Gut Health Glossary

A complete reference covering the gut microbiome, probiotics, prebiotics, gut barrier biology, short-chain fatty acids, gut conditions, and the gut-brain axis. Each definition written for clarity without sacrificing scientific precision.

The Gut Microbiome

Gut Microbiome

The community of trillions of microorganisms - bacteria, archaea, viruses, fungi, and protozoa - residing in the human gastrointestinal tract. The gut microbiome influences digestion, immunity, metabolism, hormone production, and brain function via the gut-brain axis.

Dysbiosis

An imbalance or disruption in the composition, diversity, or function of the gut microbiota, characterised by reduced microbial diversity and loss of beneficial species. Associated with IBS, IBD, metabolic syndrome, and immune conditions.

Alpha Diversity

A measure of microbial diversity within a single individual's gut microbiome. Higher alpha diversity is generally associated with better health outcomes. Alpha diversity consistently declines with ageing, antibiotic use, processed food diets, and chronic stress.

Akkermansia muciniphila

A mucus-degrading bacterium considered a keystone health-associated species. Its abundance is inversely correlated with obesity, type 2 diabetes, and inflammatory bowel disease. Akkermansia promotes gut barrier integrity by stimulating mucus production and tight junction expression.

Faecalibacterium prausnitzii

One of the most abundant beneficial species in a healthy adult gut and the most potent microbial butyrate producer in the human colon. Strongly anti-inflammatory. Dramatically reduced in Crohn's disease and other inflammatory bowel conditions.

Probiotics

Probiotic

Defined by the WHO and FAO as 'live microorganisms that, when administered in adequate amounts, confer a health benefit on the host'. Key elements: live organisms, adequate dose (typically 10^8 to 10^11 CFU), and documented health benefit for the specific strain at the specific dose.

CFU (Colony Forming Units)

The unit used to measure viable bacteria in probiotic products. Clinical trials typically use 10^8 to 10^11 CFU; labelled doses must be guaranteed at time of use, not just at manufacture, accounting for die-off during storage.

Strain Specificity

The principle that clinical evidence for one probiotic strain cannot be extrapolated to other strains of the same species. When selecting probiotics for specific applications, the strain designation (alphanumeric code) should match strains used in relevant clinical trials.

Synbiotic

A product combining a probiotic with a prebiotic that selectively supports the probiotic's growth and activity. The synbiotic approach improves probiotic colonisation efficiency and persistence compared to either alone.

Postbiotic

A preparation of inanimate microorganisms and/or their components that confers a health benefit on the host. Includes heat-killed bacteria, bacterial cell wall fragments, and fermentation products. Advantage over probiotics: stability at room temperature.

Psychobiotic

A probiotic (or prebiotic) with evidence for improving mental health outcomes - mood, anxiety, or stress resilience - via the gut-brain axis. Examples include Bifidobacterium longum 1714 (reduces stress and cortisol in RCTs).

Key Probiotic Strains

Lactobacillus rhamnosus GG (LGG)

The first commercially used probiotic strain and one of the most studied. Strong evidence for preventing and treating acute infectious diarrhoea, antibiotic-associated diarrhoea, and traveller's diarrhoea.

Lactobacillus plantarum 299v

The probiotic strain with the most consistent replicated RCT evidence for IBS bloating and abdominal pain reduction. Multiple independent trials from different research groups confirm significant IBS symptom improvement.

Bifidobacterium longum 35624 (Bifantis)

A strain with distinctive immunological effects in IBS patients, specifically normalising the IL-10/IL-12 cytokine ratio. The Whorwell et al. 2006 multicentre RCT (362 patients) remains the largest single-strain IBS trial. Marketed as Alflorex in the UK.

Bifidobacterium lactis BB-12

The most studied Bifidobacterium strain globally with over 300 published trials. Primary applications: constipation, antibiotic-associated diarrhoea prevention, and immune function. Notable for exceptional acid and bile tolerance.

