WikiBiome

The open encyclopedia of microbiome metallomics.

WikiBiome explores how heavy metals shape the human microbiome, drive disease, and reveal new therapeutic targets. A project of the Paleo Foundation.

What is Microbiome Metallomics?

Microbiome metallomics is the study of how metals — both essential (iron, zinc, manganese) and toxic (lead, cadmium, mercury, arsenic) — shape the composition and behavior of human-associated microbial communities. Heavy metals act as selective pressures on the microbiome, favoring metal-tolerant or metal-dependent organisms and suppressing sensitive beneficial species. This field integrates toxicology, microbial ecology, nutritional immunology, and clinical medicine to reveal how environmental metal exposures contribute to chronic disease through microbial mechanisms.

WikiBiome currently contains 714 articles covering 178 microorganisms, 29 metals, 167 biological mechanisms, and 70 disease signatures — all sourced from peer-reviewed research.

Disease Signatures

Each disease signature maps five layers of evidence: the metallomic profile (which metals are elevated or depleted), the taxonomic signature (which microbes are enriched or lost), the nutritional immunity response (how the host fights back), the ecological state (oxygen, pH, biofilm), and the virulence enzymes that connect metal availability to pathogenic function.

• Alzheimer'S Disease — Microbiome Signature
  Alzheimer's Disease is a progressive neurodegenerative disorder affecting >50 million people worldwide. Clinically, it presents as cognitive decline, memory ...
• Autism Spectrum Disorder — Microbiome Signature
  A neurodevelopmental condition affecting ~1 in 36 children, characterized by differences in social communication and repetitive behaviors. ASD presents the m...
• Cardiovascular Disease — Microbiome Signature
  Cardiovascular disease (CVD) encompasses atherosclerotic cardiovascular disease (ASCVD), heart failure (HF), hypertension, and related thrombotic events. The...
• Cerebral Palsy — Microbiome Signature
  Cerebral palsy (CP) is the most common motor disability in childhood (2 3 per 1,000 live births), arising from non progressive injury to the developing brain...
• Chronic Kidney Disease — Microbiome Signature
  CKD affects ~850 million people worldwide and is unique among diseases in this knowledge base because it occupies both sides of the metal disease equation: h...
• Colorectal Cancer — Microbiome Signature
  Colorectal cancer (CRC) is the third most common cancer worldwide, affecting ~1.9 million people annually. The conventional view treats CRC as an age related...
• Crohn'S Disease — Microbiome Signature
  Crohn's disease (CD) is a chronic inflammatory bowel disease characterized by transmural inflammation of the gastrointestinal tract, with periods of exacerba...
• Major Depressive Disorder — Microbiome Signature
  Major Depressive Disorder (MDD) is a mental health condition characterized by persistent low mood, anhedonia, cognitive disruption, and neurovegetative chang...
• Endometriosis — Microbiome Signature
  Endometriosis is a chronic estrogen dependent inflammatory condition affecting approximately 10% of reproductive age women worldwide. The conventional view t...
• Erectile Dysfunction — Microbiome Signature
  Erectile Dysfunction (ED) affects 30 50% of men aged 40 70 and serves as a 3 5 year sentinel for cardiovascular disease. The microbiome signature reveals the...
• Female Infertility — Microbiome Signature
  An umbrella signature covering microbiome driven mechanisms across infertility subtypes: premature ovarian insufficiency (POI), PCOS related infertility, dim...
• Fibromyalgia — Microbiome Signature
  Fibromyalgia (FM) presents as widespread chronic pain with fatigue, cognitive dysfunction, and sleep disturbance. The microbiome signature reveals FM as an e...
• Gastroesophageal Reflux Disease — Microbiome Signature
  GERD affects ~13.3% of the global population and has been reconceptualized from a simple "acid burn" model to a "cytokine sizzle" model — inflammation is imm...
• Graves' Disease — Microbiome Signature
  Graves' disease is the most common cause of hyperthyroidism, characterized by autoantibodies against the TSH receptor that drive diffuse thyroid enlargement ...
• Hashimoto'S Thyroiditis — Microbiome Signature
  > Clinical disclaimer: This signature page synthesizes peer reviewed evidence for practitioner education. It does not constitute medical advice. All interven...
• Long COVID — Microbiome Signature
  Post acute sequelae of SARS CoV 2 (PASC) affects 10 30% of COVID survivors with symptoms persisting >12 weeks. The signature is distinctive for its self perp...
• Multiple Sclerosis — Microbiome Signature
  Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease affecting approximately 2.8 million people worldwide, with a 3:1 female predominance. T...
• Necrotizing Enterocolitis — Microbiome Signature
  Necrotizing enterocolitis (NEC) is the most lethal GI emergency in premature infants, affecting 5 12% of VLBW neonates with 20 30% mortality. The microbiome ...
• Obesity — Microbiome Signature
