Glossary

Gut-related technical terms, briefly explained. You can also tap them directly in the chapters.

A B C D E F G H I K L M O P R S T U V

Akkermansia: A gut bacterium that lives on the mucus of the gut wall and stimulates its renewal. In studies, high levels often go along with good metabolic health. More in the chapter “The mucus layer and additives”
anaerobes: Bacteria that live without oxygen. For strict anaerobes oxygen is even toxic; they make up the large majority of the gut flora. More in the chapter “Anaerobic gut bacteria: why the good ones do not fit in a capsule”
ARFID: Avoidant/restrictive food intake disorder: someone eats too little or too narrowly, not because of body shape or weight, but out of fear of symptoms, low appetite or aversion to tastes and textures. More in the chapter “Fear of food: when your list of safe foods keeps shrinking”
Autoimmune disease: A disease in which the immune system attacks the body's own tissue, for example the thyroid in Hashimoto's or the pigment cells in vitiligo. More in the chapter “Autoimmune diseases and the gut: Hashimoto's, vitiligo, type 1 diabetes and more”
Bacteriophages: Viruses that only infect bacteria. In the gut there are probably about as many phages as bacteria, perhaps more, and they help determine which bacteria prevail. More in the chapter “Bacteriophages: the hunters in the gut”
Bile acids: Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea”
Biofilm: A community of microbes that sticks to a surface and embeds itself in a self-made protective coat, such as dental plaque. More in the chapter “Biofilms in the gut and “biofilm busters””
Breath test: After drinking a sugar solution, hydrogen and methane in the breath are measured several times. This can reveal sugar intolerances and signs of bacterial overgrowth. More in the chapter “Gut tests: what they show and what they do not”
Bristol stool form scale: A classification of stool into seven types, from hard lumps (1) to liquid (7). Types 3 and 4 are considered ideal. More in the chapter “Constipation: more than too little fibre”
Butyrate: A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids”
Calprotectin: A protein from white blood cells measured in stool. Raised levels point to inflammation in the gut. More in the chapter “Gut tests: what they show and what they do not”
CCK (cholecystokinin): A hormone from the duodenum. It is released in response to fat and protein, makes the gallbladder contract and calls up digestive enzymes from the pancreas. More in the chapter “The digestive chain: how stomach acid, bile and pancreas set each other off”
Choline: A nutrient the body needs for phosphatidylcholine and for moving fat out of the liver. Found in eggs, fish, meat, milk, soy, legumes and broccoli. More in the chapter “Bile, lipase and lecithin: what fat digestion really needs”
Clostridioides difficile: A bacterium that can spread after antibiotics and cause severe diarrhoea with its toxins. More in the chapter “After antibiotics: C. difficile and faecal transplants”
Coeliac disease: An autoimmune disease in which gluten damages the lining of the small intestine. It is diagnosed with a blood test and usually a biopsy while you are still eating gluten. More in the chapter “Lactose, fructose, gluten: making sense of intolerances”
Colostrum: The first milk after birth, rich in antibodies and growth factors. As a supplement it usually comes from cows. More in the chapter “The “leaky gut stack”: colostrum, zinc carnosine, aloe and co.”
