the body and can be converted to glucose. However, too much fructose consumption can promote insulin resistance, fatty liver and obesity.

Lactose is the sugar found in milk. Lactose is a double sugar and therefore consists of two single sugar molecules (glucose + galactose). The enzyme lactase is needed to digest lactose. If there is too less lactase in the body, lactose intolerance occurs.

Intolerance is caused by a lack or malfunction of the body’s own enzymes or transport proteins. As a result, food components, for example, cannot be digested and absorbed in the body. In case of intolerance, there is no reaction from the immune system. Symptoms of intolerance include diarrhoea, flatulence, nausea or abdominal pain.

In case of allergy, the body’s immune system overreacts to a foreign substance that is normally harmless, such as a component of food. This exacerbated reaction of the immune system can lead to rashes, watery eyes and a runny nose, swelling of the airways or ultimately to an anaphylactic shock. Some allergies can be life-threatening.

The glycemic load shows how much the carbohydrates in a specific foodstuff cause the blood sugar to rise and in what quantity this carbohydrate occurs in the food. The number therefore refers to 100g of the food.

The glycemic index shows how strongly the carbohydrates in a specific foodstuff cause the blood sugar to rise. The smaller the number, the slower the blood sugar rises after eating the foodstuff. The number refers to 100g of the carbohydrate.

Insulin is a hormone that is produced by the pancreas. Insulin ensures that our blood sugar can be absorbed into the cells and that the blood sugar is lowered again after a meal, for example. When the sugar concentration in the blood is too high, it can lead to many diseases.

Insulin sensitivity describes how quickly cells respond to insulin and take up sugar from the blood.
An improvement in insulin sensitivity means that the body’s cells absorb sugar from the blood more quickly. Sugar is a source of energy for cells.

Insulin resistance refers to a reduced or a total lack of effect of insulin. Either the body needs larger amounts of insulin, or it no longer manages to move the sugar out of the blood at all.

The term essential means that something is absolutely necessary for the body, but cannot be produced by the body itself. Therefore, it must be acquired through nutrition.

Digestion is the mechanical and chemical breakdown of ingested food into smaller components. These components can be absorbed into the body and serve as an energy source.

The brystol scale is a chart that represents different forms and consistencies of human stool. It serves as an assessment scheme for health.

Bacteria are small living organisms consisting of only one cell. They have their own DNA and are self-sufficient. Bacteria occur mainly in three forms: bacilli (rods), cocci (balls) and spirilli (spirals). Bacteria have many functions in the body such as vitamin production, protection against diarrheal pathogens, production of short-chain fatty acids to strengthen the immune system and absorption of minerals.

Archaea are small organisms that consist of one cell and do not have a nucleus. They often live in extreme environments characterized by intense heat or high salinity.

Viruses are small biological structures that have no metabolism of their own and can only reproduce by hijacking foreign cells. Therefore, they do not count as living organisms. Viruses are thus inactive until they encounter a host. Only then do they inject their genetic material and are able to multiply.

Fungi are small living organisms that consist of one cell and have a cell nucleus. Most fungi are static, and cannot move far on their own. However, fungi spread their cells through spores in small capsules. Some fungi can be beneficial to health, but others can cause disease. A well-known example is Aspergillus flavus, which produces aflatoxin, which is toxic to humans when present in high amounts in foodstuffs.

Pathogens are disease-causing organisms and viruses or influences (such as ionising radiation) that promote disease.

Taxonomy is a systematic classification of living organisms into different categories. Intestinal bacteria are taxonomically subdivided in the same way as we humans (Homo sapiens). The order of hierarchy is as follows: Kingdom, Phylum, Class, Order, Family, Genus and Species. myBioma identifies bacteria down to the lowest level, the “species”.

Species are different types of a genus.


Actinobacteria are gram-positive bacteria and contribute to the maintenance of the intestinal balance. They appear to be associated with ulcerative colitis.

Bacteroidetes are associated with weight loss in humans. They produce butyrate, counteract inflammation, and support the intestinal mucosa. Bacteroidetes are promoted by resistant starch and inhibited by high-fat diets.

