A clearer glossary for microbiome science, gut health, and probiotic terminology
Use this glossary to decode the vocabulary you see across articles, supplements, testing services, and microbiome research papers.
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Jump to a letter, then use related links inside each entry to keep exploring.
16S rRNA Sequencing
A molecular technique that identifies bacteria by sequencing a specific gene (16S ribosomal RNA) present in all bacteria. Used in most commercial microbiome tests. Can identify bacteria to genus level but often lacks strain-level resolution.
Acetate
The most abundant short-chain fatty acid produced by gut bacteria. Acetate is absorbed into the bloodstream and used as an energy source by peripheral tissues, and plays a role in appetite regulation and fat metabolism.
Akkermansia
Akkermansia muciniphila is a mucin-degrading bacterium that lives in the intestinal mucus layer. Higher abundance is associated with improved metabolic health, lower inflammation, and better gut barrier function. It thrives on polyphenol-rich foods.
Alpha Diversity
A measure of the variety of microbial species within a single sample or environment (e.g., one person's gut). Higher alpha diversity is generally associated with better health outcomes.
Antimicrobial Peptides (AMPs)
Small proteins produced by both the host (intestinal epithelial cells) and commensal bacteria that kill or inhibit pathogenic microorganisms. AMPs are a critical component of innate immunity in the gut and on the skin. Defensins, cathelicidins, and bacteriocins are common examples.
Bacteriophage
A virus that specifically infects and replicates within bacteria. Bacteriophages (phages) are the most abundant biological entities on Earth and play a significant role in shaping the composition and evolution of the gut microbiome.
Bacteroidetes
One of the two dominant bacterial phyla in the human gut (alongside Firmicutes). Bacteroidetes species are generally skilled at breaking down complex plant polysaccharides and are associated with leaner body composition in some studies. The Firmicutes-to-Bacteroidetes ratio was once considered a key health marker, though its significance is now debated.
Beta Diversity
A measure of how different microbial communities are between samples or individuals. Used in research to compare microbiome composition across populations, diets, or health conditions.
Bifidobacterium
A genus of beneficial bacteria that dominates the infant gut and remains important throughout life. Various species (B. longum, B. infantis, B. breve) are among the most studied probiotics, with evidence for IBS, immunity, and infant health.
Bifidobacterium longum
A beneficial bacterial species naturally abundant in the human gut from infancy. The strain B. longum 1714 has been studied for its effects on stress and cognitive function, showing modest benefits in human trials. B. longum subsp. infantis is particularly important for infant gut health and breast milk digestion.
Bile Acids
Compounds produced by the liver to aid fat digestion. Primary bile acids are modified by gut bacteria into secondary bile acids, which have signalling functions affecting metabolism, immune regulation, and gut motility. The microbiome's role in bile acid metabolism is a key mechanism linking gut bacteria to metabolic health.
Biofilm
A structured community of microorganisms attached to a surface and enclosed in a self-produced matrix. Biofilms in the gut can be protective (healthy mucus layer) or pathogenic (difficult-to-treat infections).
Butyrate
The most studied short-chain fatty acid, produced primarily by Faecalibacterium prausnitzii and other anaerobic bacteria. Butyrate is the primary energy source for colonocytes (colon lining cells) and has anti-inflammatory properties.
CFU
Colony-Forming Units. The standard measure of viable (living) bacteria in a probiotic product. A count of 1 billion CFU means approximately 1 billion live organisms capable of replicating.
Circadian Rhythm
The approximately 24-hour biological cycle that governs sleep-wake patterns, hormone release, and metabolism. The gut microbiome exhibits its own circadian fluctuations in composition and function, influenced by meal timing, light exposure, and host circadian clock genes.
Clostridioides difficile
A bacterium that can cause severe diarrhoea and colitis, typically after antibiotic use disrupts the normal gut flora. C. difficile infection is one of the clearest examples of how microbiome disruption leads to disease.
Colonisation Resistance
The ability of the resident microbiome to prevent colonisation by pathogenic organisms. A diverse, healthy microbiome provides strong colonisation resistance through competition for nutrients and space, and production of antimicrobial compounds.
Colonocyte
Epithelial cells lining the colon. These cells rely on butyrate (produced by gut bacteria) as their primary energy source, making them directly dependent on a healthy microbiome.
Commensal
An organism that benefits from a relationship with another organism without causing harm. Most gut bacteria are commensals — they gain food and shelter while contributing to digestion, immunity, and barrier function.