DAO (diamine oxidase): An enzyme in the gut wall that breaks down histamine from food before it reaches the blood. More in the chapter “DAO: the enzyme that intercepts histamine from food”
Diverticula: Small pouches of the gut lining that bulge through weak spots in the colon wall. When they become inflamed, it is called diverticulitis. More in the chapter “Diverticula, haemorrhoids and fissures: what can go wrong at the end of the gut”
Dysbiosis: A microbiome out of balance, for example with less diversity. The term is vague, because a universally “healthy” microbiome has not been defined. More in the chapter “Building microbial diversity”
Elemental diet: A liquid formula of individual amino acids, simple sugars and fats that is absorbed in the upper small intestine. In SIBO it replaces all other food for two to three weeks. More in the chapter “SIBO treatments compared: rifaximin, herbs, elemental diet and faecal transplant”
Emulsifiers: Additives that mix fat and water, such as carboxymethylcellulose or polysorbate 80. Some damage the mucus layer in studies. More in the chapter “The mucus layer and additives”
Endotoxin (LPS): A component of the outer coat of certain bacteria. When it reaches the blood, it triggers inflammatory responses. More in the chapter “The gut barrier”
Faecal microbiota transplantation: Transfer of processed stool from a healthy person to restore the gut microbiota. Well supported for recurrent C. difficile infection. More in the chapter “After antibiotics: C. difficile and faecal transplants”
FODMAP: Short for fermentable sugars and sugar alcohols that are poorly absorbed in the small intestine, such as fructans, lactose, fructose and sorbitol. More in the chapter “Doing low-FODMAP right”
Gastroparesis: Delayed gastric emptying without a mechanical obstruction, with nausea, vomiting, early satiety and fullness. More in the chapter “Gastroparesis: when the stomach empties too slowly”
GLP-1: A hormone from the gut wall that controls insulin release after eating, slows the stomach and makes you feel full. Weight-loss injections mimic it. More in the chapter “GLP-1 from the gut: what bacteria do and what “natural Ozempic” cannot do”
Histamine: A messenger substance of the body that is also found in aged and fermented foods. Too much can cause headache, flushing or diarrhoea. More in the chapter “Histamine intolerance: much searched, little proven”
IgA (secretory IgA): The antibody of the mucous membranes. It is released into the gut in large amounts, where it holds germs in the mucus without causing inflammation. More in the chapter “IgA: the antibody that keeps the gut clean, and what vitamin A, D and omega-3 have to do with it”
IgE: The antibody of classic allergy. It sits on mast cells and triggers their alarm on contact with the allergen. More in the chapter “Allergies and intolerances: how the gut learns to tolerate food”
Ileum: The last section of the small intestine. It recovers bile acids, absorbs vitamin B12 and joins the colon via the ileocaecal valve. More in the chapter “Where the small intestine meets the colon: ileum, valve and caecum”
IMO (intestinal methanogen overgrowth): Too many methane-producing archaea in the gut, shown by methane of 10 ppm or more on a breath test. Often goes along with constipation. More in the chapter “Hydrogen sulfide and methane: the other gases in the gut”
Inflammatory bowel disease: Umbrella term for Crohn’s disease and ulcerative colitis: long-term, relapsing inflammation of the gut that needs medical treatment. More in the chapter “Immune system and inflammation”
Irritable bowel syndrome: Recurring abdominal pain linked to bowel movements, without tests finding another cause. Today it is understood as a disorder of gut–brain interaction. More in the chapter “The gut-brain axis”
Ketone bodies: Energy carriers that the liver makes from fat during fasting or a very low-carbohydrate diet. The brain and muscles can use them instead of sugar. More in the chapter “Longer fasting: water fasting, therapeutic fasting and fasting-mimicking”
Lecithin: A mixture of choline phospholipids, obtained from soy or sunflower. In bile it keeps cholesterol dissolved; as a capsule for fat digestion it is not proven. More in the chapter “Bile, lipase and lecithin: what fat digestion really needs”
Mast cell activation syndrome (MCAS): A rare condition with repeated attacks caused by mast cell messengers in several organs. The diagnosis needs lab evidence during an attack. More in the chapter “Mast cells: alarm cells in the gut, histamine and the disputed MCAS”
Mast cells: Immune cells beneath the skin and mucous membranes, filled with histamine and other messengers. They raise the alarm in allergies, infections and stress. More in the chapter “Mast cells: alarm cells in the gut, histamine and the disputed MCAS”
Meta-analysis: An analysis that combines the results of several studies. It is only as good as the studies it includes.
Microbiome, gut microbiota: The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity”
Migrating motor complex: A wave of muscle contractions that sweeps the stomach and small intestine empty about every one and a half to two hours when fasting. Eating interrupts it. More in the chapter “Intermittent fasting and meal timing: 16:8, 5:2 and Ramadan”
Molecular mimicry: A bacterium or virus carries a protein that resembles one of the body's own. Immune cells fighting the germ can then accidentally attack the body's own tissue as well. More in the chapter “Autoimmune diseases and the gut: Hashimoto's, vitiligo, type 1 diabetes and more”
Mucus layer: A gel layer of mucins on the gut wall that keeps bacteria at a distance. In the colon, the inner layer is almost free of microbes. More in the chapter “The mucus layer and additives”
Mycotoxins: Toxins from moulds, such as aflatoxins or deoxynivalenol, taken in mainly through mouldy or contaminated food. More in the chapter “Mould: mycotoxins in food and damp in the home”
Off-label: An approved medicine is prescribed for a disease or at a dose for which it is not approved. This is permitted in many countries, but more responsibility lies with the doctor. More in the chapter “Low-dose naltrexone (LDN): hope, studies and limits”
Oral tolerance: The ability of the immune system to tolerate food protein taken up via the gut as harmless, mediated mainly by regulatory T cells. More in the chapter “Allergies and intolerances: how the gut learns to tolerate food”
Oxalate: Plant compound found e.g. in spinach, rhubarb and nuts. Binds to calcium in the gut and is excreted. Too much in the urine can form kidney stones. More in the chapter “Oxalate, salicylate, lectins: hidden culprits or internet myth?”
