WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
16S rRNA gene sequencing is the most widely used method for characterizing bacterial communities in this wiki. It targets the ~1,500 base pair 16S ribosomal RNA gene, which contains nine hypervariable regions (V1–V9) flanked by conserved sequences. Universal primers amp…
A Gram-negative, aerobic, non-fermenting coccobacillus and a member of the ESKAPE group of priority pathogens (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter). Acinetobacter baumannii is among the most problematic nosocomial pathogens…
The Autoimmune Protocol (AIP) diet is an elimination diet that removes foods associated with increased intestinal permeability and autoimmune activation. In Hashimoto's thyroiditis, it targets the gut-thyroid connection by reducing antigenic triggers that drive molecula…
Bacteroidetes (recently reclassified as Bacteroidota) is one of the two dominant bacterial phyla in the human gut, together with firmicutes typically comprising 90% of the intestinal microbiota. Bacteroidetes are Gram-negative, obligately anaerobic, non-spore-forming ro…
Bipolar disorder is a chronic neuropsychiatric condition characterized by recurrent episodes of mania (or hypomania) and depression, affecting approximately 1-2.4% of the global population. It carries significant morbidity -- reduced life expectancy by 10-15 years, high…
A genus of Gram-negative intracellular pathogens causing brucellosis, the most common bacterial zoonosis worldwide. Brucella species depend on nickel-activated urease for gastrointestinal survival during the initial phase of infection, and urease immunization has been s…
The most abundant mineral in the human body, with ~99% stored in bones and teeth. Calcium's biological significance extends far beyond structural support -- it is the universal second messenger in cell signaling, controlling neurotransmitter release, muscle contraction,…
A heterodimer of S100A8 and S100A9 calcium-binding proteins that constitutes approximately 60% of the cytosolic protein content of neutrophils. Calprotectin is a central effector of nutritional immunity, sequestering essential transition metals from invading pathogens a…
Candidozyma auris is the current name for NCBITaxon:498019. Liu and colleagues established the combination in 2024 as MycoBank MB 848169; Candida auris Satoh & Makimura 2009 is its basionym, not a separate species ncbi taxonomy candidozyma auris index fungorum candidozy…
A large, polyphyletic genus of Gram-positive, obligate anaerobic, spore-forming bacteria encompassing both critical beneficial commensals and dangerous pathogens. Former Clostridium clusters IV and XIVa are now reclassified into ruminococcus-family Ruminococcaceae and l…
The process by which selection pressure from one agent — typically a heavy metal — simultaneously selects for resistance to a structurally unrelated agent such as an antibiotic, because the resistance determinants are genetically linked on the same mobile genetic elemen…
An essential trace element with a striking dual nature: required for survival as a cofactor for critical enzymes (SOD1, cytochrome c oxidase, ceruloplasmin), yet toxic in excess through Fenton-like redox cycling and mis metallation of iron-sulfur clusters. Copper is ele…
Perhaps the most pervasive metallomic finding across human disease: copper is elevated in nearly every pathological condition examined in this wiki -- cancer (pan-cancer), PCOS, cardiovascular disease, depression, schizophrenia, IBD, and rheumatoid arthritis. Simultaneo…
Corynebacterium is a large genus of Gram-positive, club-shaped bacteria with over 130 species spanning commensals, opportunistic pathogens, and the classic pathogen C. diphtheriae. In the WikiBiome context, Corynebacterium is most notable for its dominance in the male r…
Cyclooxygenase-2 (COX-2) is the inducible enzyme that converts arachidonic acid to prostaglandin H₂ — the precursor of prostaglandin E₂ (PGE₂), prostacyclin, and thromboxane. Unlike COX-1 (constitutive, homeostatic), COX-2 is transcriptionally induced by nf kappa b duri…
Dermatitis herpetiformis (DH) is the cutaneous manifestation of celiac disease, presenting as intensely pruritic, grouped vesicles on the elbows, knees, buttocks, and scalp. It is driven by IgA antibodies against epidermal transglutaminase (eTG), the skin homolog of tis…
This page unifies the infant formula contamination, pregnancy complications, autism spectrum disorder, necrotizing enterocolitis, and neurodevelopmental toxicity threads around a single organizing insight: metal toxicity is disproportionately severe during specific deve…
arsenic (As) is unique among dietary heavy metals because it exists in two fundamentally different forms with dramatically different toxicities: inorganic arsenic (iAs, the dangerous form) and organic arsenic (arsenobetaine, arsenosugars — largely non-toxic). Understand…
Drug repurposing (also called drug repositioning) is the strategy of identifying new therapeutic uses for existing approved drugs. It dramatically accelerates the path from bench to bedside because safety, pharmacokinetics, and manufacturing are already established. In …
Membrane-spanning protein complexes that actively export substrates from the bacterial cell, using energy from ATP hydrolysis or the proton motive force. In the context of metal-microbiome biology, efflux pumps serve a dual role that has profound clinical consequences: …
Endocrine-disrupting chemicals (EDCs) are exogenous substances that interfere with hormone synthesis, secretion, transport, binding, action, or elimination. The classical EDC list -- BPA, phthalates, dioxins, PCBs, pesticides -- is well established. What WikiBiome adds …
