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 343 articles covering 91 microorganisms, 20 metals, 75 biological mechanisms, and 28 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...
Browse by Category
- Microbe (91 articles) — Bacteria, fungi, and archaea — their metal dependencies, virulence enzymes, and ecological roles in the human microbiome
- Mechanism (75 articles) — Biological mechanisms connecting heavy metals to microbiome disruption, including nutritional immunity, mis-metallation, and siderophore competition
- Disease (36 articles) — Conditions linked to heavy metal exposure and microbiome disruption, from autoimmune to neurodegenerative disorders
- Stop (33 articles) — Interventions that are counterproductive despite conventional wisdom — where standard-of-care may feed the disease
- Signature (28 articles) — Multi-layer disease signatures mapping metallomic, taxonomic, ecological, and virulence features
- Intervention (21 articles) — Evidence-based therapeutic approaches validated through the Triangle Test framework
- Metal (20 articles) — Essential and toxic metals — their biological roles, exposure routes, and impact on microbial ecology
- Defense (14 articles) — Host defense systems including calprotectin, lactoferrin, hepcidin, and other nutritional immunity proteins
- Analysis (14 articles) — Cross-cutting comparisons and syntheses across conditions, metals, and mechanisms
- Other (8 articles)
- Reference (2 articles)
- Entity (1 articles)
Recent Articles
- Cerebral Palsy — Cerebral palsy (CP) is the most common motor disability in childhood, affecting 2 3 per 1,000 live births. Characteri...
- Erectile Dysfunction — Erectile dysfunction (ED) affects 30 50% of men aged 40 70, with prevalence increasing with age. Conventionally under...
- Female Infertility — Affects approximately 48 million women worldwide. From a microbiome metallomics perspective, female infertility sits ...
- Fibromyalgia — Fibromyalgia (FM) is a chronic pain syndrome affecting 2 4% of the global population, characterized by widespread mus...
- Long COVID — Post acute sequelae of SARS CoV 2 infection (PASC), affecting an estimated 10 30% of COVID 19 survivors with symptoms...
- Necrotizing Enterocolitis — Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal emergency in premature infants, affect...
- Premenstrual Dysphoric Disorder — Premenstrual Dysphoric Disorder (PMDD) affects 3 8% of menstruating individuals, causing severe mood disturbances, ir...
- 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 pr...
- 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 disea...
- Female Infertility — Microbiome Signature — An umbrella signature covering microbiome driven mechanisms across infertility subtypes: premature ovarian insufficie...
- Fibromyalgia — Microbiome Signature — Fibromyalgia (FM) presents as widespread chronic pain with fatigue, cognitive dysfunction, and sleep disturbance. The...
- Long COVID — Microbiome Signature — Post acute sequelae of SARS CoV 2 (PASC) affects 10 30% of COVID survivors with symptoms persisting >12 weeks. The si...
- Necrotizing Enterocolitis — Microbiome Signature — Necrotizing enterocolitis (NEC) is the most lethal GI emergency in premature infants, affecting 5 12% of VLBW neonate...
- Premenstrual Dysphoric Disorder — Microbiome Signature — Premenstrual Dysphoric Disorder (PMDD) affects 3 8% of menstruating individuals with severe luteal phase mood disturb...
- Author Outreach Campaign — Operational Plan — Every paper in WikiBiome represents a relationship we have not yet opened. The ingestion step — reading the source ca...
- Anaerostipes — A genus of Gram positive obligate anaerobes in the family Lachnospiraceae (Clostridium cluster XIVa) that occupy a cr...
- Bismuth — A heavy metal traditionally considered safe enough for over the counter gastrointestinal remedies (Pepto Bismol), bis...
- Flavonifractor — A Gram positive obligate anaerobe in the family Ruminococcaceae (Clostridium cluster IV) whose defining metabolic act...
- Gallium — A group 13 metal with no known biological function in any organism yet one of the most promising antimicrobial metals...
- Platinum — A dense, chemically inert noble metal with no known biological function yet platinum compounds are the backbone of ch...