WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
Cadaverine (1,5-diaminopentane) is a biogenic amine produced by bacterial lysine decarboxylase — primarily by Enterobacteriaceae, Fusobacterium, and Clostridium — during proteolytic fermentation of undigested protein in the distal colon. It is a product of putrefaction …
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cadmium (Cd) enters the human body primarily through food. Unlike nickel, which has high-concentration food categories that can be avoided, cadmium contamination is diffuse — embedded in staple crops, leafy greens, and grains that form the basis of most dietary patterns…
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…
A Gram-negative, aerobic, non-fermenting coccobacillus and a member of the ESKAPE group of priority pathogens (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter). Acinetobacter baumannii is among the most problematic nosocomial pathogens…
WHO Priority 1: Critical. A Gram-negative, strictly aerobic coccobacillus and one of the most dangerous nosocomial pathogens on the planet. A. baumannii belongs to the ESKAPE group and causes ventilator-associated pneumonia, wound infections, and bloodstream infections …
A Gram-negative, obligate anaerobic, mucin-degrading bacterium that colonizes the intestinal mucus layer and has emerged as one of the most important next-generation probiotics. A. muciniphila is consistently depleted in disease states associated with metal dyshomeostas…
A 140-amino-acid presynaptic protein whose misfolding into insoluble fibrils and their deposition in Lewy bodies is the defining neuropathological hallmark of parkinsons disease and the broader family of synucleinopathies (including Lewy body dementia and multiple syste…
The most common form of dementia, affecting an estimated 55 million people worldwide and projected to triple by 2050 zhang 2024 recent advances alzheimers mechanisms trials. Characterized by progressive memory loss, cognitive decline, amyloid-beta plaques, and neurofibr…
The process by which soluble amyloid-beta (Aβ) monomers assemble into neurotoxic oligomers and insoluble fibrillar plaques in the brain -- the defining neuropathological event of alzheimers disease. What distinguishes WikiBiome's treatment of this process from conventio…
A genus of Gram-positive obligate anaerobes in the family Lachnospiraceae (Clostridium cluster XIVa) that occupy a critical metabolic relay position in gut ecosystem stability: converting lactate to butyrate. Anaerostipes is one of the most consistently depleted genera …
A metalloid that sits in the shadows of better-studied toxic metals like lead, cadmium, and mercury, yet appears with surprising consistency in metallomic studies of endocrine and inflammatory conditions. Antimony (symbol Sb, from Latin stibium; atomic number 51) exists…
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Progressive inflammatory disease of the arterial wall characterized by lipid accumulation, immune cell infiltration, and fibrous plaque formation. In the metallomics framework, atherosclerosis sits at the convergence of three interacting systems: heavy metal toxicity, g…
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A neurodevelopmental condition affecting approximately 1 in 36 children (US CDC 2023 estimate), characterized by differences in social communication, restricted interests, and repetitive behaviors. From a metallomics perspective, ASD presents a compelling convergence of…
Autoimmunity occurs when the immune system attacks the body's own tissues. What has emerged over the past two decades is that the gut microbiome is not merely associated with autoimmune disease -- it is a mechanistic driver of immune tolerance breakdown. Metals add a se…
Autophagy (from Greek, "self-eating") is the cellular process of degrading and recycling damaged organelles, misfolded proteins, and intracellular pathogens through lysosomal digestion. It is the cell's primary quality control mechanism -- a housekeeping system that bec…
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Bacterial vaginosis (BV) is the most common vaginal infection in women of reproductive age, affecting an estimated 29% of women globally. Rather than an infection by a single pathogen, BV represents a polymicrobial dysbiotic state -- a collapse of the protective Lactoba…
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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,…
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Christensenellaceae is a family of Gram-negative, strictly anaerobic bacteria within the order Clostridiales (phylum Firmicutes) that has emerged as one of the most consistently health-associated and heritable members of the human gut microbiome. First formally describe…
A progressive loss of kidney function affecting approximately 850 million people worldwide (10–14% of adults), causing 1.2 million deaths annually. CKD is unique among diseases in this wiki because it occupies both sides of the metal-disease equation: heavy metals (Cd, …
The collective ability of the resident gut microbiome to prevent colonization by exogenous pathogens and suppress expansion of resident pathobionts. Colonization resistance is not a property of any single organism but an emergent function of the whole microbial communit…
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An essential trace element with a striking dual nature: required for survival as a cofactor for critical enzymes (SOD1, cytochrome c oxidase, ceruloplasmin), yet toxic in excess through Fenton-like redox cycling and mis metallation of iron-sulfur clusters. Copper is ele…
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A chronic, relapsing-remitting inflammatory bowel disease (IBD) characterized by transmural inflammation of the gastrointestinal tract, most commonly affecting the terminal ileum and colon but capable of involving any segment from mouth to anus zhang 2017 intestinal mic…
Depression is the most prevalent mental health disorder globally, affecting over 280 million people zhu 2025 microbiota gut brain axis depression review, and one of the most metal-sensitive conditions in this wiki. It sits at the convergence of nearly every pathway cata…
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A synthesis of how dietary heavy metal exposure varies across the human lifespan, highlighting that the same metals present different risks at different developmental stages due to changing absorption rates, detoxification capacity, dietary patterns, and organ vulnerabi…