Saccharomyces boulardii

A non-pathogenic yeast with strong evidence for preventing antibiotic-associated diarrhoea and reducing Clostridium difficile recurrence. Distinct advantage: not inhibited by antibiotics, making it uniquely appropriate during antibiotic courses.

Bifidobacterium longum 1714

A psychobiotic strain with RCT evidence for reducing perceived stress, anxiety, and cortisol reactivity in healthy volunteers. Represents the leading human clinical evidence for a specific probiotic improving stress-related outcomes via the gut-brain axis.

Prebiotics

Prebiotic

A substrate that is selectively utilised by host microorganisms conferring a health benefit. Must resist gastric acid and mammalian enzymes (reaching the colon intact), be fermented by gut microbiota, and selectively stimulate beneficial microorganisms.

Inulin

A polysaccharide prebiotic fibre found naturally in chicory root, Jerusalem artichoke, garlic, and onion. The most studied and consistently bifidogenic prebiotic - selectively stimulates Bifidobacterium via inulinase enzymes.

Fructooligosaccharides (FOS)

Short-chain inulin-type fructans produced by partial hydrolysis of chicory inulin. Fermented rapidly in the proximal colon, producing a faster bifidogenic effect than long-chain inulin.

Partially Hydrolysed Guar Gum (PHGG)

A water-soluble, flavourless prebiotic fibre. FODMAP-tolerant - suitable for IBS patients who cannot tolerate inulin or FOS. Well-evidenced for constipation improvement and IBS symptom relief.

Gut Barrier and Permeability

Intestinal Permeability

A measure of the gut barrier's selectivity. Increased permeability (loosened tight junctions) allows bacterial endotoxins, incompletely digested food antigens, and bacterial metabolites to enter systemic circulation, triggering immune activation.

Leaky Gut

A colloquial term for increased intestinal permeability - a measurable physiological change associated with IBS, IBD, chronic stress, heavy exercise, NSAID use, alcohol, and antibiotic-related dysbiosis. Targeted by L-glutamine, zinc carnosine, and specific probiotics.

Tight Junctions

Protein complexes that form the paracellular seal between adjacent intestinal epithelial cells, controlling what can pass through the intercellular space. Composed of occludin, claudin proteins, and ZO-1/ZO-2 scaffolding proteins.

Secretory IgA (sIgA)

The predominant immunoglobulin in the gut lumen, produced by plasma cells in the lamina propria. sIgA coats and neutralises pathogens and toxins in the gut lumen without triggering inflammatory responses. B. lactis BB-12 and L. rhamnosus GG significantly increase faecal sIgA in RCTs.

Lipopolysaccharide (LPS)

A structural component of gram-negative bacterial cell walls that acts as a potent inflammatory endotoxin when it enters systemic circulation. LPS translocation through a leaky gut epithelium triggers systemic low-grade inflammation associated with metabolic syndrome and depression.

Short-Chain Fatty Acids and Fermentation

Short-Chain Fatty Acids (SCFAs)

Organic acids produced by anaerobic bacterial fermentation of dietary fibre in the large intestine. The primary SCFAs are butyrate, propionate, and acetate. SCFAs are the primary energy source for colonocytes and regulate gene expression, immune function, and the gut-brain axis.

Butyrate

A four-carbon SCFA and the primary energy source for colonocytes (80% of their energy needs). Potently anti-inflammatory via NF-kB inhibition. Maintains gut barrier integrity by upregulating tight junction proteins and mucin production. Reduced in dysbiosis and IBD.

Propionate

A three-carbon SCFA produced primarily by Bacteroides species. Transported to the liver where it regulates gluconeogenesis and lipid metabolism. Signals satiety via free fatty acid receptors on colonic epithelium, stimulating PYY and GLP-1 release.

Gut Conditions

IBS (Irritable Bowel Syndrome)

A functional gastrointestinal disorder characterised by recurrent abdominal pain associated with defecation or a change in stool frequency. Affects approximately 10-15% of Western adults. Subtypes: IBS-C, IBS-D, IBS-M, and IBS-U.