  Obesity is a chronic metabolic disorder characterized by excessive adipose tissue accumulation and whole body metabolic dysfunction. The conventional view tr...
• Ovarian Cancer — Microbiome Signature
  The most lethal gynecological malignancy (~314,000 new cases, ~207,000 deaths annually), with >70% diagnosed at stage III/IV. The microbiome signature of ova...
• Pancreatic Cancer — Microbiome Signature
  > Clinical disclaimer: This signature page synthesizes peer reviewed evidence for practitioner education. It does not constitute medical advice. All interven...
• Parkinson'S Disease — Microbiome Signature
  Parkinson's Disease (PD) is the second most common neurodegenerative disorder, characterized by progressive loss of dopaminergic neurons in the substantia ni...
• Polycystic Ovary Syndrome — Microbiome Signature
  Polycystic Ovary Syndrome (PCOS) is the most common endocrine disorder in reproductive age women, affecting approximately 6 20% depending on diagnostic crite...
• Premenstrual Dysphoric Disorder — Microbiome Signature
  Premenstrual Dysphoric Disorder (PMDD) affects 3 8% of menstruating individuals with severe luteal phase mood disturbance, irritability, and anxiety. The mic...
• Postpartum Depression — Microbiome Signature
  Postpartum depression (PPD) affects 10–20% of new mothers worldwide, making it the most common serious complication of childbirth. The conventional framing e...
• Schizophrenia — Microbiome Signature
  A severe neuropsychiatric disorder affecting ~1% of the global population, with 15 20 years of reduced life expectancy driven largely by metabolic comorbidit...
• Type 1 Diabetes — Microbiome Signature
  Type 1 Diabetes (T1D) is an autoimmune disease in which CD4+ and CD8+ T cells destroy pancreatic beta cells, eliminating insulin production. It affects appro...
• Type 2 Diabetes — Microbiome Signature
  Type 2 Diabetes (T2D) is a metabolic disorder characterized by insulin resistance and hyperglycemia. The microbiome signature framework reveals T2D as an eco...
• Alzheimer'S Disease Microbiome Signature
  Alzheimer's disease (AD) is the most common form of dementia, affecting approximately 55 million people worldwide and projected to triple by 2050 zhang 2024 ...
• Anxiety Disorders — Microbiome Signature
  Anxiety disorders are the most prevalent mental health conditions globally (~280 million affected, ~4.8% of world population), encompassing generalized anxie...
• Atherosclerosis — Microbiome Signature
  Atherosclerosis is a chronic inflammatory disease of arterial walls characterized by lipid laden plaque formation, endothelial dysfunction, and progressive v...
• Autism Spectrum Disorder Microbiome Signature
  Autism spectrum disorder (ASD) is a neurodevelopmental condition affecting approximately 1 in 36 children (US CDC 2023 estimate), characterized by difference...
• Barrett'S Esophagus — Microbiome Signature
  Barrett's esophagus (BE) is a premalignant condition in which the normal squamous epithelium of the distal esophagus is replaced by intestinal type columnar ...
• Breast Cancer — Microbiome Signature
  Breast cancer is the most common cancer in women worldwide (~2.3 million new cases annually). The signature reveals a distinctive convergence of metalloestro...
• Cardiovascular Disease — Microbiome Signature
  Cardiovascular disease (CVD) encompassing atherosclerosis, coronary artery disease, hypertension, myocardial infarction, heart failure, and stroke is the lea...
• Celiac Disease — Microbiome Signature
  Celiac disease is a chronic autoimmune condition triggered by dietary gluten in genetically susceptible individuals (HLA DQ2/DQ8). Gluten exposure causes imm...
• Cerebral Palsy — Microbiome Signature
  Cerebral palsy (CP) is the most common motor disability in childhood (2 3 per 1,000 live births), traditionally attributed to perinatal asphyxia but increasi...
• Chronic Kidney Disease — Microbiome Signature
  Chronic kidney disease affects approximately 850 million people worldwide (10 14% of adults), causing 1.2 million deaths annually. CKD is unique among diseas...
• Colorectal Cancer — Microbiome Signature
  Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer death. Over 90% of cases are sporadic, shaped by the...
• Crohn'S Disease Microbiome Signature
  Crohn's disease (CD) is a chronic, relapsing remitting inflammatory bowel disease characterized by transmural inflammation of the gastrointestinal tract, mos...
• Depression — Microbiome Signature
  Major depressive disorder (MDD) affects over 280 million people globally and sits at the convergence of nearly every pathway catalogued in this knowledge bas...
• Endometriosis Microbiome Signature
  Endometriosis is a chronic estrogen dependent inflammatory condition affecting approximately 10% of reproductive age women, characterized by growth of endome...
• Epilepsy — Microbiome Signature
  Epilepsy affects ~50 million people worldwide, with ~30% experiencing drug resistant seizures. The gut brain axis provides a mechanistic framework for unders...
• Erectile Dysfunction — Microbiome Signature
  Erectile dysfunction (ED) affects 30 50% of men aged 40 70 (Feldman et al. 1994). Conventionally understood as a vascular and/or neurogenic disorder, ED is n...
