Gut Health & Microbiome Glossary
A comprehensive reference guide to the key terms used in gut health, microbiome science, and functional medicine — written and reviewed by Elena Rolt IFMCP, BANT, CNHC. Each definition links to relevant in-depth articles and condition guides for further reading.
B
Butyrate
Butyrate is a short-chain fatty acid produced by the fermentation of dietary fibre by colonic bacteria, particularly Faecalibacterium prausnitzii and Roseburia species. It is the primary energy source for colonocytes, maintains the integrity of the gut lining, reduces intestinal inflammation, and has anti-cancer properties. Low butyrate production — common in dysbiosis — is associated with leaky gut, IBD, and colorectal cancer risk.
C
Candida Overgrowth
Candida is a genus of yeast that naturally inhabits the gut in small amounts. Candida overgrowth (candidiasis) occurs when Candida albicans or related species proliferate beyond normal levels, typically following antibiotic use, a high-sugar diet, or immune suppression. Symptoms include bloating, fatigue, brain fog, recurrent thrush, and sugar cravings. Diagnosis requires stool testing and treatment involves dietary modification and antifungal protocols.
D
Dysbiosis
Dysbiosis refers to an imbalance in the gut microbiome — either a reduction in microbial diversity, an overgrowth of potentially harmful species, or a depletion of beneficial bacteria. It is associated with a wide range of conditions including IBS, inflammatory bowel disease, obesity, anxiety, autoimmune disease, and skin conditions. Dysbiosis can be identified through gut microbiome testing and addressed with targeted dietary and supplement protocols.
E
Enteric Nervous System
The enteric nervous system (ENS) is the intrinsic nervous system of the gastrointestinal tract, comprising approximately 500 million neurons embedded in the gut wall. Often called the 'second brain', the ENS can function independently of the central nervous system and controls gut motility, secretion, and blood flow. It communicates bidirectionally with the brain via the vagus nerve and plays a central role in the gut-brain axis.
F
Functional Medicine
Functional medicine is a systems biology-based approach to healthcare that focuses on identifying and addressing the root causes of disease rather than managing symptoms. It uses advanced diagnostic testing — including comprehensive blood panels, gut microbiome analysis, hormone testing, and nutrient assessments — to build a personalised picture of each patient's biochemistry and develop targeted therapeutic protocols.
Food Intolerance
A food intolerance is a non-immune-mediated adverse reaction to a food or food component, typically involving digestive symptoms such as bloating, gas, abdominal pain, and altered bowel habits. Common intolerances include lactose intolerance (due to insufficient lactase enzyme) and fructose malabsorption. Food intolerances are distinct from food allergies, which involve an IgE-mediated immune response.
Fermented Foods
Fermented foods are foods that have been transformed by microbial activity — typically bacteria or yeasts — through the process of fermentation. Examples include yoghurt, kefir, sauerkraut, kimchi, miso, tempeh, and kombucha. They are natural sources of live bacteria (probiotics), organic acids, and bioactive compounds that support gut microbiome diversity and intestinal health.
G
Gut Microbiome
The gut microbiome is the collective community of trillions of microorganisms — bacteria, fungi, viruses, and archaea — that live in the gastrointestinal tract, particularly the large intestine. It plays a central role in digestion, immune regulation, hormone metabolism, neurotransmitter production, and protection against pathogens. Each person's microbiome is as unique as a fingerprint and is shaped by genetics, diet, birth mode, antibiotic exposure, and lifestyle.
Gut-Brain Axis
The gut-brain axis is the bidirectional communication network between the gastrointestinal tract and the central nervous system, mediated by the vagus nerve, the enteric nervous system, the immune system, and gut-derived neurotransmitters and hormones. Approximately 90–95% of the body's serotonin is produced in the gut. Disruptions to this axis are associated with anxiety, depression, cognitive impairment, and stress-related digestive disorders.
H
Histamine Intolerance
Histamine intolerance occurs when the body accumulates more histamine than it can break down, typically due to impaired activity of the enzyme diamine oxidase (DAO) or histamine N-methyltransferase (HNMT). Symptoms include headaches, flushing, hives, nasal congestion, digestive upset, and heart palpitations after consuming histamine-rich foods. Gut dysbiosis can worsen histamine intolerance by increasing histamine-producing bacteria.