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…
Epilepsy is a chronic neurological disorder characterized by recurrent unprovoked seizures, affecting ~50 million people worldwide. Approximately 30% of patients have drug-resistant epilepsy -- a population where microbiome-targeted interventions (particularly the ketog…
The only known cellular iron exporter in mammals. Encoded by the SLC40A1 gene, ferroportin (FPN) sits on the basolateral membrane of enterocytes, the surface of macrophages, and the membrane of hepatocytes, controlling the flow of iron from these cells into the bloodstr…
See also the genus page: gardnerella Gardnerella vaginalis is the primary causative agent of bacterial vaginosis (BV), the most common vaginal infection worldwide. This species page focuses on the species-level biology — particularly the vaginolysin cytotoxin and biofil…
Gingipains are the zinc-dependent cysteine proteases that serve as the master virulence factors of porphyromonas gingivalis. Three gingipains exist: RgpA and RgpB (arginine-specific) and Kgp (lysine-specific). They require zinc as a catalytic cofactor, making gingipain …
The most abundant intracellular thiol and the master antioxidant of mammalian cells. Glutathione is a tripeptide (gamma-glutamyl-cysteinyl-glycine) whose sulfhydryl (-SH) group makes it both a critical antioxidant and a primary target for heavy metal binding. GSH deplet…
The third nickel-dependent enzyme class in human pathogens, after urease and hydrogenase. Glyoxalase I detoxifies methylglyoxal, a reactive and toxic byproduct of glycolysis. While less well-known than urease or hydrogenase as a virulence factor, GloI is emerging as a s…
Graves' disease (GD) is an autoimmune thyroid disorder characterized by TSH receptor antibodies (TRAb) that stimulate the thyroid gland, causing hyperthyroidism kahaly 2022 graves disease targeted therapy review. It is the most common cause of hyperthyroidism, with conc…
The gut-gonadal axis describes the bidirectional communication between the intestinal microbiome and the reproductive endocrine system. Gut bacteria modulate sex hormone levels through enzymatic activity (particularly beta glucuronidase-mediated estrogen deconjugation),…
A Gram-negative, microaerophilic bacterium within the Epsilonproteobacteria (family Helicobacteraceae) that is the primary murine model of hepatobiliary and intestinal disease. Unlike its more famous relative helicobacter pylori, which colonizes the stomach, H. hepaticu…
A gastric pathogen that is arguably the most nickel-dependent human pathogen known. Two of its key virulence factors — urease and [NiFe] hydrogenase — require nickel, and the bacterium has evolved an elaborate nickel trafficking, storage, and regulation system to suppor…
Horizontal gene transfer (HGT) is the movement of genetic material between organisms outside of parent-to-offspring inheritance. In the gut microbiome, HGT -- primarily mediated by mobile genetic elements (MGEs) including plasmids, transposons, integrons, and integrativ…
Interleukin-17 (primarily IL-17A and IL-17F) is the signature cytokine of Th17 cells. At physiological levels, IL-17 maintains mucosal barrier defense by recruiting neutrophils and inducing antimicrobial peptide production. At pathological levels (Th17/Treg imbalance), …
Immunotherapy harnesses the patient's own immune system to fight disease, most notably cancer. Immune checkpoint inhibitors (ICIs) -- antibodies that block PD-1, PD-L1, or CTLA-4 -- have revolutionized oncology since their introduction in the 2010s, producing durable re…
Interleukin-22 (IL-22) is an immune signaling protein that helps coordinate host responses at epithelial surfaces. In the gut evidence represented by WikiBiome, group 3 innate lymphoid cells (ILC3s) are a prominent source, while Th17-associated responses can also includ…
The intestinal epithelium is a single-cell-thick barrier separating the lumen -- home to trillions of microbes and ingested metals -- from the systemic circulation. When this barrier fails, the consequences cascade: microbial products translocate, metals gain unrestrict…
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…
Iron-sulfur (Fe-S) clusters are among the most ancient and ubiquitous metal cofactors in biology, present in all domains of life. These inorganic prosthetic groups -- typically [2Fe-2S] or [4Fe-4S] configurations -- mediate electron transfer, enzymatic catalysis, and re…
The labile metal pool (LMP) is the fraction of intracellular metal that is bioavailable -- loosely coordinated with small molecules, transiently protein-bound, or truly "free" in solution. This pool is vanishingly small (often <1 free atom per cell for zinc and copper) …
Lactobacillus plantarum is one of the most versatile probiotic species — found in fermented foods (kimchi, sauerkraut, sourdough), the human gut, and the vaginal microbiome. It has the largest genome among Lactobacillus species (~3.3 Mb), encoding extensive stress toler…
Lipocalin-2 (also known as NGAL — neutrophil gelatinase-associated lipocalin, or siderocalin) is a 25 kDa secreted protein produced by activated neutrophils, epithelial cells, and other innate immune cells. Its primary antimicrobial function is to sequester bacterial si…
Research summary — not medical advice. This page synthesizes published research on a mechanism-level intervention. It is not a clinical recommendation. Consult a qualified healthcare provider before making any changes to diet, supplementation, or treatment.
