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 248 articles covering 83 microorganisms, 17 metals, 69 biological mechanisms, and 12 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...
- 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 ...
- 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...
- 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 (83 articles) — Bacteria, fungi, and archaea — their metal dependencies, virulence enzymes, and ecological roles in the human microbiome
- Mechanism (69 articles) — Biological mechanisms connecting heavy metals to microbiome disruption, including nutritional immunity, mis-metallation, and siderophore competition
- Disease (24 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
- Defense (14 articles) — Host defense systems including calprotectin, lactoferrin, hepcidin, and other nutritional immunity proteins
- Signature (13 articles) — Multi-layer disease signatures mapping metallomic, taxonomic, ecological, and virulence features
- Stop (11 articles) — Interventions that are counterproductive despite conventional wisdom — where standard-of-care may feed the disease
- Other (6 articles)
- Intervention (5 articles) — Evidence-based therapeutic approaches validated through the Triangle Test framework
- Analysis (5 articles) — Cross-cutting comparisons and syntheses across conditions, metals, and mechanisms
- Entity (1 articles)
Recent Articles
- Escherichia Coli — A Gram negative bacterium that spans the commensal pathogen spectrum, with pathogenic variants (UPEC, STEC, EHEC) dep...
- Helicobacter Pylori — A gastric pathogen that is arguably the most nickel dependent human pathogen known. Two of its key virulence factors ...
- Hungatella — Hungatella hathewayi is a Gram positive, obligate anaerobic bacterium within the Firmicutes phylum (family Clostridia...
- Intestinibacter — Intestinibacter bartlettii is a Gram positive, obligate anaerobic, spore forming bacterium within the Firmicutes phyl...
- Iodine — An essential halogen required for thyroid hormone synthesis (T3 and T4). The thyroid gland is the primary iodine conc...
- Lachnospira — Lachnospira is a genus of Gram positive, obligate anaerobic bacteria within the lachnospiraceae family (Firmicutes). ...
- Odoribacter — Odoribacter splanchnicus is a Gram negative, obligate anaerobic bacterium belonging to the family Odoribacteraceae wi...
- Parasutterella — Parasutterella excrementihominis is a Gram negative, obligate anaerobic bacterium within the Betaproteobacteria class...
- Parvimonas — Parvimonas micra is a Gram positive, obligate anaerobic coccus of oral origin that has emerged as one of the most con...
- Proteus Mirabilis — A Gram negative uropathogen whose Ni dependent urease is the central driver of catheter associated urinary tract infe...
- Pseudomonas Aeruginosa — An opportunistic Gram negative pathogen with a unique dual use siderophore system: its pyoverdine and pyochelin serve...
- Salmonella Enterica Serovar Typhimurium — A Gram negative enteric pathogen that possesses four distinct [NiFe] hydrogenases the most of any well characterized ...
- Staphylococcus Aureus — A versatile Gram positive pathogen with one of the best characterized nutritional immunity evasion systems known. S. ...
- Streptococcus Pneumoniae — A Gram positive pathogen (the "pneumococcus") that depends on iron, manganese, and zinc for virulence and has evolved...
- Dietary Arsenic Exposure — arsenic (As) is unique among dietary heavy metals because it exists in two fundamentally different forms with dramati...
- Dietary Cadmium Exposure — cadmium (Cd) enters the human body primarily through food. Unlike nickel, which has high concentration food categorie...
- Dietary Iron And Gut Ecology — iron occupies a unique position among dietary metals: it is both an essential nutrient and a selective pressure that ...
- Dietary Lead Exposure — lead (Pb) has no safe level of exposure. Unlike most dietary metals, lead does not play any known biological role — e...
- Dietary Metal Microbiome Interactions — Every meal delivers metals to the gut lumen — essential minerals, trace elements, and contaminants alike. These metal...
- Heavy Metals In Infant Foods — The 6 24 month developmental window — when infants transition from breast milk to solid foods — represents a converge...