Antibiotic-Associated Diarrhoea (AAD)

Diarrhoea occurring during or after antibiotic use, caused by disruption of the protective gut microbiome. Affects 5-25% of antibiotic users. Most effectively prevented by Lactobacillus rhamnosus GG and Saccharomyces boulardii, both with Cochrane-level evidence.

FODMAPs

Fermentable Oligosaccharides, Disaccharides, Monosaccharides, And Polyols - short-chain carbohydrates poorly absorbed and rapidly fermented by gut bacteria. In IBS, FODMAP ingestion exacerbates symptoms via luminal distension. The low-FODMAP diet effectively reduces IBS symptoms in 50-80% of patients.

SIBO (Small Intestinal Bacterial Overgrowth)

An abnormal increase in bacterial concentrations in the small intestine. Causes bloating, abdominal pain, diarrhoea, and nutrient malabsorption. Diagnosed by hydrogen/methane breath test.

Gut-Brain Axis

Gut-Brain Axis

The bidirectional communication network between the gastrointestinal tract and the central nervous system, operating via the vagus nerve, SCFAs and hormones, immune signalling, and microbially produced neurotransmitter precursors. The gut contains approximately 500 million neurons and produces approximately 95% of the body's serotonin.

Vagus Nerve

The primary neural highway of the gut-brain axis. Approximately 80-90% of vagal fibres are afferent (gut-to-brain), relaying gut microbiome signals to the brainstem and limbic system via emotional and autonomic regulation centres.

HPA Axis and Gut Interactions

The hypothalamic-pituitary-adrenal axis and the gut microbiome interact bidirectionally. Cortisol increases intestinal permeability and alters gut microbiome composition. Conversely, gut bacteria modulate HPA axis reactivity - psychobiotic probiotics reduce cortisol in human RCTs.

Gut Barrier and Supplement Ingredients

L-Glutamine

The most abundant amino acid in plasma and the primary energy source for enterocytes. At 5-10g daily, L-glutamine supplementation reduces measured intestinal permeability in IBS-D and stress-induced permeability contexts. Also directly stimulates tight junction protein expression.

Zinc Carnosine (Polaprezinc)

A chelated compound of zinc and L-carnosine that adheres to the gut mucosal surface. Licensed as a pharmaceutical drug in Japan for gastric ulcer treatment. At 75mg twice daily, RCTs show significant reduction in NSAID-induced intestinal permeability and exercise-induced gut damage.

Berberine

An alkaloid with evidence for gut microbiome modulation, blood glucose reduction, and anti-inflammatory effects. Increases Akkermansia muciniphila and reduces pathogenic bacteria. Caution: significant drug interactions via CYP3A4 inhibition; avoid concurrent with statins.

Diet and Microbiome

Dietary Fibre

Plant-derived carbohydrates that resist digestion and reach the colon intact, serving as fermentable substrate for gut bacteria. UK adults average 18g/day against a recommended 30g/day. The diversity of fibre types consumed drives gut microbiome diversity.

Fermented Foods

Foods produced by microbial fermentation including yoghurt, kefir, sauerkraut, kimchi, and miso. A 2021 Stanford study found a high-fermented-food diet for 10 weeks significantly increased gut microbiome diversity and decreased inflammatory markers.

Polyphenols

Plant secondary metabolites found in berries, tea, coffee, and dark chocolate. Approximately 90-95% of ingested polyphenols reach the colon unabsorbed, where they are biotransformed by gut bacteria. Polyphenols increase Akkermansia muciniphila and Bifidobacterium while reducing potentially harmful taxa.

Low-FODMAP Diet

A dietary protocol developed at Monash University that restricts fermentable carbohydrates. Effective in 50-80% of IBS patients but reduces Bifidobacterium populations - requiring post-restriction prebiotic or probiotic support.