Science · Basics

Microbiome 101

What lives in your gut and what does it do there? Get to know the gut microbiome, its roles in the body and the difference between probiotics, prebiotics and fermented foods.

The community that lives in your gut

The gut microbiome consists of bacteria and other microorganisms together with their genes and the environment in which they live. Its composition differs from person to person and changes throughout life.

1 : 1 approximate ratio of bacteria to human cells in the body of an adult

Trillions of bacteria live in the human body; most of them are in the large intestine

Day 1 colonisation of the gut by microorganisms starts at birth

First years a period of marked change, when the microbiome gradually comes to resemble the adult one

Microbiota refers to the microorganisms themselves; the microbiome also includes their genes and environment. The older term “gut microflora” names this community. Cell ratio: Sender et al., 2016. Development in childhood: Stewart et al., 2018.

What the microbiome does in the body

Processes fibre

Gut bacteria break down part of the fibre that reaches the large intestine. This produces short-chain fatty acids. One of them, butyrate, serves as a source of energy for the cells of the intestinal lining.

It plays a part in the development of immunity

The gut wall contains immune cells that respond to signals from the gut. Contact with microorganisms contributes to the maturation of the immune system and to how it reacts to its surroundings.

It is part of the gut–brain axis

The gut and the brain exchange signals through nerves, including the vagus nerve, hormones and the immune system. Substances produced by gut microorganisms also take part in this communication. Research is exploring what role these signals play in humans.

What shapes your microbiome

The composition of the microbiome is influenced by diet, age, environment and the medicines taken. Scientists follow the diversity of microorganisms, their relative representation and the substances they produce. These data are assessed together with the health status of the individual person.

Influences

What changes its composition

Diet composition and the amount of fibre you take in
Antibiotics, which also affect the bacteria that normally live in the gut
Age and changes in environment or lifestyle

Diet

Diversity starts on the plate

Alternate vegetables, fruit, pulses, nuts and wholegrain foods.
EFSA gives an adequate intake of fibre for adults of 25 g per day.
Add fibre to your diet gradually and make sure you drink enough fluids.

A simple start: add a portion of vegetables or pulses to today’s lunch. Fibre data: EFSA, 2010.

Why targeted probiotics Studies and research

Four questions about the microbiome

How are probiotics related to the microbiome?

The microbiome is the whole community in the gut together with its environment. Probiotics are live microorganisms that we take in from outside. Their health benefit is verified for specific strains, amounts and uses.

What do yoghurt and sauerkraut have in common?

These are examples of fermented foods. In their production, microorganisms transform the components of the food and create its typical taste. The content of live cultures also depends on further processing, for example heat treatment.

Can the microbiome be tested?

Analysis of a stool sample can show which microorganisms are present in it. It captures the state at the time of collection. The meaning of the result depends on the method used and is assessed together with diet, medicines and health status.

How quickly does the microbiome change?

Changes in diet can show up in its composition within a few days. How long they last depends on several factors, including the original composition of the microbiome and long-term eating habits.

How to read the results of microbiome studies

A study may follow the composition of the microbiome, the substances produced by its activity, or a change in health status. Our science team explains how to read these results and put them in context.

Article

Who lives in the gut, what they are doing there and whether it helps the person

Microbiomics vs. metabolomics vs. clinical endpoint

Imagine the gut microbiome as a busy city. Microbiomics takes a census of its inhabitants and shows who is in it. Metabolomics looks into the shops and factories and finds out what is being produced in the city. The clinical endpoint finally asks the most practical question: is life in this city better for its inhabitant? Each of these views brings a different part of the answer (1, 2).

In study results we often read that a certain diet, probiotic or other intervention “changed the microbiome”, “increased the level of a beneficial metabolite” or “improved clinical outcomes”. Although all three statements may sound positive, they do not mean the same thing. A biological change does not necessarily bring a health benefit that a person feels in everyday life (3, 8).

Perspective	What does it monitor?	What do we still not know from the result?
Microbiomics	Which microorganisms, genes and metabolic pathways are present in the gut	Whether the genes present are actually active and whether the change brings a health benefit
Metabolomics	What small molecules are found in stool, blood or urine	Who exactly produced the metabolite and whether its change improved health
Clinical endpoint	Pain, bloating, stool frequency and consistency, quality of life, remission or occurrence of diseases	By what biological mechanism the improvement came about

Table 1: Microbiomics, metabolomics and clinical endpoints capture different but complementary levels of information (2–6).

Microbiomics: Who lives in the gut?

Microbiome analysis examines the microorganisms that live in our gut. With it, scientists find out which bacteria are present, in what proportions and which genes or metabolic pathways they carry. It is a bit like a list of a city’s residents together with information about what occupations they might have. The mere entry “baker”, however, does not prove that the person is baking bread right now. Similarly, the presence of a microbial gene does not mean it is active at that moment (4, 5).

The situation is further complicated by so-called functional redundancy. Behind this technical name lies a fairly simple idea: different microorganisms can perform a similar role. In one large study, unrelated people shared on average only 43 % of microbial species, but as many as 82 % of metabolic pathways. The composition of their microbiome therefore differed, but its functional potential was much more similar. That is why the health of the microbiome cannot be judged solely by the presence or absence of a single bacterium (4).

Metabolomics: What is really going on in the gut?

Metabolomics does not assess microorganisms directly, but the small molecules produced during metabolism. These include, for example, short-chain fatty acids, bile acids, indoles, amino acids or products of polyphenol processing. Their abundance in stool, blood or urine creates a kind of chemical fingerprint of what was going on in the body at the time the sample was taken (5, 6).