Firmicutes are gram-negative bacteria and carry low cytosine and guanine levels in their DNA. A high-fat content in the diet is know to promote the growth of Firmicutes.

Proteobacteria are gram-negative bacteria. They seem to be associated with chronic intestinal diseases. A high-fat diet seems to increase Proteobacteria.

Verrucomicrobia are difficult to cultivate and make up only a small percentage of the total bacterial composition in the intestine compared to the previous 4 bacterial phyla.

Lactobacilli have a positive effect on cholesterol levels and inflammation. To boost the growth of Lactobacilli, you can use garlic, blueberries, cooled potatoes and cold chickpeas.

Akkermansia has been found to help with weight loss, strengthen the intestinal barrier and protect against leaky gut, irritable bowel syndrome and liver disease. They are inhibited by high-fat diets and promoted by cranberries, linseed oil and grape juice.

Bacteroides metabolise polysaccharides, animal protein and saturated fatty acids. They protect against inflammation, leaky gut and irritable bowel syndrome. Bacteroides seem to have a negative effect on the gut-skin axis. They love protein and abhor carbohydrates, especially inulin.

Bifidobacteria are gram-positive and change the pH value in the gastrointestinal tract. Bifidobacteria support weight loss and help keep pathogens at bay. They also have a positive effect on inflammation, irritable bowel syndrome and leaky gut. These bacteria metabolise milk into lactate. Bifidobacteria are promoted by starch, inulin, linseed oil and green tea. A low carb diet inhibits this genus of bacteria.

Faecalibacteria metabolise insoluble dietary fibre to short-chain fatty acids (SCFA) and form butyrate. They protect against leaky gut, irritable bowel syndrome and cardiovascular diseases. Faecalibacteria have a positive effect on the gut-liver as well as the gut-brain axis. They are promoted by black salsify, jerusalem artichokes, bananas and psyllium husks and inhibited by a low-carb diet.

Ruminococcus produce enzymes to break down indigestible carbohydrates and degrade mucous proteins of the intestinal mucosa. They can relieve infectious diarrhoea. Ruminococci are associated with ulcerative colitis, Chron’s disease, psoirasis and irritable bowel syndrome. They can negatively affect the gut-liver axis and positively affect the gut-brain axis.

Prevotellare are very good carbohydrate utilisers, they primarily break down sugar-protein complexes of the mucus of the intestinal mucosa. Prevotella-bacteria sprotect against psoriasis and cardiovascular diseases and favour liver diseases. This bacterial genus produces thiamine and folic acid. Carbohydrates increase Prevotella growth, whereas protein does the opposite.

Collinsella decrease the expression of tight junctions. They are associated with leaky gut and the gut-skin axis. This bacterial genus has a pro-inflammatory effect by promoting epithelial production of pro-inflammatory cytokines, such as IL-17A, CXCL1 and CXCL5. Sleep deprivation increases the growth of Collinsella.

Roseburia mainly break down insoluble dietary fibre and produce buyrat. They protect against cardiovascular disease, leaky gut and inflammation. Starch stimulates bacterial growth and a very low carbohydrate diet inhibits this genus of bacteria.

Desulfovibrio are potent hydrogen sulphide producers and appear to be involved in the development of intestinal and cardiovascular disease. They are promoted by a high-fat and high-protein diet. Inulin and starch inhibit Desulfovibrio bacteria.


Butyrate is a short-chain fatty acid produced by bacteria in the large intestine. Carbohydrates that cannot be digested in the small intestine are converted into short-chain fatty acids in the large intestine by the bacteria located there. Functions of butyrate include: maintaining the intestinal barrier, strengthening the immune system, stabilising blood sugar levels, protecting against inflammation-related diseases and influencing our satiety.

Diversity is made up of species richness and species equality and describes how diverse our intestinal colonisation is. The more different microorganisms we harbour, the higher the resistance of the microbiome.

Species evenness describes how often a bacterial species occurs in comparison to other bacterial species. The higher the species evenness the more balanced the different bacteria are distributed between the species.

The Firmicutes to Bacteroidetes ratio describes the calorie intake. A high. Firmicutes to Bacteroidetes ratio is often associated with obesity, as Firmicutes can store excess calories from indigestible fibre as a reserve. A low ratio is often associated with being underweight, as calorie utilisation is poorer.

