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 279 articles covering 87 microorganisms, 17 metals, 71 biological mechanisms, and 15 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
  Autism Spectrum Disorder (ASD) is characterized by a distinctive dysbiotic microbiota signature — a coordinated shift in taxonomic composition, loss of metab...
• Cardiovascular Disease — Microbiome Signature
  Cardiovascular disease (CVD) encompasses atherosclerotic cardiovascular disease (ASCVD), heart failure (HF), hypertension, and related thrombotic events. The...
• 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...
• 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...
• 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...
• Obesity — Microbiome Signature
  Obesity is a chronic metabolic disorder characterized by excessive adipose tissue accumulation and whole body metabolic dysfunction. The conventional view tr...
• 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...
• 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...

Browse by Category

• Microbe (87 articles) — Bacteria, fungi, and archaea — their metal dependencies, virulence enzymes, and ecological roles in the human microbiome
• Mechanism (71 articles) — Biological mechanisms connecting heavy metals to microbiome disruption, including nutritional immunity, mis-metallation, and siderophore competition
• Disease (29 articles) — Conditions linked to heavy metal exposure and microbiome disruption, from autoimmune to neurodegenerative disorders
• Metal (17 articles) — Essential and toxic metals — their biological roles, exposure routes, and impact on microbial ecology
• Signature (15 articles) — Multi-layer disease signatures mapping metallomic, taxonomic, ecological, and virulence features
• Defense (14 articles) — Host defense systems including calprotectin, lactoferrin, hepcidin, and other nutritional immunity proteins
• Stop (14 articles) — Interventions that are counterproductive despite conventional wisdom — where standard-of-care may feed the disease
• Intervention (13 articles) — Evidence-based therapeutic approaches validated through the Triangle Test framework
• Analysis (10 articles) — Cross-cutting comparisons and syntheses across conditions, metals, and mechanisms
• Other (6 articles)
• Reference (2 articles)
• Entity (1 articles)

Recent Articles

• Aeromonas — Aeromonas is a genus of Gram negative, facultatively anaerobic bacteria found in aquatic environments and, increasing...
• Bacteroides Thetaiotaomicron — Bacteroides thetaiotaomicron is one of the most abundant and metabolically versatile commensals of the human gut. It ...
• Candida Auris — Candida auris is an emerging multidrug resistant fungal pathogen first identified in 2009 and now classified as a cri...
• Candida Tropicalis — Candida tropicalis is an opportunistic fungal pathogen and occasional gut commensal. It is the second or third most c...
• Celiac Disease — Celiac disease is a chronic autoimmune condition triggered by dietary gluten (gliadin proteins from wheat, barley, an...
• AhR (Aryl Hydrocarbon Receptor) — The aryl hydrocarbon receptor (AhR) is a ligand activated transcription factor that functions as a master sensor at t...
• Amyloid Beta — Amyloid beta (Aβ) is a peptide derived from the proteolytic cleavage of amyloid precursor protein (APP), predominantl...
• Major Depressive Disorder — Microbiome Signature — Major Depressive Disorder (MDD) is a mental health condition characterized by persistent low mood, anhedonia, cogniti...
• Endometriosis — Microbiome Signature — Endometriosis is a chronic estrogen dependent inflammatory condition affecting approximately 10% of reproductive age ...
• Graves' Disease — Microbiome Signature — Graves' disease is the most common cause of hyperthyroidism, characterized by autoantibodies against the TSH receptor...
• Hashimoto'S Thyroiditis — Microbiome Signature — > Clinical disclaimer: This signature page synthesizes peer reviewed evidence for practitioner education. It does not...
• Multiple Sclerosis — Microbiome Signature — Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease affecting approximately 2.8 million people worl...
• Obesity — Microbiome Signature — Obesity is a chronic metabolic disorder characterized by excessive adipose tissue accumulation and whole body metabol...
• Pancreatic Cancer — Microbiome Signature — > Clinical disclaimer: This signature page synthesizes peer reviewed evidence for practitioner education. It does not...
• Parkinson'S Disease — Microbiome Signature — Parkinson's Disease (PD) is the second most common neurodegenerative disorder, characterized by progressive loss of d...
• Polycystic Ovary Syndrome — Microbiome Signature — Polycystic Ovary Syndrome (PCOS) is the most common endocrine disorder in reproductive age women, affecting approxima...
• Type 2 Diabetes — Microbiome Signature — Type 2 Diabetes (T2D) is a metabolic disorder characterized by insulin resistance and hyperglycemia. The microbiome s...
• STOP: Iodine Supplementation For Hashimoto'S Thyroiditis — > Warning: Clinical Disclaimer: This STOP page represents a hypothesis based on mechanistic evidence and should NOT r...
• STOP: Iron Supplementation For Alzheimer'S Disease — > Warning: Clinical Disclaimer: This STOP page represents a hypothesis based on mechanistic evidence and should NOT r...
• STOP: Iron Supplementation For Colorectal Cancer — > Warning: Clinical Disclaimer: This STOP page represents a hypothesis based on mechanistic evidence and should NOT r...