Terminology
A single-place glossary of the microbiological, clinical and diagnostic terms used throughout the book, generated automatically.
Terminology
Acetate — The most abundant short-chain fatty acid (SCFA) produced by bacterial fermentation in the gut, accounting for roughly 60% of total SCFAs. Generated from fermentable fiber, it enters the circulation and acts as a metabolic substrate for peripheral tissues and as a lipogenesis precursor in hepatocytes. It modulates appetite through the brain's energy-sensing system and stimulates IgA production by B lymphocytes. Its level reflects overall microbial fermentation activity.
Akkermansia muciniphila — A bacterial species that inhabits the intestinal mucus layer. Reduced abundance is associated with weakened mucus barrier function and increased LPS translocation. A fiber-rich diet and polyphenols promote its growth.
Archaea — Microorganisms distinct from bacteria, some of which live in the human gut and contribute to metabolic processes such as methane production. They are a minor but relevant component of the gut ecosystem transferred during FMT.
Baseline — The patient's starting condition before treatment begins. It serves as the reference point against which later changes are measured. Accurate baseline assessment is essential for interpreting treatment outcomes.
Bifidobacterium — A beneficial bacterial genus in the colon. It produces lactic acid and acetate and stimulates IgA secretion. Reduced abundance is associated with impaired SCFA production and weakened gut barrier integrity.
Bile acids — Molecules produced by the liver to aid fat digestion and then modified by gut bacteria into secondary bile acids. These microbial transformations influence metabolism and help suppress certain pathogens. Restoring bile acid conversion is one way FMT re-establishes ecological function.
BMAL1 / CLOCK — Key transcription factors regulating the molecular circadian clock. They form a 24-hour feedback loop — not only in the brain, but also in peripheral clocks of the liver, gut, and adipose tissue.
Butyrate — The most important short-chain fatty acid (SCFA), accounting for roughly 15–20% of total SCFAs. It is the primary energy source for colonic epithelial cells (colonocytes) and, as an HDAC inhibitor, reinforces tight junction proteins and activates anti-inflammatory genes, thereby supporting intestinal barrier integrity. Its deficiency increases gut permeability. Restoring butyrate production is a key goal and a marker of successful FMT-supported recovery.
Capsule-based FMT — Oral administration of microbiota in encapsulated form. It allows repeated dosing over time and is less invasive than endoscopic delivery. It is especially useful in extended treatment protocols.
Circadian rhythm — The body's internal clock that regulates sleep, metabolism, and hormonal cycles. It also influences microbial activity and composition over a 24-hour cycle. Disruption of circadian rhythm can negatively affect microbiota stability. The body's internal ~24-hour biological clock, which regulates sleep, hormone secretion, metabolism, and the immune system. Irregular schedules, late-night eating, and artificial light can disrupt it.
Colostrum — The dense, yellowish milk secreted by mammals in the first days after birth; rich in immunoglobulins, oligosaccharides, and growth factors.
Cortisol — The "stress hormone" produced by the adrenal cortex. It is naturally elevated in the morning (the cortisol awakening response) and declines throughout the day. Chronically elevated levels increase gut permeability, impair insulin sensitivity, and promote visceral fat accumulation.
Cytokine — Small signaling proteins secreted by immune cells that regulate inflammatory and immune responses through cell-to-cell communication.
Dietary fiber — Plant-based carbohydrates that are not digested by human enzymes but are fermented by gut bacteria, producing metabolites such as SCFAs. Adequate fiber intake helps support microbial function and stability after FMT.
Donor — A healthy individual whose stool is used for FMT. Donors undergo extensive screening to reduce the risk of transmitting infections or other unwanted traits. Donor selection is a critical factor in treatment safety and effectiveness.
Dysbiosis — An imbalance in the composition, diversity, or functional capacity of the gut microbiota, associated with a range of clinical conditions. Dysbiosis may involve loss of beneficial species, overgrowth of pathogenic or pro-inflammatory taxa, reduced diversity, or disrupted metabolic output. It is not a disease in itself but an ecological imbalance. FMT is used to shift the system toward functional stability.
Enteric nervous system — An autonomous nervous system within the gut wall, consisting of about 500 million neurons; independently regulates peristalsis, secretion, and blood flow.
Epigenetics — The regulation of gene activity without altering the DNA sequence. Butyrate, for example, acts as an HDAC inhibitor and modulates the expression of tight junction proteins.
Faecalibacterium prausnitzii — A commensal bacterium of the Firmicutes phylum, consistently associated with gut health in human studies. It produces butyrate and has anti-inflammatory properties. Its abundance is frequently reduced in dysbiotic states and may be partially restored after FMT.
