WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to mechanism.
An acidic microenvironment is a local drop in pH — typically into the 4.5–6.5 range — inside a tissue, organ, or ecological niche. Acidification arises from three recurring sources: bacterial fermentative metabolism that releases short-chain fatty acids and lactate (lou…
Bile acids are cholesterol-derived amphipathic molecules synthesized in the liver, secreted into the duodenum, and extensively modified by gut bacteria. The host-microbe co-metabolism of bile acids creates a signaling network with profound effects on lipid metabolism, g…
Catalase is a heme-iron enzyme that decomposes hydrogen peroxide into water and oxygen. In microbial peroxide defense, it acts downstream of superoxide dismutase: superoxide dismutase converts superoxide to hydrogen peroxide, and catalase removes that hydrogen peroxide …
Membrane-spanning protein complexes that actively export substrates from the bacterial cell, using energy from ATP hydrolysis or the proton motive force. In the context of metal-microbiome biology, efflux pumps serve a dual role that has profound clinical consequences: …
The farnesoid X receptor (FXR), also known as NR1H4, is a nuclear receptor that functions as the primary bile acid sensor in the body. Activated by bile acids — especially chenodeoxycholic acid (CDCA) — FXR regulates bile acid synthesis, cholesterol metabolism, glucose …
Ferroptosis is a form of iron-dependent regulated cell death driven by the accumulation of lipid peroxides on cellular membranes pendergrass 2026 microbial metallomics parkinsons ferroptosis, riederer 2021 iron concert master parkinsons. Unlike apoptosis or necrosis, fe…
Bidirectional communication between the gut microbiota and the central nervous system, mediated by neural (vagus nerve, enteric nervous system), immune (cytokines, microglia), endocrine (HPA axis), and metabolic (SCFAs, neurotransmitter precursors, tryptophan metabolite…
The gut-thyroid axis describes the bidirectional communication between the gut microbiome and the thyroid gland. The thyroid regulates metabolism, energy homeostasis, and immune function -- and the microbiome influences thyroid physiology at every level: mineral absorpt…
Hyperparathyroidism is the overproduction of parathyroid hormone (PTH), a master regulator of calcium homeostasis. While primary hyperparathyroidism (from parathyroid adenoma) is well described, the WikiBiome framework highlights secondary hyperparathyroidism -- the com…
A condition in which cells fail to respond normally to insulin, requiring progressively higher insulin levels to maintain glucose homeostasis. Insulin resistance is central to PCOS, type 2 diabetes, and metabolic syndrome, and has extensive but complex connections to me…
A fundamental ordering of divalent transition metal ion binding affinities, established by Harry Irving and Robert Williams in 1953: Mg2+ < Mn2+ < Fe2+ < Co2+ < Ni2+ < Cu2+ Zn2+ This series holds for virtually all ligands and biological chelators. It means that copper b…
Lipid metabolism — the synthesis, transport, and degradation of fats — is profoundly modulated by both the gut microbiome and metal homeostasis. The microbiome influences lipid metabolism through bile acid transformation, SCFA production, TMAO generation, and direct enz…
Metal sensing is the set of regulatory mechanisms bacteria use to detect intracellular metal concentrations and adjust gene expression accordingly. Because metal ions cannot be synthesized or degraded -- only imported, exported, sequestered, or trafficked -- sensing and…
Metallomics is the systematic study of metals and metalloids in a biological system. The metallome is the set of metal and metalloid species present in a defined organism, tissue, cell, fluid, or microbial community; metallomics is the measurement and interpretation of …
Protein-based transcription factors that sense intracellular metal concentrations and regulate gene expression accordingly. Metalloregulators are the decision-making layer of bacterial metal homeostasis -- they read the labile metal pool, determine whether a specific me…
A family of small (6-7 kDa), cysteine-rich proteins that bind heavy metals with extraordinary affinity. Metallothioneins (MTs) are the cell's primary chemical defense against metal toxicity -- they sequester cadmium, mercury, lead, and other toxic metals, preventing the…
An umbrella concept encompassing the metallomic dimensions of Alzheimer's disease, Parkinson's disease, and other neurodegenerative conditions. The brain is uniquely vulnerable to metal toxicity: it has high metabolic demand, limited regenerative capacity, region-specif…