Mechanisms8 sources
Hypoxic Signaling (HIF-1α Pathway)
Activation of the hypoxia-inducible factor pathway under normoxic conditions is a hallmark mechanism of nickel carcinogenesis, distinguishing it from arsenic and chromium.
Search: “signaling”
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44 records in this view
Mechanisms9 sources
NF-kB Signaling Pathway
Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) is a family of transcription factors that regulate inflammation, immune responses, cell survival, and proliferation. NF-kB is a convergence point where metal toxicity, pathogen signaling, and chronic…
Mechanisms8 sources
Aryl Hydrocarbon Receptor (AhR)
This page serves as a cross-reference point for the existing ahr concept page, which provides comprehensive coverage of AhR signaling, microbiome-derived ligands, and immune regulation. The aryl hydrocarbon receptor is a ligand-activated transcription factor that integr…
Mechanisms11 sources
Bacterial Contamination Hypothesis
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Microorganisms4 sources
Bacteroides thetaiotaomicron
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Microorganisms5 sources
Bifidobacterium breve
Bifidobacterium breve is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria, predominantly found in the infant gut and breast milk. It is among the earliest colonizers of the neonatal intestine and plays a key role in human milk oligosaccharide…
Mechanisms8 sources
Bile Acid Metabolism
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…
Mechanisms3 sources
Butyrate
The most biologically potent short-chain fatty acid (C4). Butyrate is the primary energy source for colonocytes, a histone deacetylase (HDAC) inhibitor with broad epigenetic effects, and a key anti-inflammatory mediator. Its depletion -- driven by loss of butyrate-produ…
Microorganisms3 sources
Butyrivibrio
Butyrivibrio is a genus of Gram-positive, obligate anaerobic bacteria within the family Lachnospiraceae (phylum Firmicutes). Originally characterized as a dominant fiber-fermenting genus in the rumen, Butyrivibrio species are also found in the human colon where they con…
Metals14 sources
Calcium
The most abundant mineral in the human body, with ~99% stored in bones and teeth. Calcium's biological significance extends far beyond structural support -- it is the universal second messenger in cell signaling, controlling neurotransmitter release, muscle contraction,…
Metals32 sources
Chromium
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Microorganisms7 sources
Clostridium symbiosum
Clostridium symbiosum is a Gram-positive, obligately anaerobic bacterium within the Clostridium cluster XIVa — a taxonomic group enriched for short-chain fatty acid (SCFA) producers and specialized bile acid metabolizers. Despite its ambiguous name (suggesting symbiotic…
Entity indexes8 sources
Dopamine
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Diseases8 sources
Fibromyalgia
Fibromyalgia (FM) is a chronic pain syndrome affecting 2-4% of the global population Heidari et al. 2017, characterized by widespread musculoskeletal pain, fatigue, cognitive dysfunction ("fibro fog"), and sleep disturbances. Conventionally attributed to central sensiti…
Microorganisms5 sources
Fusobacterium
A Gram-negative, obligate anaerobic bacterium that has emerged as the most consistently CRC-associated microorganism in human gut microbiome studies. F. nucleatum is the primary species of concern, originally a commensal of the oral cavity that translocates to colorecta…
Reference0 sources
Glossary
Alphabetical definitions of specialist terms used throughout this wiki. Where a full concept page exists, the term links to it. --- AhR (aryl hydrocarbon receptor) -- A ligand-activated transcription factor that senses microbial metabolites (especially indoles from tryp…
Mechanisms10 sources
Gut Barrier Dysfunction
Gut barrier dysfunction -- colloquially "leaky gut" -- is the pathological increase in intestinal permeability that permits translocation of bacteria, bacterial products (LPS, peptidoglycan), metals, and dietary antigens from the gut lumen into the systemic circulation.…
Mechanisms16 sources
Gut-Brain Axis
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…
Mechanisms6 sources
Hydrogen Sulfide (H₂S)
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Mechanisms8 sources
Hypoxia
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Mechanisms3 sources
Immunotherapy
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms13 sources
Interleukin-6 (IL-6)
Interleukin-6 is a pleiotropic cytokine that sits at the crossroads of innate immunity, adaptive immunity, and metabolism. It is one of the most frequently elevated inflammatory mediators across conditions in this wiki — appearing in disease signatures spanning IBD, aut…