Fecal microbiota transplantation (FMT) — The transfer of a processed stool preparation from a healthy, screened donor into the gastrointestinal tract of a recipient. It delivers a complex microbial community with the aim of restoring disrupted ecological functions. It is the central therapeutic intervention described in this guide.
Fermentation — The process by which gut bacteria break down dietary fibers and other substrates in the absence of oxygen. This process produces metabolites such as SCFAs and is a core functional activity of a healthy gut microbiota.
Fermented foods — Foods produced by microbial or enzymatic transformation (e.g., yogurt, kefir, sauerkraut, kimchi, miso); many contain live microorganisms.
Fusobacterium nucleatum — A Gram-negative bacterium normally found in the oral cavity that accumulates in colorectal tumor tissue, promoting inflammation and immune evasion.
GABA – Gamma-aminobutyric acid — The main inhibitory neurotransmitter of the brain. Certain microbiota members (e.g., Lactobacillus) influence the GABA/glutamate balance — one of the mechanisms by which gut microbial status affects mood.
Ghrelin — The "hunger hormone" produced by the stomach. It rises before meals and stimulates appetite. After weight loss it can remain chronically elevated — one of the reasons the body tends to drift back toward its previous weight.
GLP-1 receptor agonists — Drugs that activate the glucagon-like peptide-1 receptor (e.g., semaglutide, liraglutide), lowering blood glucose, reducing appetite, and supporting weight loss.
Gluten-free diet — A diet that fully avoids gluten-containing proteins in wheat, barley, rye, and their derivatives; essential treatment for celiac disease and severe gluten sensitivity.
Glycemic index (GI) — A measure of how rapidly a food raises blood glucose (on a 0–100 scale). On its own it can be misleading, as it does not account for portion size — the glycemic load (GL) is a more accurate indicator.
Gut motility — The rate at which intestinal contents are propelled by peristaltic contractions. Slow motility leads to constipation and a shift toward protein fermentation. It can be modulated through exercise, fiber intake, and hydration.
Gut permeability — The permeability of the intestinal epithelial layer. Normally, tight junctions prevent bacteria and toxins from entering the circulation. When they weaken, the basis for LPS translocation is established.
Gut-brain axis (GBA) — A bidirectional communication system between the gut and the nervous system, in which the gut microbiota also participates.
HDAC – Histone deacetylase — An enzyme that removes acetyl groups from histone proteins. Butyrate acts as an HDAC inhibitor — it enhances expression of tight junction proteins and activates anti-inflammatory genes.
Helicobacter pylori — A Gram-negative, spiral-shaped bacterium that colonizes the gastric mucosa; a risk factor for peptic ulcer, chronic gastritis, and gastric cancer.
Histamine — A biogenic amine involved in allergic reactions, gastric acid secretion, and neurotransmission; also produced by gut microbiota.
IBD – Inflammatory Bowel Disease — Immune-mediated intestinal disease with tissue inflammation (Crohn's disease, ulcerative colitis). Distinct from IBS. During an active flare, restrictive diets may worsen symptoms.
IBS – Irritable Bowel Syndrome — A functional bowel disorder without tissue inflammation — symptoms arise from gut-brain axis and microbiota dysregulation. The low-FODMAP diet is its strongest evidence-based dietary intervention.
IL-6 – Interleukin-6 — A pro-inflammatory cytokine produced by immune cells and adipose tissue. Chronically elevated levels indicate low-grade systemic inflammation and are associated with insulin resistance.
Immune tolerance — The immune system's ability to avoid overreacting to harmless stimuli, including beneficial microbes. A healthy microbiota helps maintain this balance. FMT may influence tolerance by restoring appropriate microbial inputs.
Inflammation — The body's response to injury, infection, or other threats. While necessary for protection, prolonged inflammation can contribute to disease. The microbiota plays an important role in shaping inflammatory processes.
Insulin — Hormone produced by pancreatic beta cells in response to elevated blood glucose. It transports glucose into cells and promotes glycogen and fat storage. Chronically elevated levels drive fat storage and insulin resistance.
Insulin resistance — A reduced sensitivity of cells to insulin. The pancreas must secrete progressively more insulin to compensate. Contributors include visceral adipose inflammation, sleep deprivation, and dysbiosis. It can be estimated by HOMA-IR and reversed through lifestyle change.
Insulin sensitivity — A measure of how effectively cells respond to insulin. With high insulin sensitivity, small amounts of insulin are sufficient. It can be improved through exercise, fiber intake, sleep, and stress reduction.