This fingerprint is closer to function than a mere list of microorganisms, but even it does not give a complete answer. A metabolite may be produced by the microbiome or by the human body, or may come from food. It often arises only through their combined action. The result is also influenced by the last meal, medicines taken, speed of digestion and the time of sampling. Metabolomics therefore works best in combination with microbiome analysis and other data on a person’s state of health (5, 7).

An association does not necessarily mean a cause

If scientists find a certain bacterium or metabolite more often in people with specific complaints, it does not yet prove that the microorganism or substance causes those complaints. The change may also be their consequence or may be linked to diet, medication or other factors. Proving cause requires interventional studies and results that link a change in the microbiome, its function and a person’s state of health (11).

Clinical endpoint: What did the person get out of it?

A clinical endpoint is an outcome that shows how a person feels or functions. For gut health it may be a relief of pain and bloating, more regular stools, fewer days with digestive complaints or better quality of life. Even subjective complaints can be a valuable scientific outcome if they are measured using validated questionnaires and in a well-designed clinical study (2, 3).

Here we often run into a small terminological trap. A change in a bacterium or metabolite may be labelled in a study as the “primary endpoint”. The word primary, however, only means that it is the main, pre-specified outcome of the study. It does not automatically mean that a health benefit was demonstrated. A biological marker can replace a clinical outcome only when it has been reliably verified that its change predicts a change in health status. For most microbiome and metabolomic markers we do not yet have such verification (3, 8).

What if individual results point in different directions?

A good example is the low-FODMAP diet in irritable bowel syndrome. A summary of clinical studies shows that it can ease overall IBS symptoms, abdominal pain and bloating. A separate meta-analysis, however, found that during this diet there was a fall in the abundance of bifidobacteria, which are commonly regarded as a beneficial part of the microbiome. A clear change in overall microbial diversity or in the concentrations of short-chain fatty acids was not confirmed (9, 10).

It is not proof that a low-FODMAP diet is “good” according to the clinic but “bad” according to the microbiome. It shows that one isolated data point cannot capture the whole gut ecosystem or a person’s state of health. A fall in one group of bacteria does not have to cancel out clinical improvement and, conversely, even a favourable change in a metabolite does not yet guarantee relief of complaints. Results must always be interpreted together and in the context of the specific person, intervention and disease (10, 11).

So how should study results be read?

What did the scientists measure? If a study reports an “improvement in the microbiome”, look at whether it actually monitored the participants’ state of health or only a change in the proportions of bacteria. Both pieces of information are valuable, but they answer a different question (3).

How was the study designed? A result carries more weight if it was pre-specified, the study had a control group, a sufficient number of participants and also tracked diet, medication and other factors that influence the microbiome. Without this information even an interesting finding is harder to interpret (1, 12).

Do the individual layers of evidence agree? A result is more convincing if a change in the microbiome is accompanied by a change in its function and, at the same time, an improvement in health. If the results do not agree, the study does not automatically lose its value – the mechanism may be more complex than we assumed (1, 11).

One change is not the whole story

Microbiome science is not moving from one method to another, but towards linking them. The better it can follow the path from microorganisms through their metabolites to a person’s state of health, the more precisely we understand not only that something has changed, but also why and with what significance (1, 2, 11).

Scientific sources used

Schierwagen R, Carraturo F, Iyappan A, et al. Multidisciplinary Delphi consensus statement on minimal standards for clinical metadata and end points in microbiome studies. Nature Reviews Gastroenterology & Hepatology. 2026. doi: 10.1038/s41575-026-01229-1.
Marco ML, Cunningham M, Bischoff SC, et al. The ISAPP consensus statement on the definition and scope of gut health. Nature Reviews Gastroenterology & Hepatology. 2026;23:432–448. doi: 10.1038/s41575-026-01176-x.
Califf RM. Biomarker definitions and their applications. Experimental Biology and Medicine. 2018;243(3):213–221. doi: 10.1177/1535370217750088.
Visconti A, Le Roy CI, Rosa F, et al. Interplay between the human gut microbiome and host metabolism. Nature Communications. 2019;10:4505. doi: 10.1038/s41467-019-12476-z.
Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nature Metabolism. 2024;6:1225–1236. doi: 10.1038/s42255-024-01074-z.
Zierer J, Jackson MA, Kastenmüller G, et al. The fecal metabolome as a functional readout of the gut microbiome. Nature Genetics. 2018;50:790–795. doi: 10.1038/s41588-018-0135-7.
Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569:655–662. doi: 10.1038/s41586-019-1237-9.
Fleming TR, DeMets DL. Surrogate end points in clinical trials: are we being misled? Annals of Internal Medicine. 1996;125(7):605–613. doi: 10.7326/0003-4819-125-7-199610010-00011.
Black CJ, Staudacher HM, Ford AC. Efficacy of a low FODMAP diet in irritable bowel syndrome: systematic review and network meta-analysis. Gut. 2022;71(6):1117–1126. doi: 10.1136/gutjnl-2021-325214.
So D, Loughman A, Staudacher HM. Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis. The American Journal of Clinical Nutrition. 2022;116(4):943–952. doi: 10.1093/ajcn/nqac176.
Metwaly A, Kriaa A, Hassani Z, et al. A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research. Nature Reviews Gastroenterology & Hepatology. 2025;22:343–356. doi: 10.1038/s41575-025-01041-3.
Porcari S, Mullish BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology. 2025;10(2):154–167. doi: 10.1016/S2468-1253(24)00311-X.

Probiotics, prebiotics and other terms

Similar names refer to different things. This is a brief overview based on the definitions of the International Scientific Association for Probiotics and Prebiotics (ISAPP).