Mechanisms3 sources
Ketone Bodies
Ketone bodies (beta-hydroxybutyrate [BHB], acetoacetate, acetone) are produced by hepatic fatty acid oxidation during carbohydrate restriction, fasting, or ketogenic diet consumption. BHB is the most abundant and is structurally and functionally analogous to butyrate — …
Mechanisms4 sources
Leptin
Leptin is an adipokine (hormone produced by adipose tissue) that signals satiety to the hypothalamus — suppressing appetite and increasing energy expenditure. Leptin resistance (elevated leptin with impaired signaling) is a hallmark of obesity, paralleling insulin resis…
Mechanisms6 sources
Lipopolysaccharide
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms3 sources
Metalloestrogen
A metal ion that activates estrogen receptors and mimics the biological effects of estradiol. Metalloestrogens represent a distinct class of endocrine-disrupting compounds where the active agent is an inorganic metal rather than an organic xenoestrogen like BPA or phtha…
Mechanisms13 sources
Metalloestrogens
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms7 sources
Microbial Metabolites
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Mechanisms7 sources
Microbiome-Derived Metabolites
Small molecules produced, modified, or activated by gut microbiota that function as the primary chemical language between the microbiome and its host. These metabolites are not passive byproducts — they regulate gene expression, immune cell differentiation, gut barrier …
Mechanisms22 sources
Mis-Metallation
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms10 sources
Mitochondrial Dysfunction
Mitochondrial dysfunction refers to the impairment of mitochondrial energy production, redox balance, and signaling functions. Mitochondria are the primary targets of heavy metal toxicity in human cells, and they are also the organelles most dependent on metal cofactors…
Mechanisms3 sources
Mycobiome
The fungal component of the human microbiome, comprising ~0.1-1% of the total gut microbial community by abundance but disproportionately active in immune signaling and cross-kingdom interactions. While bacterial communities dominate microbiome research, emerging eviden…
Mechanisms9 sources
Neuroinflammation
Chronic inflammatory activation within the central nervous system, driven by microglia, astrocytes, and infiltrating peripheral immune cells. Neuroinflammation is a convergent pathological mechanism across alzheimers disease, parkinsons disease, multiple sclerosis, and …
Diseases6 sources
Ovarian Cancer
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Microorganisms8 sources
Peptostreptococcus anaerobius
A Gram-positive, obligate anaerobic bacterium within the Firmicutes phylum (family Peptostreptococcaceae) that has emerged as a consistently enriched organism in the colorectal cancer tumor microenvironment. While fusobacterium nucleatum receives the most attention as a…
Mechanisms4 sources
Quorum Sensing
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms9 sources
Short-Chain Fatty Acids (SCFAs)
The most extensively referenced missing concept in this wiki. SCFAs -- acetate (C2), propionate (C3), and butyrate (C4) -- are the primary metabolic products of anaerobic bacterial fermentation of dietary fiber in the colon. They serve as the critical molecular link bet…
Clinical cautions6 sources
STOP: Calcium Supplementation with Cadmium Exposure
Research summary -- not medical advice. This page synthesizes published research on why a commonly recommended intervention requires careful consideration in the context of cadmium exposure. Consult a qualified healthcare provider before making changes to supplementatio…
Mechanisms3 sources
Succinate
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms10 sources
Tau Phosphorylation
Tau is a microtubule-associated protein essential for maintaining the structural integrity of neuronal axons. In health, tau binds to and stabilizes microtubules, enabling axonal transport of organelles, vesicles, and signaling molecules. When tau becomes hyperphosphory…
Mechanisms8 sources
TLR4
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mechanisms3 sources
Toll-Like Receptors
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Mechanisms3 sources
Tryptamine
Tryptamine is a microbial decarboxylation product of tryptophan, produced by bacterial tryptophan decarboxylase (found in ruminococcus gnavus, Clostridium sporogenes, and others). It is a serotonin receptor agonist (particularly 5-HT4) that stimulates gut motility and f…
Metals62 sources
Zinc
This knowledge-base record is being expanded from WikiBiome’s evidence graph.