Three enterotypes are distinguished. The enterotype describes which bacterial genus dominates in the intestine. Among other things, the enterotype is shaped by our diet and influences which food components can be utilised well in the body. However, genetics also play a decisive role.

In enterotype 1, Bacteroides are the dominant genus of bacteria. This type is often found in people who eat a diet rich in meat, protein and saturated fats.

In enterotype 2, Prevotella are the dominant bacterial genus. This type is often found in people who eat a vegetarian diet high in carbohydrates.

In enterotype 3, Ruminococcus is the dominant bacterial genus. This type is often found in people who eat a mixed and balanced diet.

Dysbiosis describes an imbalance in the microbiome.

Mucus is a viscous, organic secretion that is secreted mainly by mucous membranes. The mucus layer covers the mucous membranes as a fine film and protects them from dehydration, foreign particles and makes them more slippery.

Mucosa is the name given to the inner lining of the intestine, the intestinal mucosa. It is an important barrier and only allows certain substances to enter our body. It also forms the mucus layer and can produce the body’s own antibiotics (defesins).

Tight junctions are located between the mucosa cells of the intestinal mucosa. Tight junctions provide a tight barrier against pathogenic germs and bacteria or toxins.

Enterotoxins are proteins. When a bacterium decays, parts of lypolysaccharides are secreted and have a toxic effect. These parts are called endotoxins. These toxins can have a negative effect on the intestine and cause symptoms such as traveller’s diarrhoea.

Lipopolysaccharides are so named because they consist of components similar to fat (lipo) and sugar (polysaccharides). They can be used to recognise bacteria because they act as antigens. Lipolysaccharides are located in the outer membrane of gram-negative bacteria.

The intestinal barrier protects against toxins and pathogens from entering the bloodstream from inside the intestine. The intestinal barrier includes those intestinal bacteria that prevent pathogenic bacteria from colonising. Furthermore, the thick layer of mucus formed by mucosal cells in the intestine protects the intestine against pathogens. Tight junctions between the mucosal cells provide a tight barrier against toxins or pathogens. The immune defence cells located in the intestinal wall are also part of the intestinal barrier.

The intestinal mucosa and skin both have contact with the environment and protect the organs from pollutants. Both harbour bacteria and can become inflamed. The intestine and skin contain nerve fibres and communicate via hormones, immune system and metabolism. An imbalance of intestinal bacteria can have a negative effect on the skin.

The gut-brain axis describes the complex communication between the gut and the brain and vice versa. The gut-brain axis is related to the stress axis. The neuroendocrine system plays an important role in the stress response by means of the stress axis (= hypothalamus-pituitary-adrenal axis). If the communication between the gut-brain axis is disturbed, this can have a negative effect on the psyche and well-being.

An imbalance of the microbiome can negatively affect liver metabolism. It can lead to bile acid, fat digestion problems or fatty liver. If the function is disturbed, bacteria can transport lipolysaccharides, migrate through the intestinal wall and promote inflammatory messengers in the liver.

If an imbalance of those intestinal bacteria dominates that break down the mucus more, this can lead to a reduction of the intestinal barrier and thus to “leaky gut”. “Leaky gut” describes the loosening of the tight junctions between the mucosal cells. Toxins can penetrate through the resulting gaps and enter the bloodstream.

Irritable bowel syndrome (IBS) is a functional disorder of the digestive system. IBS is one of the chornical recurrent systemic disorders of the gastrointestinal tract.

SIBO stands for “Small Intestinal Bacterial Overgrowth” and describes a bacterial overgrowth in the small intestine that is 100-fold increased. With SIBO, bacteria are found that are (hardly) present in healthy people, as bacteria from the large intestine penetrate into the small intestine.

The composition of the microbiome influences insulin levels. Bacteria can have a positive or negative influence on insulin levels. Intestinal bacteria that ferment indigestible food components have a positive influence on insulin balance, whereas those bacteria that promote chronic inflammation disrupt the feeling of satiety and have a negative influence on insulin balance.