Probiotics

Live microorganisms that, when administered in adequate amounts, bring a health benefit. For a specific preparation, the identified strains, their amount and the evidence for the given benefit are what matter.

ISAPP consensus, Hill et al., 2014

Prebiotics

Substances that certain microorganisms in the body use, thereby bringing a health benefit. These include, for example, some types of fibre.

The “prebiotic” label requires evidence of this use as well as of a health benefit. ISAPP consensus, Gibson et al., 2017

Synbiotics

A mixture of live microorganisms and substances that are selectively used by microorganisms in the body. This combination must bring a health benefit.

ISAPP consensus, Swanson et al., 2020

Postbiotics

A preparation of inactivated microorganisms or their components with a demonstrated health benefit. Inactivated means the microorganisms are no longer alive.

A postbiotic includes microbial cells or their components. Isolated butyrate on its own is a metabolite. ISAPP consensus, Salminen et al., 2021

Fermented foods

Foods made by the targeted growth of microorganisms and the transformation of the food’s components. They include, for example, yoghurt, sauerkraut or sourdough bread.

The content of live cultures depends on processing. The “probiotic” label also requires meeting the definition of probiotics. ISAPP consensus, Marco et al., 2021

When reading a package, start with the ingredients. For probiotics, look for the strain designation and its amount in the daily dose. Research then shows what has been studied with those strains and doses.

A glossary from A to Z

Come across an unfamiliar word? Look it up in the glossary or open the explanation next to the ⓘ symbol on our science pages.

#

95 % CI: 95 % confidence interval – an interval expressing the uncertainty around an estimated value.

A

Acetate: Acetic acid, one of the most abundant short-chain fatty acids produced by gut bacteria
Acidophilic: Acidophilic is a term for microorganisms that grow and thrive best in an acidic environment with a low pH. Typical examples include lactic acid bacteria, which are key to food fermentation and the health of the gut microbiome. Opposite: Alkaliphilic (or neutrophilic/basophilic, depending on the degree) is its counterpart, characterising organisms that prefer an alkaline environment with a high pH. These microorganisms occur in specific ecosystems such as salt lakes or alkaline soils.
Adherens junction: A type of cell junction that provides mechanical cohesion between neighbouring cells of a tissue.
Aerobic: A process or organism that absolutely requires oxygen for its life and metabolism.
Allergy: An inappropriate reaction of the immune system to harmless foreign substances, in which histamine is released.
Anaerobic: A process or organism that lives and metabolises in an environment without oxygen.
Antibiotic: A medicine intended to destroy bacteria or stop their growth, but which can also disturb a person’s natural microbiome.
Antifungal: A medicine used to treat infections caused by fungi (yeasts and moulds).
Antioxidant: A substance that slows down or stops the oxidation of other molecules and helps protect cells from damage caused by free radicals.
Apolipoprotein: An apolipoprotein is a specialised protein that binds to lipids (fats) and forms transport particles with them, called lipoproteins (e.g. LDL or HDL). These proteins keep the fat particles stable in blood plasma, act as signalling molecules for receptors on the surface of cells and activate enzymes needed for the proper metabolism and transport of cholesterol in the body.
Atopic dermatitis: A chronic inflammatory skin disease, often associated with an impaired skin barrier and immune hypersensitivity.
Autoaggregation: A process in which cells of the same bacterial species or strain clump and bind together, increasing their ability to colonise surfaces and the intestinal mucosa, form protective biofilms and withstand external influences or pathogens more effectively.

B

Bacterial vaginosis: An imbalance of the vaginal microbiota caused by excessive growth of organisms other than the usual lactobacilli.
Beta-glucans: Beta-glucans are natural polysaccharides (complex sugars) made up of glucose units, found naturally in the cell walls of fungi, yeasts, cereals (especially oats and barley) and some algae. In the human body they act as important immunomodulators that activate cells of the immune system (e.g. macrophages) and, thanks to their soluble fibre structure, contribute to maintaining normal cholesterol levels and stabilising blood glucose.
Biomarker: A biomarker (biological marker) is a measurable indicator of a biological state, process or the body’s response to treatment, used for the objective assessment of health or the presence of disease. It is used in medicine for early diagnosis, monitoring the course of diseases, predicting risk and for precisely directing or checking the effectiveness of therapy. Examples are levels of specific proteins, genes, enzymes or metabolites in the blood or other body fluids
Butyrate: Butyric acid, an important product of the bacterial fermentation of fibre, which nourishes the cells of the gut wall and has an anti-inflammatory effect.

