A comprehensive nutrient ontology: a structured map of macronutrients, micronutrients, conditionally essential compounds, plant bioactives, microbiota-associated modulators, and water.

1. Macronutrients and Primary Building Blocks

Compounds consumed in relatively large quantities that primarily supply energy, serve as structural precursors for body tissues, or act as major building blocks for endogenous synthesis of complex molecules. These form the bulk of dietary intake and are classified by dominant chemical nature.

1.1 Carbohydrates

  • 1.1.1 Monosaccharides and disaccharides: Simple sugars that provide rapid energy or serve as precursors. Examples: glucose, fructose, galactose, sucrose, lactose, maltose.

  • 1.1.2 Starches and digestible polysaccharides: Glucose polymers broken down for sustained energy. Examples: amylose, amylopectin, glycogen (endogenous storage form).

  • 1.1.3 Dietary fibers and non-digestible polysaccharides: Structural plant carbohydrates that resist digestion, support gut motility, and may be fermented. Note: some prebiotic overlap with microbiota category. Examples: cellulose, hemicellulose, pectin, resistant starch, beta-glucans, inulin (also functions as prebiotic).

1.2 Proteins, Amino Acids, and Derivatives

  • 1.2.1 Essential amino acids: Cannot be synthesized by humans and must be obtained from diet; required for protein synthesis and other functions. Examples: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine.

  • 1.2.2 Conditionally essential amino acids: Synthesized endogenously under normal conditions but synthesis becomes insufficient during stress, illness, rapid growth, or aging. Examples: arginine, cysteine, glutamine, glycine, proline, tyrosine (plus related ornithine).

  • 1.2.3 Non-essential amino acids: Readily synthesized by the body. Examples: alanine, aspartate, asparagine, glutamate, serine.

  • 1.2.4 Amino acid derivatives and metabolites: Modified forms with specialized roles (e.g., energy buffering, antioxidant defense, neurotransmission support); often become more important when endogenous production declines. Examples: taurine, creatine/phosphocreatine, carnosine, anserine, beta-alanine, 4-hydroxyproline, polyamines (spermidine, spermine, putrescine).

  • 1.3.1 Essential fatty acids: Cannot be synthesized; required for membrane structure and eicosanoid production. Examples: linoleic acid (omega-6), alpha-linolenic acid (omega-3 precursor).

  • 1.3.2 Long-chain polyunsaturated fatty acids and derivatives: Often obtained directly from diet or elongated/desaturated from precursors; important for membranes, signaling, and specialized tissues. Examples: eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), arachidonic acid, docosapentaenoic acid.

  • 1.3.3 Phospholipids and membrane lipids: Amphipathic molecules forming cell membranes and acting as emulsifiers or signaling precursors. Examples: phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, sphingomyelin.

  • 1.3.4 Sterols and other neutral lipids: Structural components of membranes and precursors for hormones/bile acids. Examples: cholesterol, phytosterols/stanols, plant sterol esters.

2. Vitamins

Organic micronutrients required in small amounts for essential catalytic, regulatory, or antioxidant roles in metabolism. Deficiency produces characteristic syndromes. Humans cannot synthesize most in adequate quantities. Classified by solubility, which affects absorption, transport, and storage.

2.1 Fat-Soluble Vitamins

  • 2.1.1 Vitamin A and carotenoid precursors: Vision, epithelial integrity, immune function. Examples: retinol, retinal, retinoic acid, beta-carotene, alpha-carotene, cryptoxanthin (provitamin forms).

  • 2.1.2 Vitamin D: Calcium/phosphate homeostasis, bone health, immune modulation. Examples: cholecalciferol (D3), ergocalciferol (D2), 25-hydroxyvitamin D, 1,25-dihydroxyvitamin D (active form).

  • 2.1.3 Vitamin E: Lipid-soluble antioxidant protecting membranes. Examples: alpha-tocopherol, gamma-tocopherol, tocotrienols.

  • 2.1.4 Vitamin K: Blood clotting, bone metabolism. Examples: phylloquinone (K1), menaquinones (K2 forms, including MK-4, MK-7).

2.2 Water-Soluble Vitamins

  • 2.2.1 Thiamine (B1): Carbohydrate metabolism, nerve function. Examples: thiamine, thiamine pyrophosphate (active coenzyme).

  • 2.2.2 Riboflavin (B2): Redox reactions, energy metabolism. Examples: riboflavin, flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD).

