Gut health glossary
Reviewed by Dr. Nikita Dinger, Founder & CEO, BioMeBar. Last reviewed 7 October 2026.
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Gut health writing comes with its own vocabulary, and some terms are used loosely in marketing. This glossary gives short, plain definitions of the words you are most likely to meet, with notes where a term is often misused. It is not exhaustive, and definitions can shift as the science develops.
Core terms
| Term | Meaning |
|---|---|
| Microbiome | The community of microbes in a body site, together with their genes and surroundings. “Gut microbiome” usually means the colon community. |
| Microbiota | The microbes themselves. People often use microbiome and microbiota interchangeably. |
| Dysbiosis | A shift in the microbial community that is associated with a condition. There is no agreed standard for what a “balanced” gut looks like, so the word should be used carefully. |
| Probiotic | Live microorganisms that, when given in adequate amounts, may offer a health benefit to the host (the 2014 ISAPP consensus definition). |
| Prebiotic | A substrate that is selectively used by host microorganisms to give a health benefit (the 2017 ISAPP definition). |
| Synbiotic | A mixture of live microorganisms and substrate(s) selectively used by host microorganisms that may offer a health benefit (the 2020 ISAPP definition). It can be complementary or synergistic. |
| Postbiotic | A preparation of inanimate microorganisms and/or their components that may offer a health benefit. It is a newer category. |
| Strain | A specific version of a species, often written with letters and numbers. Probiotic effects are strain-specific. |
| CFU | Colony-forming units, a count of viable microbes in a dose. More is not automatically better. |
Digestion and fibre
| Term | Meaning |
|---|---|
| Dietary fibre | Plant carbohydrates that humans cannot digest. See fibre types and gut bacteria. |
| Short-chain fatty acids (SCFAs) | Compounds such as acetate, propionate and butyrate that bacteria make when they ferment fibre. |
| FODMAP | A group of fermentable carbohydrates that can trigger symptoms in some people. See what is FODMAP. |
| Transit time | How long food takes to move through the digestive tract. |
| Bile acids | Compounds made by the liver that help digest fat. Gut bacteria modify them. |
Gut-related conditions and terms
| Term | Meaning |
|---|---|
| IBS | Irritable bowel syndrome, a functional gut disorder diagnosed by symptom criteria (Rome IV). It does not cause visible damage to the gut. |
| IBD | Inflammatory bowel disease, mainly Crohn’s disease and ulcerative colitis, in which there is inflammation that can be seen on tests. See IBS vs IBD. |
| SIBO | Small intestinal bacterial overgrowth, a proposed condition in which excess bacteria are found in the small intestine. Testing and diagnosis are debated. |
| Intestinal permeability | How easily substances cross the gut lining. See gut barrier. |
| Coeliac disease | An autoimmune reaction to gluten. |
| Lactose intolerance | Difficulty digesting lactose because of low lactase enzyme. It is not an allergy. |
| Gut-brain axis | Two-way communication between the gut and the brain. |
| Estrobolome | Gut microbial genes that influence estrogen handling. |
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Testing and science terms
| Term | Meaning |
|---|---|
| 16S rRNA sequencing | A method that reads a marker gene to identify which bacteria are present, usually down to genus level. |
| Shotgun metagenomics | Sequencing all DNA in a sample, which can give finer identification and information about genes. |
| Alpha diversity | A measure of variety within one person’s sample. |
| Beta diversity | A measure of how different two samples are. |
| Calprotectin | A stool marker of gut inflammation, used by clinicians to help tell IBD from IBS. |
| Bristol Stool Scale | A seven-type chart for stool form. See Bristol stool chart. |
Words to read with care
- Cleanse, reset. The gut and liver already clear waste. These words are marketing, not medical terms.
- “Good” and “bad” bacteria. Many microbes act differently depending on context, location and the rest of the community.
- “Boosts immunity”. Immune function is complex, and no single product boosts it in a simple way.
Common questions
Why do definitions keep changing?
The field is young, and expert panels such as ISAPP update terms as evidence grows.
Is a food with live cultures a probiotic?
Only if the strains are defined and shown to give a benefit. Many fermented foods contain live microbes without meeting that bar.
A few more terms you may see on labels
- Live and active cultures. A phrase for products containing living microbes at the time of manufacture. It does not tell you the strain, the dose or whether they are still alive at the end of shelf life.
- Genus, species, strain. The naming levels of a microbe, for example genus Bifidobacterium, species longum, then a strain code.
- Substrate. The food or compound that microbes use. In a prebiotic, it is the ingredient that selectively feeds helpful microbes.
- Colonisation. Whether a microbe settles in the gut or only passes through. Many probiotics seem to be temporary visitors.
Related reading
- Probiotics vs prebiotics vs synbiotics
- Gut health FAQ
- Gut microbiome tests explained
- Short-chain fatty acids
Sources
- Hill C, et al. 2014. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology.
- Gibson GR, et al. 2017. The International Scientific Association for Probiotics and Prebiotics consensus statement on the definition and scope of prebiotics. Nature Reviews Gastroenterology & Hepatology.
- Swanson KS, et al. 2020. The International Scientific Association for Probiotics and Prebiotics consensus statement on the definition and scope of synbiotics. Nature Reviews Gastroenterology & Hepatology.
- Drossman DA. 2016. Functional gastrointestinal disorders: history, pathophysiology, clinical features and Rome IV. Gastroenterology.
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BioMeBar provides nutrition and gut health guidance and does not replace medical care. See a doctor for severe, persistent or worrying symptoms.