C

Caco-2 cells: A stable line of human colon adenocarcinoma cells that differentiate under laboratory conditions into a polarised monolayer resembling the enterocytes of the small intestine, which is why they are widely used to study intestinal permeability, drug transport and interactions with the gut microbiome.
CCL17/TARC: A chemokine (signalling protein) that attracts immune cells (especially Th2 lymphocytes) to sites of inflammation and serves in medicine as an important blood biomarker monitoring the activity and severity of allergic diseases, especially atopic dermatitis.
CD4+: A type of white blood cell (helper T lymphocytes) carrying the specific protein CD4 on its surface, which play a key role in coordinating the immune response and activating other immune cells in the fight against infections.
Chemokine: A small signalling protein (a type of cytokine) that acts as a chemical attractant for immune cells and directs their movement to sites of inflammation, infection or injury in the body.
Chemotherapeutic agent: A drug used to treat infections or cancer that effectively destroys or stops the growth of rapidly dividing cells.
Cholesterol: Cholesterol is an essential waxy, lipid-type substance that the body produces mainly in the liver and also takes in from food. It is a key building block of cell membranes and is used to make sex and stress hormones, vitamin D and bile acids. It is carried in the blood by lipoproteins, and the balance between its “good” (HDL) and “bad” (LDL) transport is decisive for the health of the cardiovascular system.
Targeted modulation of the gut microbiome: Strategic influencing of the composition of the microbiome by means of beneficial bacteria/probiotics or diet, for the purpose of treating or preventing specific health problems.
Clausin: Clausin is an antimicrobial substance produced by some strains of Bacillus clausii. It belongs to the lantibiotics and acts against selected gram-positive bacteria.
Cohen’s d: A statistical indicator of effect size that expresses the size of the observed difference in standardised form.
Gut barrier: A functional layer made up of epithelial cells and mucus that prevents pathogens and toxins from passing from the gut into the bloodstream.
Gut microbiota: A community of microorganisms living in the gut environment.
Gut motility: Movement of the intestines caused by muscle contractions, which moves food through the digestive tract.
Intestinal permeability: A measure of how permeable the intestinal wall is. Normally it selectively lets nutrients and water through, while impaired integrity allows toxins and bacteria to pass unwantedly into the bloodstream.
Intestinal epithelium: A single-layer lining of the inside of the intestines that absorbs nutrients and acts as a barrier against harmful substances.
Gut microbiome: The collection of gut microorganisms, their genetic material, their functions and their relationships with the host’s environment.
Crohn’s disease: A chronic inflammatory disease that can affect any part of the digestive tract from the mouth to the rectum, characterised by deep inflammation of the gut wall and closely linked to the immune response and the gut microbiome.
Bacterial cross-feeding: A relationship in which the metabolic waste products of one group of bacteria serve as food or an energy source for another group
Cytokine: A small signalling protein released by cells of the immune system to communicate and coordinate the inflammatory response.
Cytokine response: A cytokine response is a complex immune reaction of the body, controlled by signalling proteins (cytokines) that ensure communication between cells of the immune system. These molecules coordinate inflammatory processes, cell division and the body’s defences in response to infections, tissue damage or other stimuli. If activation is excessive and uncontrolled, it can progress to a so-called cytokine storm, which leads to serious damage to the body’s own tissues and organs.

D

Deconjugated bile acids: Deconjugated bile acids are primary bile acids stripped of their bond to amino acids (glycine or taurine) through the action of bacterial enzymes in the gut. This process, known as deconjugation, changes their physicochemical properties: free bile acids are reabsorbed more easily or undergo further conversion into secondary bile acids. Their excessive presence in the small intestine may signal a microbiome imbalance or impaired function of the digestive tract.
Diversity: A measure of the diversity of microorganism species in the microbiome; higher diversity is generally associated with better health.
Dopamine pathway: A nerve pathway that uses dopamine and plays a key role in the reward system, motivation, the experience of pleasure and the control of movement; its activity is also influenced by signals from the gut microbiome.
dp-ucMGP (dephospho-uncarboxylated matrix Gla protein): The inactive form of matrix Gla protein in the blood, whose raised level serves as a sensitive and reliable biomarker of vitamin K deficiency in the body.
Double-blind study: A design in which neither the participant nor the researcher assessing the outcomes knows, during the study, who is receiving the intervention under study and who is receiving the control intervention.

E

Emollients: Softening and moisturising preparations (creams, ointments, oils) that soften and smooth the skin, help restore its protective barrier and reduce moisture loss, which is key especially in the treatment of atopic dermatitis.
Endotoxaemia: The presence of bacterial toxins (such as LPS) in the blood, which triggers chronic systemic inflammation.
Endpoint: A pre-specified outcome or parameter by which the research question of a study is evaluated.
Enteropathogen: An enteropathogen is an infectious microorganism (bacterium, virus or parasite) that, after entering the digestive tract, causes a disease affecting the intestinal mucosa. These pathogens cause inflammatory processes that most often manifest as diarrhoea, abdominal pain, nausea and fever. Typical examples include specific strains of bacteria such as Escherichia coli or Salmonella.
Enzyme: A protein that works as a biological catalyst, that is, it speeds up chemical reactions in the body without being used up itself.
Eradication therapy: Targeted treatment (most often a combination of antibiotics and other medicines) aimed at the complete removal and eradication of a specific pathogenic microorganism, for example the bacterium Helicobacter pylori, from the body.
ex vivo: An experiment carried out on tissues or cells removed from an organism and maintained under body-like conditions.
Expression (gene expression): The process by which genetic information from DNA is turned into functional molecules (mainly proteins), thereby controlling the formation and activity of cellular structures.

F

Fermentation: A process in which microorganisms (bacteria, yeasts) break down organic substances, for example carbohydrates, into other substances, such as lactic acid or alcohol.
Fermented foods: Foods made by the controlled growth of microorganisms. Bryndza (a Slovak sheep’s cheese), sauerkraut and kombucha contain live and active cultures. They are not probiotics — they lack a defined strain, a dose and a study. ISAPP consensus, Marco et al., 2021
FOXO1 (FOXO1 transcription factor): An important protein that regulates gene activity and helps control metabolism, the cell cycle and the body’s defence against oxidative stress.
FOXP3: A key transcription factor (protein) that acts as the master regulator of the development and function of regulatory T lymphocytes (T-reg cells), and is essential for maintaining immune tolerance, controlling inflammatory processes and protecting against autoimmune reactions, especially in the digestive tract.
Fructooligosaccharides (FOS): Short chains of sugars that act as prebiotics and selectively serve as food for beneficial gut bacteria. They support their growth, activity and the overall balance of the gut microbiome.