Manganese is an essential trace element with a narrow therapeutic window: required as a cofactor for critical enzymes including Mn-SOD (SOD2), pyruvate carboxylase, arginase, and ribonucleotide reductase, yet profoundly neurotoxic at elevated levels martin 2022 manganes…
Metabolomics is the comprehensive measurement of small-molecule metabolites (<1,500 Da) in a biological sample -- the functional readout of what the genome, transcriptome, and microbiome are actually doing. While genomics tells you what organisms are present and metagen…
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…
Specialized proteins that escort metal ions from their point of entry to specific metalloenzyme targets, ensuring correct metalation in a cytoplasm crowded with competing metal-binding sites. Metallochaperones solve a fundamental problem in metal biology: how does the r…
Protein-based transcription factors that sense intracellular metal concentrations and regulate gene expression accordingly. Metalloregulators are the decision-making layer of bacterial metal homeostasis -- they read the labile metal pool, determine whether a specific me…
A family of small (6-7 kDa), cysteine-rich proteins that bind heavy metals with extraordinary affinity. Metallothioneins (MTs) are the cell's primary chemical defense against metal toxicity -- they sequester cadmium, mercury, lead, and other toxic metals, preventing the…
Microglia are the resident immune cells of the central nervous system, constituting 5-12% of all brain cells. They function as the brain's surveillance and defense system -- scanning for damage, clearing debris, pruning synapses during development, and mounting inflamma…
Mitochondrial dysfunction refers to the impairment of mitochondrial energy production, redox balance, and signaling functions. Mitochondria are the primary targets of heavy metal toxicity in human cells, and they are also the organelles most dependent on metal cofactors…
Molecular mimicry occurs when microbial antigens share structural similarity with host proteins, triggering cross-reactive immune responses that attack host tissue. It is a primary mechanism linking infections and dysbiosis to autoimmune disease — the immune system corr…
An essential trace element that serves as a cofactor for a small but critical family of enzymes -- the molybdoenzymes -- involved in purine catabolism, sulfite detoxification, and aldehyde metabolism smovrsnik 2025 trace elements pcos. Molybdenum appears in this wiki pr…
Multi-strain synbiotic supplementation (probiotic + prebiotic) as adjunctive therapy alongside antipsychotics. This is the strongest validated microbiome-targeted intervention for schizophrenia, with both psychiatric symptom improvement and metabolic benefit demonstrate…
N-Acetylcysteine (NAC) is a glutathione precursor and glutamatergic modulator that addresses two key features of ASD pathophysiology: oxidative stress and excitatory-inhibitory imbalance. A pilot RCT demonstrated large effect sizes for irritability reduction.
Nakaseomyces glabratus is the current name for NCBITaxon:5478. Takashima and Sugita established the current combination in 2022 as MycoBank MB 843854; Candida glabrata is a homotypic synonym and former combination, while Cryptococcus glabratus H.W. Anderson 1917 is the …
Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal emergency in premature infants, affecting 5-12% of very low birth weight neonates (<1500 g) with mortality rates of 20-30%. Characterized by intestinal inflammation, necrosis, and perforation…
Specialized membrane proteins that import nickel into bacterial cells, supplying the essential cofactor for virulence enzymes including urease, NiFe hydrogenase, and Ni-glyoxalase. Because mammals produce no known nickel-requiring proteins, these transporters represent …
Nickel-glyoxalase (Ni-GlxI) is a bacterial variant of the glyoxalase I enzyme system that depends on nickel as its essential metal cofactor. This enzyme detoxifies methylglyoxal (MG), a toxic glycolysis byproduct that accumulates under glucose fermentation. Unlike the h…
Nickel-urease (urease, EC 3.5.1.5) is a metalloenzyme that catalyzes the hydrolysis of urea (NH₂-CO-NH₂) to ammonia (NH₃) and carbon dioxide (CO₂). The active site contains two nickel ions (Ni²⁺) coordinated by histidine and cysteine residues. Nickel-urease is expressed…
Nrf2 is a master transcription factor that regulates the expression of antioxidant and cytoprotective genes. It plays a central role in cellular defense against oxidative stress, electrophilic stress, and inflammation. Under normal conditions, Nrf2 is sequestered in the…
The strategy by which mammalian hosts withhold essential metals from invading pathogens to limit their growth. Well-established for iron and zinc; underexplored but potentially powerful for nickel.