Intermittent fasting — A dietary strategy alternating eating windows and fasting periods (e.g., 16:8 time window, 5:2 day pattern, alternate-day fasting).
Intestinal permeability ('leaky gut') — Increased passage of microbial products (e.g., lipopolysaccharide) and other molecules through the gut epithelium into systemic circulation. This can activate innate immune responses and contribute to low-grade systemic inflammation. FMT may help restore barrier integrity through microbial and metabolic mechanisms.
Inulin — A fermentable prebiotic fiber found mainly in onion, garlic, and artichoke. It preferentially stimulates Bifidobacterium strains. Large doses can cause bloating — gradual introduction is recommended.
Jet lag — A circadian desynchrony caused by crossing time zones: sleep disturbance, appetite loss, mental fatigue, and digestive issues.
Kefir — A milk- or water-based fermented beverage made with kefir grains (a bacteria-yeast symbiosis); contains dozens of microorganisms.
Lactobacillus — A group of lactic acid bacteria in the gut. They produce lactic acid and acetate and stimulate IgA secretion. Found in many commercial probiotic products.
Lactose intolerance — Bloating, diarrhea, and abdominal discomfort caused by reduced lactase enzyme activity that normally digests lactose (milk sugar).
LPS – Lipopolysaccharide — A component of the Gram-negative bacterial cell wall ("endotoxin"). With increased gut permeability it translocates into the circulation, where it drives metabolic endotoxemia.
Melatonin — The "sleep hormone" produced by the pineal gland in darkness. Through the MTNR1B receptor it suppresses pancreatic insulin secretion — which is why late-evening carbohydrate intake produces higher blood glucose.
Metabolic syndrome — The co-occurrence of abdominal obesity, hypertension, dyslipidemia, and insulin resistance; a major risk for cardiovascular disease and type 2 diabetes.
Metformin — The first-line drug for type 2 diabetes. It suppresses hepatic glucose output. Long-term use impairs vitamin B12 absorption — periodic monitoring is recommended.
Microbial community — A group of interacting microorganisms within a shared environment. In the gut, this community is shaped by cooperation and competition between species. FMT works by introducing a functioning community rather than single strains.
Microbial diversity — The variety of microbial species present within the microbiota. Higher diversity is generally associated with greater resilience and functional redundancy. FMT often aims to restore diversity as part of rebuilding ecological balance.
Microbial ecosystem — The microbiota viewed as an interconnected system of organisms, metabolites, and environmental conditions. It emphasises that function arises from relationships between species rather than isolated microbes. FMT targets this ecosystem as a whole.
Microbiome — The complete collection of microorganisms (bacteria, archaea, fungi, viruses, phages) and their genetic material in a defined environment. In clinical usage, 'gut microbiome' and 'gut microbiota' are often used interchangeably, though technically 'microbiome' includes the genes and 'microbiota' refers to the organisms. It describes not only which organisms are present, but what they do and how they influence physiological processes. In this guide, restoring the microbiome means restoring these functional processes rather than individual species.
Microbiota — The collection of microorganisms (bacteria, archaea, fungi, viruses) inhabiting the gut and other mucosal surfaces, which influences digestion, immunity, and metabolism. Distinct from the microbiome: that is a broader concept encompassing the microorganisms together with their collective genes and genetic activity.
Microbiota transfer therapy (MTT) — The broader therapeutic framework in which FMT is combined with targeted lifestyle and environmental interventions including diet, sleep, stress management, and other factors that influence microbial survival and integration. This is the term used in this guide for the full treatment model within which FMT is embedded.
Mucin — Heavily glycosylated proteins that form the mucus protective layer of the gut mucosa; key components of the gut barrier.
Mucus (intestinal mucus) — The mucus layer covering the intestinal epithelium. It acts as a physical barrier between bacteria and the epithelium. On a low-fiber diet, bacteria begin to digest the mucus, thinning the protective layer.
Omega-3 fatty acids — Essential polyunsaturated fatty acids (EPA, DHA, ALA) that are key components of cell membranes and anti-inflammatory mediators.
Peristalsis — The wave-like contractions of intestinal smooth muscle that propel contents toward the rectum. Stress inhibits it; the vagus nerve and the gastrocolic reflex stimulate it. Physical activity also augments it mechanically.
Polyphenols — A family of plant-derived phenolic compounds (e.g., flavonoids, anthocyanins) with antioxidant effects that serve as important substrates for gut microbiota.
Postbiotic — A preparation of inactivated microorganisms or their components that confers a health benefit on the host.