G

GABA (gamma-aminobutyric acid): The main inhibitory neurotransmitter in the central nervous system, which helps reduce neuronal activity and induce calm, and which can also be produced in the gut by selected bacterial strains.
Galactooligosaccharides (GOS): A type of prebiotic fibre that supports the growth of beneficial bacteria in the gut and has a favourable influence on health.
Gastroenteritis: Inflammation of the stomach and intestines, most often caused by viral or bacterial infections, which shows up as diarrhoea, vomiting and abdominal pain and markedly but temporarily disrupts the balance of the gut microbiome.
Genome: The complete set of genetic information of a given organism or bacterium.
Gliadin: Gliadin is the main alcohol-soluble protein fraction of gluten, found in cereals such as wheat, barley and rye. Thanks to its unique structure it gives dough its elasticity and viscosity, but it is also the main trigger of autoimmune and adverse reactions in people with coeliac disease, non-coeliac gluten intolerance or wheat allergy.
Glutathione: An important tripeptide (protein) that works as a powerful antioxidant and protects cells from toxins and oxidative stress
Glutathione system: The cell’s main internal antioxidant mechanism, which uses enzymes and glutathione to neutralise harmful reactive oxygen species.
Glutathione peroxidase: An enzyme that protects cells from oxidative damage by breaking down harmful peroxides using glutathione
Glutathione reductase: An enzyme that recycles oxidised glutathione back to its active antioxidant form, thereby maintaining the cell’s defences.
Gram-negative bacterium: A type of bacterium with a thin layer of peptidoglycan and an outer membrane containing lipopolysaccharides; often more resistant to some antibiotics.
Gram-positive bacterium: A type of bacterium with a thick cell wall of peptidoglycan that appears purple when Gram stained.

H

Histamine: A substance the body releases during an allergic reaction that causes swelling, itching and inflammation.
Histamine intolerance: A disorder in which the body cannot properly break down histamine taken in with food, causing digestive and other problems.
HS-LC extract: a standardised polyphenol combination of extracts from hibiscus (Hibiscus sabdariffa, HS) and lemon verbena (Lippia citriodora, LC). It contains mainly anthocyanins and verbascoside and is investigated in research in connection with metabolic markers, appetite regulation and blood pressure

I

IBS: Irritable bowel syndrome, a functional digestive disorder associated with abdominal pain and changes in bowel movements, often linked to the microbiome.
IGF1 (Insulin-like growth factor 1): A hormone that stimulates the growth, division and regeneration of cells and influences overall metabolism and the development of the organism in an important way.
IL-10 (interleukin-10): A powerful anti-inflammatory cytokine (signalling protein) produced mainly by regulatory T lymphocytes and other immune cells, which crucially dampens excessive immune reactions, suppresses inflammation in the gut and helps maintain immune tolerance.
IL-6: An interleukin that acts as an important cytokine controlling the immune response and inflammation in the body.
IL-8: Chemokine (a type of cytokine) that works as a “navigation” and attracts immune cells to the site of inflammation.
Immunodeficiency: A state of reduced immune system function in which the body is more susceptible to infections.
Immunomodulation: The ability of a substance to adjust or balance the activity of the immune system.
in vitro: A laboratory experiment carried out outside a living organism, for example in a test tube or on a cell culture.
in vivo: An experiment carried out directly in a living organism.
Indoxyl sulfate: A metabolite formed from tryptophan in the gut that is toxic to the body in patients with kidney disease.
Inhibition: The process of suppressing or stopping a particular biological, chemical or enzymatic reaction.
Incubation: The period during which microorganisms grow under optimal conditions (temperature, humidity) in a laboratory culture medium.
INR (International Normalised Ratio): international normalised ratio. It is a value from a blood test that shows how quickly the blood clots. It is used mainly to monitor treatment with vitamin K antagonists, for example warfarin or acenocoumarol (Sintrom)
Barrier integrity: The intact state of the intestinal lining, which is key to the proper functioning of immunity and digestion.
Intervention: A predefined intervention or procedure whose effect is systematically monitored during the research.
Lactose intolerance: A set of clinical symptoms (abdominal pain, diarrhoea) that appear after consuming lactose in people who have lactose maldigestion.
Insulin sensitivity: Insulin sensitivity (responsiveness to insulin) expresses the ability of the body’s cells to respond to the hormone insulin and take up glucose from the bloodstream efficiently. High sensitivity means that the body needs only a small amount of insulin to keep blood sugar stable. Conversely, a decline in sensitivity (insulin resistance) forces the pancreas to produce much more of this hormone, which puts long-term strain on metabolism and raises the risk of developing type 2 diabetes.
Irinotecan: A medicine used in chemotherapy to treat tumours, which can have side effects on the gut microbiome and cause diarrhoea