This page identifies the contradictions and clinical dilemmas that become visible only when the 236 source pages in this wiki are read together. Each paradox describes a situation where evidence-based dietary or supplementation advice -- advice that is correct for most …
The pathological disruption of normal metal homeostasis — the tightly regulated balance of essential trace elements (iron, zinc, copper, manganese, selenium, cobalt) and the effective exclusion of toxic metals (cadmium, lead, mercury, arsenic). Dyshomeostasis is a conve…
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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: …
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Exogenous chemicals that interfere with hormone synthesis, secretion, transport, binding, or elimination, mimicking or blocking endogenous hormones at physiologically relevant concentrations. In the metallomics-microbiome framework, endocrine disruptors occupy a critica…
A genus of Gram-positive bacteria (primarily E. faecalis and E. faecium) that exemplifies the metal-antibiotic resistance co-selection crisis. Enterococci carry diverse metal tolerance genes for mercury, arsenic, copper, and cadmium on the same mobile genetic elements a…
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Epigenetics is the study of heritable changes in gene expression that occur without alterations to the DNA sequence itself. These changes -- primarily DNA methylation, histone modifications, and non-coding RNA regulation -- represent a molecular memory system that can b…
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Erectile dysfunction (ED) affects 30-50% of men aged 40-70 Feldman et al. 1994, with prevalence increasing with age. Conventionally understood as a vascular and/or neurogenic disorder, ED is now recognized as a condition with a significant gut microbiome component -- th…
The most abundant bacterium in the healthy human colon (5-15% of total fecal microbiota), F. prausnitzii is the premier butyrate producer in the gut and a cornerstone of anti-inflammatory intestinal homeostasis. Its depletion is one of the most consistent microbiome sig…
Affects approximately 48 million women worldwide (WHO global infertility prevalence estimates). From a microbiome-metallomics perspective, female infertility sits at the intersection of the estrobolome (microbial estrogen metabolism), heavy metal reproductive toxicity (…
The most common malignancy of the stomach, accounting for over 95% of gastric cancers. helicobacter pylori infection is the strongest known risk factor, classified as a Group 1 carcinogen by IARC. In the metallomics framework, gastric adenocarcinoma reveals a striking d…
The fifth most common cancer worldwide and third leading cause of cancer death, with over 1 million new cases annually. Gastric cancer stands unique in this wiki as the disease where a single microorganism -- helicobacter pylori -- provides the dominant causal pathway, …
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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…
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This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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Heavy metals exert some of their most devastating effects on the nervous system. lead, mercury, and arsenic are the three metals with the most extensively documented neurotoxic mechanisms, but cadmium, manganese, aluminum, and nickel also contribute to neurological dama…
The 6-24 month developmental window — when infants transition from breast milk to solid foods — represents a convergence of maximum vulnerability and maximum exposure. Immature detoxification systems, rapid organ development, and high food-to-body-weight ratios mean tha…
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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…
Sustained elevation of systemic blood pressure, affecting an estimated 1.3 billion adults worldwide and the leading modifiable risk factor for cardiovascular disease, stroke, and chronic kidney disease. The gut microbiome-blood pressure axis has emerged as a major resea…
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…
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The intestinal epithelium is a single-cell-thick barrier separating the lumen -- home to trillions of microbes and ingested metals -- from the systemic circulation. When this barrier fails, the consequences cascade: microbial products translocate, metals gain unrestrict…
A Gram-positive, obligate anaerobic genus within the Firmicutes phylum (family Oscillospiraceae or Ruminococcaceae depending on classification) that possesses a unique metabolic capability: butyrate production from lysine fermentation rather than from dietary fiber. Thi…
An essential halogen required for thyroid hormone synthesis (T3 and T4). The thyroid gland is the primary iodine-concentrating organ, containing 70-80% of total body iodine. Iodine occupies a unique position in the metallomics landscape: it is not a metal, but its inter…
The kynurenine pathway (KP) is the dominant route of tryptophan catabolism, accounting for approximately 95% of dietary tryptophan degradation. It produces a cascade of neuroactive, immunomodulatory, and potentially neurotoxic metabolites whose balance determines whethe…
This page serves as the family-level hub for Lachnospiraceae, connecting the individual genus and species pages (roseburia, blautia, anaerostipes, eubacterium rectale) with the overarching ecological and metabolic framework that defines the family. For the primary entit…
Lactobacillus iners is a Gram-positive, facultatively anaerobic bacterium that dominates the vaginal microbiome of many women worldwide, defining Community State Type III (CST-III) in vaginal microbiome classification. For decades, all vaginal Lactobacillus species were…
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This page synthesizes findings across 1,426 source pages to map the relationships between metals and disease. Where individual source pages document a single study's findings, this page identifies the patterns that emerge when those findings are laid side by side. ADVER…
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…
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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…
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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…