Cortisol
The primary stress hormone produced by the adrenal glands in response to HPA axis activation. Chronic cortisol elevation can increase intestinal permeability, alter gut motility, reduce mucus production, and shift the composition of the gut microbiome toward less diverse states.
Cutibacterium acnes
The dominant bacterium on the human face (formerly classified as Propionibacterium acnes). It metabolises sebum and helps maintain the skin's acid mantle. Certain strains are associated with acne vulgaris, while others are found on healthy skin — the issue is strain imbalance rather than the species itself.
Dysbiosis
An imbalance in the composition or function of the microbiome, typically characterised by reduced diversity, loss of beneficial bacteria, or overgrowth of potentially harmful species.
Endotoxin
A toxic component of the outer membrane of gram-negative bacteria, released when the bacteria die. The most common endotoxin is lipopolysaccharide (LPS). When endotoxins cross a compromised intestinal barrier into the bloodstream, they trigger systemic inflammation — a process called metabolic endotoxaemia.
Enterochromaffin Cells
Specialised cells in the gut lining that produce approximately 95% of the body's serotonin. Their activity is directly influenced by the gut microbiome, making them a key link in the gut-brain axis.
Enterotype
A classification of the human gut microbiome into distinct community types, first proposed in 2011. Three enterotypes were identified based on dominant genera: Bacteroides, Prevotella, and Ruminococcus.
Eubiosis
A balanced, healthy state of the microbiome with high diversity and appropriate proportions of bacterial species. The opposite of dysbiosis.
Faecal Microbiota Transplant (FMT)
A medical procedure that transfers stool from a healthy donor into a patient's gut to restore microbial diversity. Currently approved primarily for recurrent Clostridioides difficile infection, with research ongoing for other conditions.
Faecalibacterium prausnitzii
One of the most abundant and important bacteria in the healthy human gut. A major butyrate producer with strong anti-inflammatory properties. Reduced abundance is consistently associated with Crohn's disease and other inflammatory conditions.
Fermentation
The metabolic process by which bacteria break down substrates (such as dietary fibre) in the absence of oxygen. In the gut, fermentation of fibre produces short-chain fatty acids, gases, and other metabolites essential for colon health.
Firmicutes
The largest bacterial phylum in the human gut, encompassing diverse genera including Lactobacillus, Clostridium, Faecalibacterium, and Ruminococcus. Many important SCFA producers belong to this phylum. An elevated Firmicutes-to-Bacteroidetes ratio has been associated with obesity in some studies, though the relationship is complex and inconsistent.
FODMAP
Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols — a group of short-chain carbohydrates that are poorly absorbed and rapidly fermented by gut bacteria. The low-FODMAP diet is an evidence-based treatment for IBS symptoms, developed at Monash University.
GABA (Gamma-Aminobutyric Acid)
The brain's primary inhibitory neurotransmitter, responsible for reducing neuronal excitability. Several gut bacteria, including Lactobacillus and Bifidobacterium species, produce GABA. Research suggests that microbially produced GABA may influence brain function via the vagus nerve, with implications for anxiety and stress.
GALT
Gut-Associated Lymphoid Tissue. The immune tissue distributed throughout the intestinal lining, containing approximately 70% of the body's immune cells. The microbiome plays a critical role in training and regulating GALT function.
GOS (Galactooligosaccharides)
Prebiotic carbohydrates structurally similar to human milk oligosaccharides. Found naturally in legumes and available as supplements. GOS has evidence for promoting Bifidobacterium growth and reducing symptoms of IBS.
Gut-Brain Axis
The bidirectional communication system between the gastrointestinal tract and the central nervous system, involving neural, hormonal, and immune pathways. The microbiome plays a central role in this communication.
HPA Axis
The hypothalamic-pituitary-adrenal axis — a neuroendocrine system that regulates the body's stress response. When activated, it triggers cortisol release, which affects gut motility, intestinal permeability, and microbial composition. Chronic HPA axis activation is implicated in IBS and other gut disorders.
Human Milk Oligosaccharides (HMOs)
Complex sugars found in human breast milk that selectively feed beneficial Bifidobacterium species in the infant gut. HMOs are the third most abundant component of breast milk and are critical for establishing the infant microbiome.
IBS (Irritable Bowel Syndrome)
A chronic functional gastrointestinal disorder characterised by abdominal pain, bloating, and altered bowel habits without identifiable structural cause. The microbiome is increasingly recognised as a contributing factor, with IBS patients typically showing reduced microbial diversity and altered bacterial composition compared to healthy controls.