FODMAP stands for “fermentable oligosaccharides, disaccharides, monosaccharides and polyols” and describes certain sugar and alcohol compounds contained in food. Intestinal bacteria ferment FODMAP, which can produce gases. This causes discomfort in people who suffer from irritable bowel syndrome, for example. A low-FODMAP diet can relieve these symptoms.

Hashimoto’s is a chronic thyroid disease where the body’s immune system produces antibodies against thyroid proteins. In the long run, this can lead to hypothyroidism (underactive thyroid). Small intestinal bacterial overgrowth (SIBO) and “leaky gut” can be related to Hashimoto’s.

The thyroid gland looks like a butterfly and is located below the larynx. It is a vital hormone gland and produces more or less hormones depending on the situation. The thyroid gland influences growth, metabolism and various bodily functions. The composition of the microbiome affects the availability of essential micronutrients such as iodine, iron, copper, selenium, zinc and vitamine D, which play an important role for the thyroid gland.

Chronic inflammatory joint diseases include rheumatoid arthritis. It is an autoimmune disease because the body fights against its own cell structures, which leads to constant inflammation and destruction of the body’s own joints. Bacterial imbalances and “leaky gut” play an important role here, as they throw the immune system out of balance.

Inflammatory bowel diseases (IBD) are chronic recurrent systemic diseases of the gastrointestinal tract. These diseases include irritable bowel syndrome (IBS), Crohn’s disease, Colitis ulcerosa. The symptoms of IBD are accompanied by severe abdominal pain and even bloody diarrhoea. The causes are not yet fully understood, but it appears that intestinal dysbiosis is associated with the development of IBD.

Inflammation is the body’s response to unwanted pathogens and pathogenic organisms (parasites, viruses, fungi or bacteria). Bacteria can be anti-inflammatory as well as pro-inflammatory. For example, pro-inflammatory bacteria increase “leaky gut”, which allows toxins from bacteria to cross the intestinal barrier into the bloodstream and promote inflammation.

Healthy aging is a continuous process of optimising the possibilities for improving and maintaining mental and physical health. Healthy aging describes the preservation of quality of life as well as independence throughout the life course. From birth to old age, the microbiome plays an important role in the regulation and function of the immune system. As we age, the microbiome and immune system change, which in turn can result in increased susceptibility to infectious diseases. The microbiome influences health, life expectancy and reduction of inflammation throughout the life course.

Flatulence is caused by the metabolic processes of intestinal bacteria and describes gases that accumulate in the intestine. As soon as these gases escape from the anus, one speaks of flatulence.

Flatulence occurs when the gases produced by the metabolic processes of the intestinal bacteria cannot escape through the anus. As a result, the abdomen bloats and abdominal pain can occur.

Metorism describes a bloated belly. A bloated belly occurs when the gases produced by the metabolic processes of the intestinal bacteria cannot escape through the anus. As a result, the abdomen bloats and bacu pain can occur.

Diarrhoea, also known as diarrhoea, describes increased stool frequency and liquefied stool consistency. Diarrhoea is when you have to empty your bowels more than three times a day. A distinction is made between acute and chronic diarrhoea.

Constipation, also known as ostipation, describes an impeded evacuation of stool. One speaks of constipation when the bowels can be emptied less than three times a week. A distinction is made between acute and chronic constipation. Constipation can be a side effect of diseases such as constipation, irritable bowel syndrome or other intestinal diseases.

Cholesterol is produced in our liver and absorbed through food. It functions as a necessary building block of the cell membranes of all body cells and assists in hormone production as well as the formation of bile acids.

Quorum sensing describes the ability of bacteria to learn from each other through chemical communication, to take over functions from each other and to adapt rapidly to environments. This unique ability allows bacteria to learn from each other and exchange functions.


The 16S gene contains the genetic information for building the small subunit of the ribosome of bacteria. The ribosome is responsible for building the proteins that are the tools of the cell. Therefore, the 16S gene is very important for the cell, is therefore found in every bacterium and changes only very slowly in the course of evolution. For these reasons, it is very well suited as a fingerprint of a bacterial species, and is used to study the composition of bacterial communities of all kinds.