Pouchitis — Inflammation of the ileoanal pouch (a surgically created "neorectum"); typically occurs after colectomy for ulcerative colitis.
Prebiotic — A substrate selectively utilized by beneficial gut microbes that confers a health benefit on the host.
Probiotic — The deliberate intake of live microorganisms for a health benefit. Effects are strain- and condition-specific. Butyrate-producing strains are absent from commercial products due to their oxygen sensitivity.
Resilience — The ability of the microbiota to recover after disturbance. A resilient ecosystem can return to a functional state after stress such as antibiotic exposure or illness. FMT aims to improve this capacity.
Resistant starch — The fraction of starch that escapes absorption in the small intestine. Among the best sources are cooked-and-cooled rice and potatoes, and unripe bananas. A strong driver of butyrate production.
Response — Measurable improvement after treatment, assessed through symptoms, clinical markers, or functional changes. Evaluating response guides decisions about whether the protocol is working as intended.
Serotonin — A neurotransmitter and tissue hormone. 90–95% is produced in the gut, where it regulates motility — but it does not cross the blood-brain barrier. Brain serotonin's role in mood regulation depends indirectly on microbiota-modulated tryptophan metabolism.
Shift work — A work schedule outside the normal daytime pattern (night, rotating, or early shifts); causes chronic circadian desynchrony.
Short-chain fatty acids (SCFA) — Short (C1–C6) chain fatty acids produced by the colonic microbiota through fermentation of soluble dietary fibers. The three principal SCFAs — acetate, propionate, and butyrate — together account for roughly 95% of the total. They fuel colonocytes, reinforce the gut barrier, exert anti-inflammatory and immunomodulatory effects, and influence metabolism, appetite, and brain activity via the gut–brain axis.
Sleep quality — The depth, duration, and regularity of sleep. Poor sleep can affect hormonal and immune pathways that influence the microbiota. Consistent sleep patterns may support microbial stability after treatment.
Stress response — The body's physiological reaction to psychological or physical stress, involving hormonal changes that can alter gut motility, immune activity, and microbial composition. Chronic stress can work against stable FMT outcomes.
Symptoms — Subjective experiences reported by the patient, such as pain, bloating, fatigue, or changes in bowel habits. They reflect how the body responds to underlying biological processes. Careful symptom tracking is essential for monitoring FMT response.
Synbiotic — A combined preparation of probiotic and prebiotic that work synergistically or complementarily on host health.
Th17 cells — A CD4+ helper T-cell subset that produces IL-17 and IL-22; central to antibacterial and antifungal defense and to autoimmune inflammation.
Tight junctions — Protein complexes (claudin-1, occludin, ZO-1) between adjacent intestinal epithelial cells that seal the paracellular spaces. Their integrity is essential for preventing paracellular passage of bacteria and toxins; when they weaken, gut permeability increases. Dysbiosis-associated disruption of tight junctions contributes to epithelial permeability. Butyrate enhances their expression through its HDAC-inhibitor action.
Time-restricted eating — The daily form of intermittent fasting: eating is restricted to an 8-12 hour window (e.g., 16:8 pattern); only water or non-caloric fluids the rest of the time.
TNF-α – Tumor necrosis factor alpha — A central pro-inflammatory cytokine produced mainly by macrophages; key in inflammation, autoimmune disease, and metabolic disorders.
Trend — A pattern of change observed over time. It helps distinguish temporary fluctuations from meaningful improvement or deterioration. Trends are more informative than single observations when evaluating treatment response.
Tryptophan — An essential amino acid that serves as a precursor for serotonin (95% produced in the gut), the kynurenine pathway metabolites, and indole compounds. Gut bacteria regulate tryptophan availability and metabolic routing. FMT may influence mood, motility, and immune tone in part through restoration of tryptophan metabolism.
UPF – Ultra-Processed Foods — NOVA category 4: industrially manufactured products containing non-food-derived additives (emulsifiers, flavor enhancers, artificial sweeteners, hydrogenated fats). They are characterized by high energy density, low fiber content, rapid absorption, and enhanced activation of the brain's reward system. Higher consumption is associated with overeating, blood glucose volatility, reduced microbiota diversity, and elevated metabolic disease risk.
Vagus nerve — The tenth cranial nerve, running from the brainstem to the abdominal organs. The principal pathway of gut-brain communication: about 80% of signals from the gut reach the brain via the vagus.
Variability — Fluctuations in symptoms or measurements over time. Some variability is expected, but excessive or irregular changes may indicate instability. Understanding variability helps interpret patient progress more accurately.