Intestinal Permeability
The property of the intestinal lining that controls what passes from the gut into the bloodstream. Increased permeability (sometimes called "leaky gut") allows harmful substances to enter circulation, triggering immune responses.
Inulin
A naturally occurring prebiotic fibre found in chicory root, garlic, onions, leeks, and artichokes. It selectively feeds beneficial Bifidobacterium species and is one of the most studied and widely used prebiotic supplements.
Keystone Species
A bacterial species that has a disproportionately large effect on the structure and function of the microbial community relative to its abundance. The loss of keystone species can trigger cascading changes in the entire microbiome ecosystem.
Lactobacillus
A genus of lactic acid-producing bacteria found naturally in the gut, mouth, and vaginal tract. Certain strains (L. rhamnosus GG, L. plantarum 299v) have strong clinical evidence for specific health benefits. Now reclassified into multiple genera including Lacticaseibacillus and Limosilactobacillus.
Lactobacillus rhamnosus
One of the most extensively studied probiotic species. The strain L. rhamnosus GG has strong evidence for preventing antibiotic-associated diarrhoea and acute gastroenteritis in children. The strain L. rhamnosus JB-1 has shown anxiolytic effects in animal models via the vagus nerve, though human trials have been less conclusive.
Lipopolysaccharide (LPS)
A component of the outer membrane of gram-negative bacteria. When LPS enters the bloodstream through a compromised intestinal barrier, it triggers inflammation — a key mechanism linking gut health to systemic disease.
Mediterranean Diet
A dietary pattern emphasising vegetables, fruits, wholegrains, legumes, nuts, olive oil, and fish, with moderate dairy and limited red meat. It is the most studied dietary pattern in microbiome research, consistently linked to greater microbial diversity, higher SCFA production, and reduced inflammation.
Melatonin
A hormone primarily associated with sleep regulation, produced by the pineal gland and — in much larger quantities — by enterochromaffin cells in the gut. Gut-derived melatonin influences intestinal motility, inflammation, and epithelial barrier function, and its production is influenced by the microbiome.
Metabolic Endotoxaemia
A state of chronically elevated blood levels of bacterial lipopolysaccharide (LPS), typically caused by increased intestinal permeability. First described by Cani et al. (2007), it is linked to low-grade systemic inflammation and is proposed as a mechanism connecting gut dysbiosis to obesity, type 2 diabetes, and cardiovascular disease.
Metabolome
The complete set of small-molecule metabolites (such as short-chain fatty acids, amino acids, vitamins, and bile acids) found within a biological system. The gut metabolome — largely produced or modified by the microbiome — provides functional information about what gut bacteria are actually doing, beyond simply which species are present.
Metagenome
The collective genetic material of all microorganisms in a given environment. The human gut metagenome contains roughly 150 times more genes than the human genome.
Microbiome
The complete collection of microorganisms (bacteria, viruses, fungi, archaea) and their genetic material within a specific environment, such as the human gut.
Microbiome Diversity
The variety and abundance of different microbial species in a given environment. Greater diversity is consistently associated with better health outcomes, while reduced diversity is linked to obesity, inflammatory bowel disease, and other chronic conditions.
Microbiome-Gut-Brain Axis
The extended concept of the gut-brain axis that explicitly includes the microbiome as an active participant. Communication occurs through neural pathways (vagus nerve), immune signalling, microbial metabolites, and endocrine routes. Disruption of this axis is implicated in IBS, anxiety, depression, and neurodegenerative conditions.
Microbiota
The actual living microorganisms within an environment. Often used interchangeably with microbiome, though microbiome technically includes their genes as well.
Mucin
Glycoproteins produced by goblet cells in the intestinal lining that form the protective mucus layer. This layer provides a habitat for beneficial bacteria like Akkermansia and acts as a physical barrier against pathogens.
Omega-3 Fatty Acids
Essential polyunsaturated fatty acids found in oily fish (salmon, mackerel, sardines), walnuts, and flaxseeds. Omega-3s have anti-inflammatory properties and research suggests they may support gut microbiome diversity by increasing Bifidobacterium and Lactobacillus populations and enhancing SCFA production.
Pathobiont
A normally harmless commensal organism that can become pathogenic under certain conditions, such as immune suppression, antibiotic use, or disrupted gut barrier. Many gut bacteria are pathobionts rather than true pathogens.