I
Intestinal Permeability (Leaky Gut)
Intestinal permeability, commonly referred to as 'leaky gut', describes a condition in which the tight junctions between cells lining the gut wall become compromised, allowing partially digested food particles, toxins, and bacterial fragments to pass into the bloodstream. This triggers systemic inflammation and immune activation, and has been linked to food sensitivities, autoimmune conditions, brain fog, fatigue, and skin problems.
L
Low-FODMAP Diet
The low-FODMAP diet is a therapeutic elimination diet developed by Monash University to manage IBS symptoms. FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) are short-chain carbohydrates that are poorly absorbed in the small intestine and rapidly fermented by gut bacteria. The diet involves a strict elimination phase followed by systematic reintroduction to identify individual triggers.
M
Microbiota
Microbiota refers to the community of microorganisms living in a specific environment — in the context of gut health, the microbiota is the collection of bacteria, fungi, viruses, and other microbes inhabiting the gastrointestinal tract. The term is often used interchangeably with 'microbiome', though strictly speaking the microbiome refers to the collective genetic material of these organisms, while microbiota refers to the organisms themselves.
Microba Testing
Microba is an Australian biotechnology company that provides one of the most clinically detailed gut microbiome analyses available. Their test uses metagenomic sequencing — analysing all DNA in a stool sample — to identify thousands of microbial species and their functional capabilities. This is more comprehensive than 16S rRNA sequencing used by many consumer tests, providing actionable data on microbial diversity, keystone species, and metabolic potential.
N
Nutritional Therapy
Nutritional therapy is a complementary health discipline that uses evidence-based nutritional science and functional testing to support health and wellbeing. Registered nutritional therapists (BANT, CNHC) take a whole-body approach, addressing diet, lifestyle, and biochemical individuality to identify and correct underlying imbalances. In the UK, BANT (British Association for Nutrition and Lifestyle Medicine) and CNHC (Complementary and Natural Healthcare Council) are the primary regulatory bodies.
P
Probiotics
Probiotics are live microorganisms that, when consumed in adequate amounts, confer a health benefit on the host. They are found naturally in fermented foods such as yoghurt, kefir, sauerkraut, kimchi, and miso, and are also available as supplements. Different strains have different effects — Lactobacillus and Bifidobacterium species are the most studied — and strain selection should be based on the specific health goal.
Prebiotics
Prebiotics are non-digestible dietary fibres and compounds that selectively feed beneficial bacteria in the gut, promoting their growth and activity. Common prebiotics include inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS), and resistant starch. They are found in foods such as garlic, onions, leeks, asparagus, bananas, oats, and chicory root.
S
SIBO (Small Intestinal Bacterial Overgrowth)
SIBO is a condition in which bacteria that normally reside in the large intestine migrate into and proliferate within the small intestine. This causes fermentation of carbohydrates in the wrong location, producing hydrogen and/or methane gas, leading to bloating, abdominal pain, diarrhoea, constipation, and nutrient malabsorption. SIBO is diagnosed via a breath test and is a common underlying cause of IBS symptoms.
Short-Chain Fatty Acids (SCFAs)
Short-chain fatty acids (SCFAs) are metabolites produced when gut bacteria ferment dietary fibre in the colon. The primary SCFAs are butyrate, propionate, and acetate. Butyrate is the preferred energy source for colonocytes (gut lining cells) and plays a key role in maintaining intestinal barrier integrity, reducing inflammation, and regulating immune function. Low SCFA production is associated with dysbiosis, leaky gut, and inflammatory conditions.
Z
Zonulin
Zonulin is a protein that modulates the permeability of tight junctions between intestinal epithelial cells. Elevated zonulin levels indicate increased intestinal permeability (leaky gut). Zonulin is upregulated by gluten (via gliadin) and by gut dysbiosis. It can be measured in blood or stool as a marker of intestinal barrier function and is used in functional medicine assessments.