K

Candidiasis: Candidiasis is an inflammatory disease caused by overgrowth of yeasts, mainly of the genus Candida, which are a common but otherwise controlled part of the human microbiome. It arises when the balance of the internal environment is disrupted due to factors such as antibiotic treatment, weakened immunity or unsuitable eating habits. Depending on location, it shows up on the mucous membranes or skin as itching, redness, coatings or digestive problems.
Cardiometabolic indicator: A cardiometabolic marker is a measurable laboratory or clinical parameter used to assess the risk of developing cardiovascular disease, type 2 diabetes and metabolic disorders. The most important markers include blood lipid levels (cholesterol, triacylglycerols), fasting glycaemia, blood pressure and body mass index. These parameters help identify hidden metabolic imbalances early, before the disease itself breaks out.
Carotenoids: Carotenoids (in the skin) are natural yellow, orange to red pigments of plant origin that, after being eaten in food, are stored in human subcutaneous fat and the layers of the skin. They serve as important antioxidants that protect skin cells from oxidative stress and damage caused by UV radiation. Besides their protective function, they give the skin a naturally healthy and subtly golden tone.
Cavitated carious lesions: Advanced stages of tooth decay in which the surface structure of the tooth has been broken down and breached, creating a visible hollow (cavity) in the dental tissue.
Kimchi: A traditional Korean fermented vegetable dish that is a rich source of beneficial probiotic bacteria.
Claudins: proteins of the tight junctions between cells, which contribute to the integrity of the intestinal barrier.
Strain specificity: The fact that the health effects of probiotics depend on the specific bacterial strain, not just on its genus or species.
Coaggregation: A process in which genetically different bacterial cells bind to one another specifically and firmly, which plays an important role in the formation of microbial biofilms, colonisation of the intestinal mucosa and defensive interaction between probiotic and pathogenic bacteria.
Cognitive function: The sum of mental processes such as learning, memory, attention and decision-making, which can also be influenced by the state of the gut microbiome.
Indole-3-acetic acid: A metabolite produced by gut bacteria from tryptophan that influences the immune response and the intestinal barrier.

L

Laboratory biomarker: A biological parameter measured in the laboratory, for example from blood, stool or another biological sample.
Lactate: A salt of lactic acid, which is a common product of the metabolism of some bacteria in the gut.
Lactose: Milk sugar, which is made up of glucose and galactose and needs the enzyme lactase to be broken down.
Lactose intolerance: Inability to break down lactose due to a lack of the enzyme lactase in the small intestine.
LDL (low-density lipoproteins) and HDL: LDL (low-density lipoproteins) and HDL (high-density lipoproteins) are the two main types of transport particles that carry cholesterol through the bloodstream. LDL (often called “bad” cholesterol) supplies cells with fats, but when in excess it is deposited in the walls of blood vessels and raises the risk of atherosclerosis. HDL (known as “good” cholesterol) has a protective effect, because it collects excess cholesterol from tissues and carries it back to the liver for metabolic processing and excretion.
Lipid: An organic compound, for example a fat, that forms a basic component of cell membranes and is key to energy storage.
Lipopolysaccharide: A toxic component of the outer membrane of some bacteria (endotoxin) that can trigger a strong inflammatory response in the body.
Lymphocyte: A type of white blood cell that is a key part of the body’s specific immune defence.

M

Lactose maldigestion: Insufficient breakdown of lactose in the gut caused by a lack of the enzyme lactase.
MASLD (metabolic dysfunction-associated steatotic liver disease): a condition characterised by excessive fat accumulation in the liver that is linked to at least one cardiometabolic risk factor, for example overweight, insulin resistance, type 2 diabetes or abnormal blood lipid levels. It is the current name for a disease that used to be called non-alcoholic fatty liver disease (NAFLD).
Menaquinone: The biological form of vitamin K (vitamin K2), which, besides coming from the diet, is also largely produced by bacteria of the gut microbiome and which is key to proper blood clotting, calcium metabolism and the health of bones and blood vessels.
Mesalazine: an anti-inflammatory drug (5-aminosalicylic acid) used mainly to treat and maintain remission in non-specific inflammatory bowel diseases such as ulcerative colitis.
Metabolic activity of the microbiome: A set of biological processes through which gut microorganisms convert available substances and create their own metabolic products.
Metabolic endotoxaemia: Metabolic endotoxaemia is a condition characterised by a mildly elevated level of bacterial endotoxins (especially lipopolysaccharides from Gram-negative bacteria) in the bloodstream. It arises as a result of increased permeability of the intestinal barrier, which allows them to pass from the gut into the body. This condition triggers chronic low-grade inflammation and is closely linked to the development of insulin resistance, obesity and metabolic syndrome.
Metabolite: A substance formed as a product of metabolism in the body or in the microbiome.
AhR-associated metabolites: Biologically active substances (often products of the conversion of the amino acid tryptophan by gut bacteria) that bind to the aryl hydrocarbon receptor (AhR) and significantly influence immunity, inflammatory processes and the defences of the intestinal barrier.
Metabolisation: A process in which an organism or bacteria chemically convert substances (e.g. food or medicines) into other forms.
Microbial metabolite: A substance produced by the metabolic activity of microorganisms. Some microbial metabolites may enter into communication between the gut environment and other systems of the body.
Microbiome: The collection of all microorganisms (bacteria, viruses, fungi) living in a particular part of the body, such as the gut, which influence our health.
Microorganism: A microscopically small organism, such as bacteria, yeasts or viruses, which are invisible to the naked eye.
Mononuclear cells: Types of white blood cells (lymphocytes and monocytes) that play a key role in the immune response.
Mucin MUC13: A transmembrane glycoprotein found on the surface of epithelial cells, mainly in the digestive tract, where it forms part of the protective mucus layer and helps to maintain the integrity of the intestinal barrier.

O

Observational interventional study: A study in which participants receive the intervention being studied and researchers systematically record changes over time, without random allocation to placebo-controlled groups.
Oxalate: an ester of oxalic acid present in plant foods, which specific bacteria partly break down in the gut and which, in excessive amounts, can contribute to the formation of kidney stones.
Oxidation: A chemical reaction in which a substance loses electrons, which can lead to the formation of unstable compounds that damage cells.
Oxidative stress: An imbalance between the production of harmful free radicals and the body’s ability to neutralise them, leading to damage to cells and tissues.