Polyphenols
Plant-derived compounds found in berries, tea, coffee, dark chocolate, red wine, and olive oil. Most polyphenols are poorly absorbed in the small intestine and reach the colon, where gut bacteria metabolise them into bioactive compounds with anti-inflammatory properties.
Postbiotic
Bioactive compounds produced by probiotic bacteria during fermentation, including short-chain fatty acids, enzymes, and cell wall fragments. These can have health benefits independent of living bacteria.
Prebiotic
Non-digestible food components (typically dietary fibres) that selectively stimulate the growth or activity of beneficial gut bacteria. Common examples include inulin, FOS, and GOS.
Prevotella
A bacterial genus associated with high-fibre, plant-rich diets. Prevotella copri is dominant in populations consuming traditional, grain-based diets and is relatively rare in Western populations eating processed food. It defines one of the three proposed human gut enterotypes.
Probiotic
Live microorganisms which, when administered in adequate amounts, confer a health benefit on the host. Benefits are strain-specific, not species-wide.
Propionate
A short-chain fatty acid produced by gut bacterial fermentation of dietary fibre. Propionate is primarily metabolised by the liver and has been shown to reduce cholesterol synthesis and regulate appetite and glucose metabolism.
Proteobacteria
A bacterial phylum that includes many well-known pathogens (E. coli, Salmonella, Helicobacter). In a healthy gut, Proteobacteria are a minor component, but their expansion is considered a potential marker of dysbiosis and microbial instability. Elevated Proteobacteria levels are observed in inflammatory bowel disease and other conditions.
Psychobiotic
A live organism (probiotic) that, when ingested in adequate amounts, produces a health benefit in patients suffering from psychiatric illness. A term coined by Dinan et al. in 2013.
Quorum Sensing
A cell-to-cell communication system used by bacteria to coordinate behaviour based on population density. Bacteria release and detect signalling molecules, allowing them to collectively activate gene expression for biofilm formation, virulence, or other group behaviours.
Resistant Starch
A type of starch that resists digestion in the small intestine and reaches the colon intact, where it is fermented by bacteria to produce short-chain fatty acids. Found in cooked and cooled potatoes, green bananas, oats, and legumes.
Serotonin
A neurotransmitter commonly associated with mood regulation, of which approximately 95% is produced in the gut by enterochromaffin cells. Gut-derived serotonin influences intestinal motility, secretion, and pain perception. The microbiome modulates serotonin production, forming a key link in the gut-brain axis.
Short-Chain Fatty Acids (SCFAs)
Metabolites produced when gut bacteria ferment dietary fibre. The three main SCFAs — butyrate, propionate, and acetate — are critical for colon health, immune regulation, and energy metabolism.
Shotgun Metagenomics
A sequencing approach that reads all DNA in a sample, not just bacterial marker genes. Provides higher resolution than 16S rRNA sequencing, including strain-level identification, functional gene analysis, and detection of viruses and fungi.
SIBO
Small Intestinal Bacterial Overgrowth. A condition where excessive bacteria colonise the small intestine (which normally has relatively few), causing bloating, pain, and malabsorption.
Staphylococcus aureus
A common bacterium that colonises the skin and nasal passages. While often harmless, S. aureus is an opportunistic pathogen implicated in wound infections, food poisoning, and skin conditions. In eczema, S. aureus overgrowth during flares is a consistent finding, driving inflammation through superantigen production.
Staphylococcus epidermidis
One of the most abundant commensal bacteria on human skin. S. epidermidis produces antimicrobial peptides that inhibit pathogenic bacteria including S. aureus, communicates with the immune system, and helps maintain the skin's acidic pH. Often called the "good staph."
Tight Junctions
Protein structures that seal the gaps between intestinal epithelial cells, controlling what passes from the gut lumen into the bloodstream. Disruption of tight junctions — by stress, certain bacteria, or dietary factors — increases intestinal permeability and is a key mechanism in gut barrier dysfunction.
Vagus Nerve
The longest cranial nerve, connecting the brainstem to the abdomen. It is the primary communication channel of the gut-brain axis, with approximately 80% of its fibres carrying signals from the gut to the brain.
Zonulin
A protein that regulates the tight junctions between intestinal cells. Elevated zonulin levels increase intestinal permeability. Discovered by Alessio Fasano, zonulin is triggered by gluten exposure and certain bacteria, and is studied as a biomarker for gut barrier function.