  • 2.2.3 Niacin (B3): Redox reactions, NAD/NADP coenzymes. Examples: nicotinic acid, nicotinamide, nicotinamide riboside.

  • 2.2.4 Pantothenic acid (B5): Coenzyme A synthesis, fatty acid metabolism. Examples: pantothenic acid, pantethine.

  • 2.2.5 Vitamin B6: Amino acid metabolism, neurotransmitter synthesis. Examples: pyridoxine, pyridoxal, pyridoxamine, pyridoxal 5’-phosphate (active form).

  • 2.2.6 Biotin (B7): Carboxylation reactions, fatty acid/glucose metabolism. Examples: biotin, biocytin.

  • 2.2.7 Folate (B9): One-carbon metabolism, DNA synthesis. Examples: folic acid, 5-methyltetrahydrofolate, folinic acid.

  • 2.2.8 Vitamin B12 (Cobalamins): Methylmalonyl-CoA mutase and methionine synthase. Examples: cyanocobalamin, methylcobalamin, adenosylcobalamin, hydroxocobalamin.

  • 2.2.9 Vitamin C (Ascorbic acid): Antioxidant, collagen synthesis, iron absorption, immune support. Examples: L-ascorbic acid, dehydroascorbic acid, mineral ascorbates.

3. Minerals, Electrolytes, and Trace Elements

Inorganic elements required for structural roles (bones, teeth), electrolyte balance, osmotic regulation, enzyme cofactors, oxygen transport, and signaling. Required amounts range from grams to micrograms daily. Some ultra-trace elements have emerging or context-specific evidence of importance.

3.1 Macrominerals and Electrolytes

Inorganic elements required in larger quantities for structural integrity, fluid balance, and cellular signaling. Examples: calcium, magnesium, sodium, potassium, phosphorus, chloride, sulfur.

3.2 Trace Minerals

Essential inorganic elements required in small amounts as crucial cofactors for enzyme systems and metabolic processes. Examples: iron, zinc, copper, manganese, iodine, selenium, molybdenum, chromium, fluoride.

3.3 Ultra-Trace and Potentially Conditionally Essential Elements

Elements with lower established requirements or evidence primarily from animal models, specific deficiency states, or particular populations (e.g., long-term parenteral nutrition). Examples: boron, silicon, vanadium, nickel, lithium (trace), arsenic (ultra-trace in some contexts).

4. Conditionally Essential Nutrients and Vitamin-Like Metabolites

Organic compounds that humans can synthesize from precursors in limited quantities, but endogenous production is frequently insufficient to meet optimal needs during development, stress, illness, rapid growth, aging, pregnancy, or restricted diets (e.g., vegan). Dietary intake supports key metabolic, membrane, redox, methylation, and energy functions. These bridge classical micronutrients and bioactives.

4.1 Choline and one-carbon/methyl metabolism compounds

Phospholipid precursor, methyl donor (via betaine), neurotransmitter precursor. Examples: choline, betaine (trimethylglycine), phosphatidylcholine.

4.2 Carnitine and fatty acid transport factors

Mitochondrial fatty acid shuttle for energy production. Examples: L-carnitine, acetyl-L-carnitine, propionyl-L-carnitine.

4.3 Taurine and sulfur-containing amino acid derivatives

Osmoregulation, bile acid conjugation, membrane stabilization, antioxidant roles. Examples: taurine, hypotaurine.

4.4 Inositols

Cell signaling (phosphoinositides), insulin sensitivity, osmotic regulation. Examples: myo-inositol, D-chiro-inositol, other stereoisomers.

4.5 Creatine and high-energy phosphate compounds

Rapid ATP buffering in muscle and brain. Examples: creatine, phosphocreatine.

4.6 Coenzyme Q10 and ubiquinone system

Mitochondrial electron transport chain component and lipid-soluble antioxidant. Examples: ubiquinone-10 (CoQ10), ubiquinol (reduced form).

Mitochondrial dehydrogenase cofactor, regenerates other antioxidants (glutathione, vitamins C/E). Examples: alpha-lipoic acid (ALA), dihydrolipoic acid.

4.8 Glutathione and thiol-based antioxidants

Master intracellular antioxidant and detoxifier; synthesis often limited by precursor availability. Examples: glutathione (GSH), N-acetylcysteine (NAC, precursor), precursors: cysteine/glycine/glutamate.