• Female Infertility — Microbiome Signature
  Female infertility affects approximately 48 million women worldwide (WHO). This signature reveals three converging pathways: (1) the estrobolome — microbial ...
• Fibromyalgia — Microbiome Signature
  Fibromyalgia (FM) affects 2 4% of the global population (Heidari et al. 2017), characterized by widespread musculoskeletal pain, fatigue, cognitive dysfuncti...
• Gastric Cancer — Microbiome Signature
  Gastric cancer is the fifth most common cancer worldwide and the third leading cause of cancer death, with over 1 million new cases annually. It stands uniqu...
• Gastroesophageal Reflux Disease (GERD) — Microbiome Signature
  GERD affects approximately 20% of Western populations and is conventionally managed with proton pump inhibitors. The microbiome signature reveals GERD as far...
• Gestational Diabetes — Microbiome Signature
  <! STUB: needs expansion >
• Graves' Disease — Microbiome Signature
  Graves' disease (GD) is the most common cause of hyperthyroidism, characterized by TSH receptor antibodies (TRAb) that stimulate the thyroid gland. It affect...
• Hashimoto'S Thyroiditis — Microbiome Signature
  Hashimoto's thyroiditis (HT) is the most common autoimmune disease globally and the leading cause of hypothyroidism, with prevalence of 5 10% and a striking ...
• Hypertension — Microbiome Signature
  Hypertension affects an estimated 1.3 billion adults worldwide and is the leading modifiable risk factor for cardiovascular disease, stroke, and chronic kidn...
• Irritable Bowel Syndrome — Microbiome Signature
  Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder affecting 10 15% of the global population, characterized by chronic abdominal pain, ...
• Inflammatory Bowel Disease Microbiome Signature
  Inflammatory bowel disease (IBD) is an umbrella term for chronic relapsing remitting inflammatory conditions of the gastrointestinal tract, principally crohn...
• Long COVID — Microbiome Signature
  Long COVID (post acute sequelae of SARS CoV 2 infection, PASC) affects an estimated 10 30% of COVID 19 survivors with symptoms persisting beyond 12 weeks. Th...
• Multiple Sclerosis — Microbiome Signature
  Multiple sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system affecting approximately 2.8 million people globally. The ...
• Necrotizing Enterocolitis — Microbiome Signature
  Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal emergency in premature infants, affecting 5 12% of very low birth weight neona...
• Obesity — Microbiome Signature
  Obesity affects over 1 billion people globally and is characterized by excess adipose tissue accumulation, systemic low grade inflammation, and gut microbiom...
• Ovarian Cancer — Microbiome Signature
  Ovarian cancer is the most lethal gynecological malignancy, with approximately 314,000 new cases and 207,000 deaths annually worldwide. Its poor prognosis st...
• Pancreatic Cancer — Microbiome Signature
  Pancreatic cancer is the fifth leading cause of cancer death in Western nations. Pancreatic ductal adenocarcinoma (PDAC) accounts for >90% of cases, with fiv...
• Pancreatitis — Microbiome Signature
  Pancreatitis is inflammation of the pancreas, occurring as acute pancreatitis (AP, 34 per 100,000/year) and chronic pancreatitis (CP, 10 per 100,000). Severe...
• Parkinson'S Disease Microbiome Signature
  Parkinson's disease (PD) is the second most common neurodegenerative disease, affecting over 10 million people worldwide. Characterized by progressive loss o...
• Polycystic Ovary Syndrome — Microbiome Signature
  Polycystic ovary syndrome (PCOS) affects 6 20% of reproductive age women and is the leading cause of anovulatory infertility. From a metallomics perspective,...
• Premenstrual Dysphoric Disorder — Microbiome Signature
  Premenstrual Dysphoric Disorder (PMDD) affects 3 8% of menstruating individuals, causing severe mood disturbances, irritability, anxiety, and physical sympto...
• Postpartum Depression — Microbiome Signature
  Postpartum depression (PPD) affects 10 20% of women after delivery, with profound consequences for maternal health, infant bonding, and child neurodevelopmen...
• Rheumatoid Arthritis — Microbiome Signature
  Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by symmetric polyarthritis with progressive joint destruction, affecting app...
• Schizophrenia — Microbiome Signature
  Schizophrenia is a severe neuropsychiatric disorder affecting approximately 1% of the global population, characterized by positive symptoms (hallucinations, ...
• Type 1 Diabetes — Microbiome Signature
  Type 1 diabetes is an autoimmune disease in which immune mediated destruction of insulin producing beta cells leads to lifelong insulin dependence. T1D accou...
• Type 2 Diabetes — Microbiome Signature
  Type 2 diabetes (T2D) affects over 500 million people worldwide and is conventionally framed around caloric excess and sedentary behavior. The metallomic per...
• Ulcerative Colitis — Microbiome Signature
  Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by continuous mucosal inflammation of the colon, extending proximally from the ...