Placebo: A dummy treatment without an active ingredient. Comparing with it shows how much a remedy achieves beyond expectation and chance.
Postbiotics: Inactivated microbes or their components and metabolites, which can still have an effect. More in the chapter “Butyrate and other short-chain fatty acids”
POTS: Postural orthostatic tachycardia syndrome: the heart rate rises by at least 30 beats per minute on standing without a drop in blood pressure, with light-headedness and exhaustion. More in the chapter “POTS and hypermobility: when circulation and connective tissue drag the gut along”
Prebiotics: Food components, usually certain fibres, that specifically feed beneficial gut bacteria, such as inulin or GOS. More in the chapter “Prebiotics that build up gently”
Probiotics: Live microorganisms that are meant to provide a benefit in sufficient amounts. The effect depends on the individual strain. More in the chapter “Using fermented foods well”
Prokinetics: Drugs that stimulate movement of the stomach and gut, such as prucalopride or low-dose erythromycin. More in the chapter “Why SIBO comes back: the cleaning wave, underlying causes and prokinetics”
Proton pump inhibitors (PPIs): Acid blockers such as omeprazole or pantoprazole. They inhibit the acid pump in the stomach lining. More in the chapter “Acid blockers (PPIs): what they change in the gut and how to stop them properly”
Randomised trial: A study in which chance decides who gets the treatment and who does not, for comparison. This makes results particularly reliable.
Refeeding syndrome: A dangerous shift of blood salts such as phosphate and potassium when someone eats again too quickly after long starvation or malnutrition. More in the chapter “Longer fasting: water fasting, therapeutic fasting and fasting-mimicking”
Rome V criteria: Internationally used criteria with which experts classify IBS, functional constipation and stomach complaints based on symptoms. Rome V (2026) is the current version; it replaced the Rome IV criteria of 2016. More in the chapter “The gut-brain axis”
Secretin: A hormone from the duodenum. It is triggered by stomach acid and makes the pancreas and bile ducts release bicarbonate to neutralise it. More in the chapter “The digestive chain: how stomach acid, bile and pancreas set each other off”
Short-chain fatty acids: Acids such as acetate, propionate and butyrate that gut bacteria make from fibre. They nourish the gut wall and act throughout the body. More in the chapter “Butyrate and other short-chain fatty acids”
Small intestinal bacterial overgrowth (SIBO): Too many bacteria in the small intestine, where normally few live. Bloating and diarrhoea are typical; it is usually diagnosed with a breath test. More in the chapter “When the small intestine is too densely colonised”
Sphincter of Oddi: Ring muscle where the bile duct and pancreatic duct open into the duodenum. It controls the outflow of bile and pancreatic juice. More in the chapter “Life without a gallbladder: diarrhoea, fat and symptoms after surgery”
Sugar alcohols (polyols): Sweeteners such as sorbitol, xylitol or maltitol, which also occur in fruit. They are barely absorbed and can cause bloating and diarrhoea. More in the chapter “Lactose, fructose, gluten: making sense of intolerances”
Tight junctions: Protein connections that hold the cells of the gut wall tightly together. They determine what can pass between the cells. More in the chapter “The gut barrier”
TUDCA: Short for tauroursodeoxycholic acid, a bile acid. Not an approved medicine in Europe or the USA; sold as a capsule, but with no proven benefit for fat digestion. More in the chapter “Bile, lipase and lecithin: what fat digestion really needs”
Ursodeoxycholic acid: A bile acid used as a medicine, prescription-only in many countries. Approved among other things for dissolving gallstones and for certain liver diseases. More in the chapter “Bile, lipase and lecithin: what fat digestion really needs”
Vagus nerve: The tenth cranial nerve and the most important nerve of the rest-and-digest system. It connects the brainstem and the abdominal organs; most of its fibres tell the brain what is happening in the gut. More in the chapter “The vagus nerve: the data line between belly and head”