Next-generation sequencing (NGS) is a term for the newer second- and third-generation sequencing techniques, which can evaluate significantly more DNA at once compared to the original Sanger sequencing (first generation). This has made it possible to sequence communities of microorganisms cheaply and in large quantities and thus to study bacteria that cannot be observed with traditional cultures.

Bioinformatics is concerned with extracting knowledge and insights from raw biological data. In the case of the analysis of the intestinal microbiome, for example, the DNA sequences that were read from the genetic material of the bacteria in the intestine are purified and compared with biological databases. This allows us to find out to which species a sequence belongs and which functions it can fulfil for the cell/microbiome.

To put it simply, an algorithm is a recipe or a set of instructions for solving a specific problem. An algorithm consists of predefined individual steps that lead to the optimal solution of the problem to be addressed.
Examples of algorithms in bioinformatics can be found, for example, in sequence analysis where algorithms (e.g. Smith-Waterman, Needleman-Wunsch & BLAST) are used to compare observed sequences with known sequences, e.g. from a database, and thus obtain knowledge about their origin or function.


Resistant starch forms when starch-containing foods such as potatoes, pasta and rice cool down. Resistant starch is not water-soluble and cannot be digested by the human organism in the small intestine. It is only metabolised in the large intestine by the bacteria located there and converted into short-chain fatty acids. Resistant starch promotes intestinal health, can ensure faster and longer satiety and regulate blood sugar levels.

Prebiotics, are natural fibres that cannot be digested by the human body. They are therefore only digested in the large intestine by the bacteria located there and converted into short-chain fatty acids, such as butyrate. Prebiotics promote intestinal health and the proliferation of beneficial bacteria in the colon. They also promote the absorption of minerals and trace elements in the body and increase stool volume. This prevents pathogenic germs from entering the mucosa (and subsequently the body).

Probiotics contain living, apathogenic (=non-pathogenic) microorganisms. These survive the gastrointestinal tract and can colonise the colon. This can promote intestinal health and ensure a balanced intestinal flora. Examples of probiotic foods include: yoghurt, fermented foods and drinks, tempeh and vinegar.

Dietary fibres are carbohydrates that cannot be digested by the human body’s own digestive system and therefore end up undigested in the large intestine. In the large intestine, the dietary fibres are metabolised by the bacteria located there and converted to short-chain fatty acids, such as butyrate and propionate, among other things. Dietary fibre promotes a healthy intestine, can eliminate toxins, protects our body from pathogenic germs, prevents constipation, regulates blood sugar, ensures long-lasting satiety and promotes the growth of health-promoting bacteria.

Pectin is a dietary fibre that is found in apples and carrots, for example. Pectin has a positive influence on the composition of our microbiome. Pectin can also regulate blood sugar levels, lower cholesterol levels and ensure long-lasting satiety.

The term bioactive ingredients covers secondary plant substances, dietary fibres and substances produced by lactic acid bacteria during fermentation. Bioactive ingredients are responsible for the colour, aroma and taste of plant-based foods. They are not essential for the human organism and do not provide energy. However, when consumed regularly, they can reduce the risk of some chronic degenerative diseases such as cardiovascular disease, diabetes and Alzheimer’s disease.

Protect the body from damage by scavenging highly reactive substances and particles. Highly reactive particles (radicals) attack blood vessels, cell components, protein and fats. This can lead to damage that promotes diseases such as cancer or Alzheimer’s disease.

Is a condition in the body where the concentration of free radicals is too high and at the same time there are too few antioxidants. Oxidative stress can put a lot of strain on the body and increases the risk of various diseases such as cardiovascular diseases, diseases of the nervous system as well as cognitive diseases.

When fasting, one voluntarily abstains from food or only eats food to a limited extent. Furthermore, stimulants can also be abstained from or conditionally consumed. Fasting is said to have a detoxifying and cleansing effect on the body. There are many different forms of fasting – from therapeutic fasting to juice fasting. Fasting often has a religious or cultural background.

Are very aggressive and highly reactive substances. The radicals are missing an electron. As a result, the radical reacts with other substances to steal an electron from them. The attacked substance then also becomes a radical. A chain reaction develops. Radicals attack vessels, cell components, protein and fats. This can lead to damage that promotes diseases such as cancer or Alzheimer’s disease.