1. Terminology
A single-place glossary of the microbiological, nutritional and clinical terms used throughout the book.
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.
Bacteroidetes — One of the major phyla of the gut microbiota, primarily involved in carbohydrate fermentation. The shift in the Firmicutes/Bacteroidetes ratio documented in obesity is associated with increased energy harvest from food.
Beta-glucan — A partially water-soluble fiber found mainly in oats and barley. It forms a gel-like matrix in the gut, slows glucose absorption, and stimulates Lactobacillus strains.
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.
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.
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.
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.
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.
Firmicutes — One of the major phyla of the gut microbiota, whose members include many butyrate-producing bacteria (Faecalibacterium, Roseburia). The Firmicutes/Bacteroidetes ratio may shift in obesity.
FODMAP — Fermentable Oligosaccharides, Disaccharides, Monosaccharides And Polyols. In large amounts they ferment rapidly, causing bloating in sensitive intestines. A low-FODMAP diet is the most evidence-based dietary intervention for IBS — but it is only recommended for 4–8 weeks.
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.
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.
Glycemic load (GL) — The product of the glycemic index (GI) and the amount of carbohydrate per serving. It reflects the real glycemic burden of a meal and is clinically more relevant than the GI alone.
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-brain axis (GBA) — A bidirectional communication system between the gut and the nervous system, in which the gut microbiota also participates.
HbA1c – Glycated hemoglobin — A marker reflecting average blood glucose over the previous 2–3 months. Normal: <5.7%; prediabetes: 5.7–6.4%; diabetes: ≥6.5%.
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 modulation — The influence of the microbiota on immune function through microbial metabolites and structural components. These signals help shape immune balance and responsiveness. FMT may improve gut health partly by restoring these microbial immune signals.
Indole Derivatives — A family of compounds produced from tryptophan by gut bacteria (especially Bacteroides, Clostridium, Lactobacillus, Bifidobacterium): indole, indole-3-acetate (IAA), indole-3-aldehyde (I3A), indole-3-lactic acid (ILA), indole-3-propionate (IPA). AhR agonists, antioxidant, gut-barrier-protective, anti-inflammatory, and gut–brain-axis modulators. Decreased indole production is typical in dysbiosis, IBD, MASLD, and metabolic disease.
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 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.
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.
Kefir — A milk- or water-based fermented beverage made with kefir grains (a bacteria-yeast symbiosis); contains dozens of microorganisms.
Lactate — A byproduct of anaerobic muscle metabolism — and, in fact, an important energy substrate. The lactate threshold used in Zone-2 training is the marker of the aerobic/anaerobic transition.
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).
Leaky gut — A popular term for increased gut permeability. The mechanism itself is documented, but "leaky gut syndrome" is not a validated standalone clinical diagnosis — no standardized diagnostic test exists.
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.
MASLD – Metabolic Dysfunction-Associated Steatotic Liver Disease — The new nomenclature introduced by the 2023 AASLD/EASL/ALEH Delphi consensus, replacing the former NAFLD (non-alcoholic fatty liver disease) label. MASLD = hepatic steatosis (fat in ≥5% of hepatocytes) + at least one cardiometabolic risk factor (T2DM, hypertension, dyslipidemia, central obesity, etc.). The inflammatory progressive form is MASH (metabolic dysfunction-associated steatohepatitis, formerly NASH). The change aims to avoid stigmatization and to use positive criterion-based diagnosis.
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.
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.
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.
MUFA – Monounsaturated fatty acids — Fatty acids with a single double bond (e.g., oleic acid); major sources include olive oil, avocado, and nuts.
NF-κB — Nuclear factor kappa B — a central transcription factor of the immune response and low-grade systemic inflammation. In its inactive form it resides in the cytoplasm; upon inflammatory stimuli (LPS, cytokines, oxidative stress) it translocates to the nucleus and activates pro-inflammatory genes (TNF-α, IL-6, COX-2). Gut-derived LPS and chronic hyperinsulinemia can also activate it — one of the mechanisms linking dysbiosis to insulin resistance.
NOVA classification — A food processing classification system (Monteiro et al.): 1 = unprocessed / minimally processed, 2 = culinary ingredients, 3 = processed foods, 4 = ultra-processed foods (UPF).
Omega-3 fatty acids — Essential polyunsaturated fatty acids (EPA, DHA, ALA) that are key components of cell membranes and anti-inflammatory mediators.
Pectin — A water-soluble, gel-forming fiber found mainly in apple peel and berries. It slows glucose absorption and feeds fermentative gut bacteria.
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.
Postprandial — "After a meal". Most often refers to the postprandial glucose peak and the subsequent glucose "dip" — emerging 30–90 minutes after a meal and capable of triggering strong hunger and cravings.
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.
Propionate — A short-chain fatty acid (SCFA) produced by gut microbes from fermentable fiber, accounting for roughly 20–25% of total SCFAs. It is absorbed into the bloodstream and processed mainly in the liver, where it serves as a major gluconeogenesis substrate contributing to glucose regulation; it is antilipogenic and activates AMPK. Through GPR41/GPR43 receptors it suppresses pro-inflammatory cytokine production, promotes Treg cell differentiation, and acts as a central satiety signal. Shifts in its level are a sensitive marker of microbial activity after FMT.
Psyllium — A fiber powder made from the husk of Plantago seeds. It swells strongly in water. A mixed soluble/insoluble fiber that slows glucose absorption and increases stool bulk. Typical dose: 5–10 g daily with plenty of water.
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.
Resistant Starch Type II — A fermentable but slowly digestible form of starch that, in its raw state, behaves more like insoluble fibre. It acts as a prebiotic and is associated with broader ecosystem-level changes in the microbiota.
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.
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.
SIBO – Small Intestinal Bacterial Overgrowth — Excessive bacterial proliferation in the small intestine — causing bloating, diarrhea, and nutrient malabsorption.
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.
TNF-α – Tumor necrosis factor alpha — A central pro-inflammatory cytokine produced mainly by macrophages; key in inflammation, autoimmune disease, and metabolic disorders.
Treg – Regulatory T cell — The "brakes" of the immune system — T-lymphocytes that suppress excessive inflammatory responses. Propionate and butyrate (SCFAs) promote their differentiation in the colon.
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.
Zonulin — A protein that modulates the permeability of tight junctions in the intestinal epithelium. Elevated zonulin levels are associated with increased intestinal permeability. It is one measurable indicator of barrier dysfunction.