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…
Ovarian cancer is the most lethal gynecological malignancy, with approximately 314,000 new cases and 207,000 deaths annually worldwide. Its poor prognosis stems largely from late-stage diagnosis (70% at stage III/IV) and the development of chemoresistance. From a metall…
Pancreatitis is inflammation of the pancreas, occurring in acute (AP) and chronic (CP) forms. Acute pancreatitis ranges from mild self-limiting disease to severe necrotizing pancreatitis with 20-30% mortality. Chronic pancreatitis is a risk factor for pancreatic cancer …
Parvimonas micra is a small (0.5–1.0 µm), Gram-positive, obligately anaerobic coccus originally isolated from the human oral cavity that has emerged as one of the most consistent and universally enriched pathobionts in colorectal cancer across all geographic regions, ag…
Phage therapy uses bacteriophages — viruses that infect and lyse specific bacteria — as precision antimicrobials. Unlike broad-spectrum antibiotics, phages target specific bacterial species or strains, sparing the commensal microbiome. In the WikiBiome framework, phage …
Phosphodiesterases (PDEs) are a family of enzymes that hydrolyze cyclic nucleotides (cAMP and cGMP), regulating intracellular signaling cascades. PDE5, the isoform targeted by sildenafil and tadalafil, is best known for its role in erectile dysfunction pharmacotherapy, …
Probiotic supplementation targeting the dysbiosis-thyroid axis aims to restore Lactobacillus and Bifidobacterium populations depleted in Hashimoto's thyroiditis, with potential downstream effects on iodine and selenium metabolism.
Probiotic supplementation targeting depleted Bifidobacterium and Lactobacillus in the postpartum period aims to restore gut-brain axis signaling disrupted during the dramatic hormonal shifts following delivery.
Propionibacterium (largely reclassified as Cutibacterium for skin species) is a genus of Gram-positive, anaerobic to aerotolerant bacteria that produce propionic acid as their primary fermentation product. P. acnes (now Cutibacterium acnes) is the dominant skin commensa…
Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by symmetric polyarthritis with progressive joint destruction, affecting approximately 1% of the global population. The conventional framing centers on genetic susceptibility (HLA-DRB1 shar…
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…
Saccharomyces cerevisiae is a unicellular budding fungus (ascomycete) ubiquitous in fermentation, brewing, bread-making, and increasingly used as a pharmaceutical probiotic (Hatoum et al. 2012). The strain S. boulardii (also called S. cerevisiae var. boulardii) is the m…
A severe neuropsychiatric disorder affecting approximately 1% of the global population, characterized by positive symptoms (hallucinations, delusions), negative symptoms (anhedonia, social withdrawal, flat affect), and cognitive deficits. Life expectancy is reduced by 1…
Shotgun metagenomics is a sequencing approach that fragments and sequences all DNA in a sample -- bacterial, archaeal, fungal, viral, and host -- without prior amplification of a specific gene target. Unlike 16S rRNA amplicon sequencing, which identifies "who is there" …
Siderophores and metallophores are small-molecule chelators secreted by pathogens to scavenge metals from the metal-scarce host environment. They represent the extracellular arm of pathogen metal acquisition -- how pathogens reach out into the surrounding milieu to capt…
A non-essential metal with a 5,000-year history of antimicrobial use, silver has re-emerged as a critical tool in the post-antibiotic era. What makes silver particularly interesting from a metallomics perspective is not that it kills bacteria -- many metals do -- but ho…
A genus of Gram-positive, facultative anaerobic cocci that includes some of the most clinically significant human pathogens. Staphylococci are defined by their exceptionally comprehensive metal acquisition arsenal -- arguably the most thoroughly characterized of any bac…
Statins (HMG-CoA reductase inhibitors) are the most widely prescribed drug class globally, used primarily for cholesterol lowering and cardiovascular risk reduction. Over 200 million people take statins worldwide. Beyond their canonical mechanism of inhibiting cholester…