Building blocks for RNA/DNA, energy carriers, signaling; important for gut repair and rapid cell turnover. Examples: AMP, GMP, IMP, uridine, adenosine, queuine (tRNA modifier humans cannot synthesize).

4.10 Polyamines

Regulate cell growth/proliferation, gene expression, autophagy, and membrane stability; endogenous synthesis declines with age. Examples: spermidine, spermine, putrescine.

4.11 Other vitamin-like factors

Emerging or accessory redox/mitochondrial compounds with demonstrated deficiency-like responses in models. Examples: pyrroloquinoline quinone (PQQ), S-adenosylmethionine (SAMe, major methyl donor).

5. Phytochemicals and Plant Secondary Metabolites

Structurally diverse, non-nutritive compounds synthesized by plants (often as defense or signaling molecules). Not required to prevent classical deficiency diseases but consumed regularly in plant foods and associated with antioxidant, anti-inflammatory, metabolic, and preventive health effects via multiple mechanisms. Classified primarily by core chemical structure and biosynthetic origin.

5.1 Polyphenols and Phenolic Compounds

Largest and most studied class of plant secondary metabolites, defined by the presence of multiple phenolic rings. Examples: flavonoids (quercetin, kaempferol, catechins/EGCG, anthocyanins, genistein, apigenin, naringenin, proanthocyanidins), phenolic acids (gallic acid, caffeic acid, ferulic acid, chlorogenic acid), stilbenes (resveratrol), lignans, tannins, curcuminoids (curcumin).

5.2 Terpenoids and Isoprenoids

Diverse structural class derived from five-carbon isoprene units, including plant pigments and volatile compounds. Note: some overlap as vitamin precursors. Examples: carotenoids (lutein, zeaxanthin, astaxanthin, lycopene, beta-carotene), monoterpenes (limonene, menthol), diterpenes, triterpenes, saponins/ginsenosides, phytosterols.

5.3 Alkaloids

Naturally occurring nitrogen-containing heterocyclic compounds that often exhibit pronounced physiological activity. Examples: caffeine, theobromine, berberine, capsaicin, morphine (plant-derived reference), nicotine.

5.4 Organosulfur Compounds

Sulfur-containing organic metabolites synthesized by specific plant families, noted for their distinct aromas and defensive roles. Examples: glucosinolates and isothiocyanates (sulforaphane, indole-3-carbinol), alliin/allicin and diallyl sulfides (garlic-derived).

5.5 Other Phytochemical Classes

Additional distinct molecular configurations synthesized by plant systems that exhibit biological actions in biological models. Note: some overlap with lipids. Examples: betalains (betanin), polyacetylenes, phytosterols/stanols.

6. Microbiota-Associated and Microbial Metabolites/Modulators

Compounds that selectively stimulate or are produced by beneficial gut microorganisms, or preparations of microbial components/metabolites that confer host benefits independent of live cells. These influence digestion, immune function, barrier integrity, and systemic metabolism via the gut–host axis.

6.1 Prebiotics

Selectively fermented ingredients that allow specific changes, both in the composition and/or activity in the gastrointestinal microbiota, that confer benefits upon host well-being. Examples: inulin, fructooligosaccharides (FOS), galactooligosaccharides (GOS), resistant starch, beta-glucans, pectin, human milk oligosaccharides.

6.2 Probiotics and live microbial modulators

Live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Examples: specific strains of Lactobacillus, Bifidobacterium, Saccharomyces boulardii, Akkermansia muciniphila (pasteurized forms sometimes considered in postbiotic context).

6.3 Postbiotics and microbial metabolites

Inanimate microbial preparations and/or their components, or metabolic byproducts generated through microbial action, that provide health benefits to the host. Examples: short-chain fatty acids (butyrate, propionate, acetate), exopolysaccharides, bacteriocins, cell wall peptidoglycans/teichoic acids, microbial peptides, certain vitamins produced by gut bacteria.

7. Water

Universal solvent and reaction medium essential for all physiological processes, thermoregulation, nutrient transport, and waste elimination. Required in the largest quantities of any nutrient; deficiency rapidly impairs function.

7.1 Forms and Sources of Hydration

Distinct vehicles of water delivery utilized by the body to maintain biological fluid homeostasis. Examples: potable water, water from food sources, electrolyte solutions (when needed for rehydration).