WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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 Gram-negative obligate anaerobe identified as a histamine-producing bacterium enriched in dysbiotic microbiota associated with obesity, metabolic syndrome, and metabolic endotoxemia. Allisonella is a minor but functionally significant genus whose primary clinical rele…
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Cephalosporins are a class of beta-lactam antibiotics (five generations) that inhibit bacterial cell wall synthesis by binding penicillin-binding proteins. They are among the most prescribed antibiotic classes and among the most disruptive to the gut microbiome.
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 …
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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…
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…
Indoxyl sulfate (IS) is a protein-bound uremic toxin produced through a two-step process: gut bacteria convert dietary tryptophan to indole, which is then absorbed and sulfated by hepatic sulfotransferases (SULT1A1). IS exemplifies how dysbiosis-driven metabolite overpr…
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 most abundant transition metal in the human body and arguably the most consequential metal in biology. Iron sits at the center of a paradox that drives pathology across virtually every disease domain: organisms need it for oxygen transport, energy metabolism, DNA sy…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
An essential macromineral required as a cofactor for over 300 enzymatic reactions in the body, including energy metabolism, protein synthesis, DNA/RNA stability, and neuromuscular function. Magnesium is not a heavy metal or trace element but is frequently measured along…
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A family of Gram-positive obligate anaerobes (formerly classified as the genus Oscillospira, now reclassified into Oscillibacter and related genera within Oscillospiraceae) that serve as keystone butyrate producers in the healthy human distal colonic microbiota (Konikof…
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A Gram-positive, obligate anaerobic genus that has emerged as one of the most consistently enriched taxa in colorectal cancer. The key pathogenic species P. anaerobius promotes colorectal carcinogenesis through multiple mechanisms including cholesterol biosynthesis indu…
A Gram-positive, obligate anaerobic bacterium within the Firmicutes phylum (family Peptostreptococcaceae) that has emerged as a consistently enriched organism in the colorectal cancer tumor microenvironment. While fusobacterium nucleatum receives the most attention as a…
Peptostreptococcus stomatis is a Gram-positive, obligately anaerobic coccus originally isolated from the human oral cavity (oral streptococcal species) that has emerged as a carcinogenic oral pathobiont enriched in colorectal cancer, particularly in advanced stages. Unl…
A Gram-positive obligate anaerobe that has emerged as a pro-inflammatory pathobiont enriched across multiple disease states including crohns disease, depression, and multiple sclerosis. R. gnavus produces a species-specific inflammatory polysaccharide that activates int…
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Harm potential: YELLOW — True iron deficiency anemia requires supplementation regardless of inflammatory state.
Vitamin C (ascorbate) is broadly protective: it reduces nickel absorption from food (acting as a competitive inhibitor in the GI tract), is the most commonly recommended adjunct to low-nickel diets zirwas 2009 dietary nickel dermatitis, and is a critical cofactor for DN…
Copper is elevated in the blood/serum of nearly every disease state examined in this wiki: | Disease | Cu Direction | Evidence | |---|---|---| | PCOS | Elevated | SMD = 0.51, p < 0.0001 (meta-analysis of 9 studies) | | Breast cancer | Elevated | SMD 2.44 in plasma/serum…
Fish is the primary dietary source of methylmercury (MeHg) -- a potent neurotoxin that crosses the blood-brain barrier, depletes glutathione, and can increase amyloid-beta production and tau phosphorylation mercury. MeHg is 95-100% absorbed in the intestinal tract. An e…
Celiac patients achieve serological remission on a gluten-free diet (GFD), confirming that the diet is working at the immunological level. Yet a subset develops NEW or WORSENING gastrointestinal and extraintestinal symptoms on prolonged GFD. The cause: gluten-free subst…
Iron deficiency is common and clinically significant across multiple conditions: postpartum anemia increases PPD risk 1.89-fold (RR = 1.887), low ferritin (<1 ug) increases PPD risk 3.98-fold azami 2019 anemia ppd meta analysis, iron deficiency impairs thyroid peroxidas…
Restricting dietary nickel has clear benefits for nickel-sensitive individuals: it resolves SNAS symptoms, improves Ni ACM, and even enhances H. pylori eradication. Campanale et al. (2014) found that adding a nickel-free diet to standard triple therapy increased H. pylo…
Anti-inflammatory and plant-forward diets are the standard nutritional recommendation for endometriosis, PCOS, rheumatoid arthritis, and IBD. These diets emphasize legumes, whole grains, nuts, seeds, dark chocolate, and cruciferous vegetables -- precisely the foods with…
Probiotics protect the gut barrier from heavy metal toxicity. Zhai et al. (2016) demonstrated that L. plantarum CCFM8610 protected intestinal epithelial cells from cadmium through a four-part mechanism: metal sequestration in the gut lumen, alleviation of oxidative stre…
Zinc is depleted in nearly every disease state examined in this wiki -- cancer (breast, prostate, lung, pancreatic, esophageal, colorectal), type 2 diabetes, PCOS, autism, postpartum depression, and IBD. Zinc supplementation is generally beneficial: it reduces PPD risk …
Autoimmune thyroid diseases (AITDs) -- hashimotos thyroiditis and graves disease -- are the most common organ-specific autoimmune conditions, affecting 5-10% of the global population. The thyroid gland sits at a remarkable intersection of metal biology and immune regula…
A gut microbiome-derived metabolite that has emerged as one of the strongest microbial biomarkers for cardiovascular disease risk. TMAO exemplifies how microbial metabolism of dietary nutrients can generate systemically toxic products -- a fundamentally different paradi…
Tryptamine is a microbial decarboxylation product of tryptophan, produced by bacterial tryptophan decarboxylase (found in ruminococcus gnavus, Clostridium sporogenes, and others). It is a serotonin receptor agonist (particularly 5-HT4) that stimulates gut motility and f…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.