P

p-value: A statistical value used in hypothesis testing. It helps to judge how compatible the observed data are with the assumption that there is no difference between the conditions being compared.
p-cresyl sulfate: A metabolite produced by the action of gut bacteria from proteins, which accumulates in the blood in kidney failure and is toxic.
Periodontium: The set of tissues that hold a tooth in the jaw (gum, ligament, bone), whose health is closely linked to the oral microbiome.
Pasteurisation: Pasteurisation is a gentle heat treatment of foods and drinks that aims to destroy pathogenic microorganisms and extend their shelf life without a significant loss of nutritional value. It is carried out by heating the product to a precisely specified temperature below boiling point for a certain time, followed by rapid cooling. This method effectively eliminates disease-causing germs but, unlike sterilisation, does not kill all harmless spores, which is why it requires subsequent chilling.
Pathogen: A microorganism (bacterium, virus, fungus) that is capable of causing disease in a host.
Peripheral blood: Blood circulating throughout the body outside the central system (heart, lungs), from which samples are often taken for analysis.
PandA perinatal formulation: A specific combination of probiotic strains given to expectant mothers in late pregnancy and to newborns, designed to support the development of the immune system and the prevention of atopic diseases in children.
Oral administration: A way of administering a medicine or supplement through the mouth into the digestive tract.
Personalised probiotics and personalisation: An approach in which the choice of probiotics is tailored to the individual composition of the microbiome and the health status of a specific person.
Placebo: A placebo is an inert substance or ineffective procedure with no real pharmacological effects, used in medicine and research for comparison with real treatment. It produces a demonstrable improvement in a patient’s condition (the so-called placebo effect), which results from a psychological belief in the effectiveness of the treatment and the expectation of relief.
Postbiotic: A preparation of inanimate microorganisms or their components that confers a health benefit. An isolated metabolite, such as butyrate, is not a postbiotic.ISAPP consensus, Salminen et al., 2021
Prebiotic: A substrate that is selectively utilised by the host’s microorganisms and confers a health benefit. They feed the bacteria already present. Fibre is not automatically a prebiotic.ISAPP consensus, Gibson et al., 2017
Primary bile acids: Bile acids that are synthesised directly from cholesterol in the liver and secreted into the digestive tract, where they aid the digestion and absorption of fats and, in the gut, serve as the starting material for the formation of secondary bile acids.
Primary endpoint: The main predefined outcome of a study, by which its main research question is assessed.
Principle of complementarity: The principle of complementarity is a biological and chemical principle of molecules complementing one another and fitting together precisely on the basis of their structure and chemical properties. In molecular biology, it ensures the specific pairing of nitrogenous bases in nucleic acids (DNA and RNA), which is key to the faithful replication and transmission of genetic information. It also applies to the binding of antigens to antibodies or of enzymes to their substrates.
Probiotic: Live microorganisms that, in adequate amounts, confer a health benefit on the host. All conditions must apply at once: live, a defined strain, a sufficient dose and a benefit documented in a human study.
Proof of concept: An initial phase of research aimed at obtaining the first systematic data, verifying the feasibility of a concept and preparing the groundwork for a more robust study.
Propionic bacterium: A propionic bacterium (a representative of the genus Propionibacterium or Cutibacterium) is an anaerobic or aerotolerant bacterium that produces propionic acid as the main product of its metabolism. These microorganisms are a natural part of human skin and the digestive tract, and play a key role, for example, in the ripening of traditional cheeses (e.g. Swiss-type), where their fermentation creates the characteristic flavour and typical holes.
Prospective non-interventional observational study: A type of observational study in which participants are followed forward in time without the research protocol determining the treatment intervention.
Prospective study: A type of study in which participants are followed forward in time from a pre-specified start of the research.
Protein: The body’s basic structural protein, made up of amino acids, which provides the structure, function and regulation of cells.
Proteolysis/proteolytic: The enzymatic breakdown of proteins into smaller peptides and amino acids, carried out in the digestive tract by the host’s digestive enzymes and by bacteria of the gut microbiome; besides feeding cells, when too much unabsorbed protein is taken in it can lead to the formation of potentially harmful metabolites.

R

Randomisation: Random allocation of participants to the groups being compared, intended to reduce systematic differences between the groups.
RCT: Randomized Controlled Trial – a randomised controlled study in which participants are randomly allocated to the groups being compared.
Reactive oxygen species: Highly unstable oxygen molecules that form as a by-product of metabolism and can damage cell structures.
Redox conversion: A chemical process involving the transfer of electrons between substances, which is the basis of cellular energy metabolism.
Remission: A period of a chronic disease during which symptoms disappear or ease markedly, with the disease under control.
Respiratory infection: An infectious disease of the respiratory tract, most often caused by viruses or bacteria.