Browse by Category

• Microbe (178 articles) — Bacteria, fungi, and archaea — their metal dependencies, virulence enzymes, and ecological roles in the human microbiome
• Mechanism (167 articles) — Biological mechanisms connecting heavy metals to microbiome disruption, including nutritional immunity, mis-metallation, and siderophore competition
• Stop (72 articles) — Interventions that are counterproductive despite conventional wisdom — where standard-of-care may feed the disease
• Intervention (71 articles) — Evidence-based therapeutic approaches validated through the Triangle Test framework
• Signature (70 articles) — Multi-layer disease signatures mapping metallomic, taxonomic, ecological, and virulence features
• Disease (56 articles) — Conditions linked to heavy metal exposure and microbiome disruption, from autoimmune to neurodegenerative disorders
• Analysis (31 articles) — Cross-cutting comparisons and syntheses across conditions, metals, and mechanisms
• Metal (29 articles) — Essential and toxic metals — their biological roles, exposure routes, and impact on microbial ecology
• Defense (24 articles) — Host defense systems including calprotectin, lactoferrin, hepcidin, and other nutritional immunity proteins
• Other (9 articles)
• Entity (5 articles)
• Reference (2 articles)

Recent Articles

• Barium — <! Auto created stub from Rule 13 scope discovery. 4 source pages mention this metal. Awaiting content expansion. >
• Citrobacter — <! Auto created stub from Rule 13 scope discovery. 10 source pages mention this taxon. Awaiting content expansion. >
• Cladosporium — <! Auto created stub from Rule 13 scope discovery. 8 source pages mention this taxon. Awaiting content expansion. >
• Corynebacterium — <! Auto created stub from Rule 13 scope discovery. 8 source pages mention this taxon. Awaiting content expansion. >
• Enterobacter — <! Auto created stub from Rule 13 scope discovery. 12 source pages mention this taxon. Awaiting content expansion. >
• Faecalibacterium — <! Auto created stub from Rule 13 scope discovery. 14 source pages mention this taxon. Awaiting content expansion. >
• Fusarium — <! Auto created stub from Rule 13 scope discovery. 6 source pages mention this taxon. Awaiting content expansion. >
• Listeria — <! Auto created stub from Rule 13 scope discovery. 6 source pages mention this taxon. Awaiting content expansion. >
• Megasphaera — <! Auto created stub from Rule 13 scope discovery. 11 source pages mention this taxon. Awaiting content expansion. >
• Propionibacterium — <! Auto created stub from Rule 13 scope discovery. 7 source pages mention this taxon. Awaiting content expansion. >
• Proteus — <! Auto created stub from Rule 13 scope discovery. 5 source pages mention this taxon. Awaiting content expansion. >
• Pseudomonas — <! Auto created stub from Rule 13 scope discovery. 6 source pages mention this taxon. Awaiting content expansion. >
• Ruminococcaceae — <! Auto created stub from Rule 13 scope discovery. 7 source pages mention this taxon. Awaiting content expansion. >
• Salmonella — <! Auto created stub from Rule 13 scope discovery. 22 source pages mention this taxon. Awaiting content expansion. >
• Shigella — <! Auto created stub from Rule 13 scope discovery. 36 source pages mention this taxon. Awaiting content expansion. >
• Strontium — <! Auto created stub from Rule 13 scope discovery. 5 source pages mention this metal. Awaiting content expansion. >
• Subdoligranulum — <! Auto created stub from Rule 13 scope discovery. 12 source pages mention this taxon. Awaiting content expansion. >
• Titanium — <! Auto created stub from Rule 13 scope discovery. 3 source pages mention this metal. Awaiting content expansion. >
• Treponema — <! Auto created stub from Rule 13 scope discovery. 9 source pages mention this taxon. Awaiting content expansion. >
• Uranium — <! Auto created stub from Rule 13 scope discovery. 4 source pages mention this metal. Awaiting content expansion. >