S

Secondary bile acids: Bile acids that are formed in the gut by the chemical conversion of primary bile acids through the action of enzymes of gut microorganisms and that play an important role in metabolism and signalling.
Secondary endpoint: Another pre-specified outcome that complements the main aim of the study and makes it possible to observe the broader picture of the intervention.
Serotonin pathway: A nerve and signalling pathway that uses the neurotransmitter serotonin and regulates mood, sleep, digestion and communication along the gut–brain axis (with most of the body’s serotonin being made in the digestive tract).
Serum MK-7 and faecal MK-6/MK-7: Indicators of the levels of various forms of vitamin K2 (menaquinones) in the blood (serum MK-7) and in stool (faecal MK-6 and MK-7), which reflect their intake from the diet, their absorption and their production directly by the gut microbiome.
Sialidase: An enzyme that cleaves sialic acid from the surface of cells or mucus, which some bacteria can use to colonise the gut.
SIBO: Small intestinal bacterial overgrowth syndrome, in which bacteria from the large intestine multiply disproportionately in the small intestine.
IBS-SSS (Irritable Bowel Syndrome Severity Scoring System) and GSRS scores: The IBS-SSS (Irritable Bowel Syndrome Severity Scoring System) and GSRS (Gastrointestinal Symptom Rating Scale) scores are standardised questionnaires for assessing the severity of symptoms of irritable bowel syndrome (IBS) and other gastrointestinal disorders.
SCORAD score: a standardised clinical tool (short for SCORing Atopic Dermatitis) developed for a comprehensive assessment of the extent, intensity and subjective symptoms (such as itching and sleep disturbance) of atopic dermatitis. https://scorad.org/
Spore: A dormant, extremely resistant form of a bacterium that allows it to survive long periods in unfavourable conditions.
Spore-forming bacterium: A bacterium capable of forming a highly resistant spore in order to survive unfavourable environmental conditions.
Consumer study: Systematic monitoring of the user experience and of subjectively assessed changes while using the product under study.
Statistical significance: A statistical assessment of whether an observed difference is large enough in view of the variability of the data and the chosen method of analysis. On its own, it does not express the size or practical significance of the change.
Stomatitis: Inflammation of the lining of the mouth, which may be of infectious, autoimmune or other origin.
Supernatant: The liquid that remains above the sediment after a mixture is centrifuged under laboratory conditions; it often contains substances released by bacteria.
Supplementation: Regular use of a defined food supplement or combination of ingredients during the observation period.
Synbiotic intervention: An intervention combining live microorganisms and substrates utilised by the host’s microorganisms in order to create a mutually complementary effect.
Synbiotic: Live microorganisms together with a substrate that feeds them — in a single preparation and with a health benefit. ISAPP consensus, Swanson et al., 2020
Systolic blood pressure: Systolic blood pressure is the highest blood pressure value measured in the arteries at the moment when the heart muscle (the ventricle) contracts and pushes blood into the circulation. In a blood pressure reading it is the first, higher number (e.g. 120 for a value of 120/80 mmHg) and reflects the force with which the heart pushes blood into the vascular system. Persistently raised values are one of the main risk factors for the development of cardiovascular disease. Diastolic blood pressure is the lowest blood pressure value measured in the arteries at the moment when the heart muscle relaxes after contraction and the ventricles fill with blood again. In a blood pressure reading it is the second, lower number (e.g. 80 for a value of 120/80 mmHg) and reflects the resistance of the blood vessels at the time when the heart is between beats. Persistently raised diastolic values also place a strain on the cardiovascular system.

T

TAG: TAG (triacylglycerol) is the main form of fat in the human body and diet, made up of one glycerol molecule bound to three fatty acid chains. It serves mainly as an efficient energy reserve stored in adipose tissue, and a raised level in the blood is among the important cardiometabolic indicators of the risk of vascular and metabolic diseases.
Taxonomy: Taxonomy (taxonomic) is a scientific discipline concerned with the classification, naming and systematic placement of organisms into hierarchical categories based on their genetic, evolutionary and morphological relatedness. In biology and the microbiome, it is used for the precise identification and division of species, from the broadest groups (such as kingdoms and phyla) down to individual genera and species.
Tight junction: A complex of proteins that tightly joins neighbouring epithelial cells in the gut and forms an impermeable barrier against the passage of harmful substances.
Th1/Th2 signal (Th1/Th2 balance): The mutual ratio and signalling balance between the two main subgroups of T helper lymphocytes (Th1, responsible for cellular immunity against intracellular pathogens, and Th2, mediating the antibody and allergic response), whose long-term disturbance in favour of the Th2 signal is a key factor in the development of allergies and atopic diseases.
TLR4: TLR4 (Toll-like receptor 4) is a key membrane receptor of the immune system belonging to the family of pattern-recognition receptors (PRRs). Its main role is to detect the presence of pathogens in the body, specifically recognising lipopolysaccharides found on the outer membrane of Gram-negative bacteria. After binding this stimulus it triggers a strong inflammatory and immune response aimed at eliminating the infection.
TNF-α: An important pro-inflammatory cytokine that triggers and regulates the body’s inflammatory response.
Tryptophan: An essential amino acid from which gut bacteria can produce substances that influence mood and immunity.

U

Ulcerative colitis: A chronic inflammatory disease affecting the inner lining of the colon and rectum, showing as ulcers, abdominal pain and diarrhoea, and closely linked to disorders of immunity and the gut microbiome.
Uraemic toxin: A substance (often a product of protein metabolism and gut bacteria) that builds up in the blood and tissues when kidney function is reduced and has a toxic effect on various organ systems in the body.
Urogenital: Urogenital is a term for the group of organs of the urinary and reproductive systems that are anatomically and functionally closely connected in the human body. In medicine and microbiology, the term is most often used in connection with the urogenital tract and its mucosal microbiome, which plays a key role in defence against infections and in maintaining a healthy internal environment.

V

Vaginitis: Vaginitis (inflammation of the vagina) is an inflammatory condition of the vaginal mucosa, most often caused by an overgrowth of yeasts, bacteria or parasites resulting from disruption of the naturally acidic environment. It shows as unpleasant itching, burning, redness and a change in the character of vaginal discharge. It arises under the influence of factors such as antibiotic treatment, hormonal fluctuations or weakened immunity.
Venous: Relating to the veins or the venous system through which blood flows towards the heart.
Vulvovaginal candidiasis: A yeast infection of the external genitalia and vagina, most commonly caused by Candida albicans.

Z

Bile acids: Steroid compounds made in the liver from cholesterol, which are secreted into the gut, where they facilitate the digestion and absorption of fats.

Β

β-galactosidase: An enzyme that catalyses the breakdown of milk sugar (lactose) into simpler sugars (glucose and galactose); it is produced by the human body and also by some gut and probiotic bacteria to make lactose easier to digest.