WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
Research summary -- not medical advice. This page synthesizes published research on why a commonly prescribed intervention may be counterproductive in this specific clinical context. Consult a qualified healthcare provider before making any changes to treatment.
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…
WHO Priority 1: Critical. A Gram-negative, strictly aerobic coccobacillus and one of the most dangerous nosocomial pathogens on the planet. A. baumannii belongs to the ESKAPE group and causes ventilator-associated pneumonia, wound infections, and bloodstream infections …
Aerococcus is a genus of Gram-positive, alpha-hemolytic, catalase-negative cocci. The primary species of clinical relevance are A. urinae (a cause of urinary tract infections, particularly in elderly men) and A. christensenii (a vaginal commensal). In the WikiBiome vaul…
Aeromonas is a genus of Gram-negative, facultatively anaerobic bacteria found in aquatic environments and, increasingly recognized as an opportunistic gut pathogen. Several species — particularly Aeromonas hydrophila, A. veronii, and A. caviae — are associated with gast…
Amyloid-beta (Aβ) is a 36–43 amino acid peptide derived from the proteolytic cleavage of amyloid precursor protein (APP) by beta-secretase (BACE1) and gamma-secretase. Its aggregation from soluble monomers into insoluble fibrillar plaques in the brain is the defining ne…
The process by which soluble amyloid-beta (Aβ) monomers assemble into neurotoxic oligomers and insoluble fibrillar plaques in the brain -- the defining neuropathological event of alzheimers disease. What distinguishes WikiBiome's treatment of this process from conventio…
Anaerococcus is a genus of Gram-positive, obligate anaerobic cocci within the phylum Firmicutes. It is a normal inhabitant of the human vaginal, skin, and gastrointestinal microbiota, but is recognized as an opportunistic pathogen in dysbiotic states, particularly when …
A ubiquitous filamentous fungal genus that is both an environmental saprophyte and an opportunistic human pathogen. A. fumigatus is the primary cause of invasive aspergillosis in immunocompromised patients, while A. niger is relevant to food contamination. The genus is …
Bacterial vaginosis (BV) is the most common vaginal infection in women of reproductive age, affecting an estimated 29% of women globally. Rather than an infection by a single pathogen, BV represents a polymicrobial dysbiotic state -- a collapse of the protective Lactoba…
Structured microbial communities encased in a self-produced extracellular polymeric substance (EPS) matrix. Biofilms are the predominant mode of bacterial and fungal growth in chronic infections, device-associated infections, and the gut. From a metallomics perspective,…
A genus of spirochete bacteria transmitted by Ixodes ticks, best known as the causative agent of Lyme disease -- the most common tick-borne illness in the Northern Hemisphere. Borrelia burgdorferi sensu lato comprises approximately 20 genospecies, with B. burgdorferi se…
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…
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…
A haploid, asexual yeast and the second most common cause of invasive candidiasis after Candida albicans. Recently reclassified into the genus Nakaseomyces (as N. glabratus), though the name C. glabrata remains in widespread clinical use. Unlike C. albicans, C. glabrata…
Chlamydia is a genus of obligate intracellular, Gram-negative bacteria with a unique biphasic developmental cycle. The genus includes three species pathogenic to humans: chlamydia trachomatis (STI and trachoma), C. pneumoniae (respiratory infections, atherosclerosis ass…
Citrobacter is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family, named for its ability to utilize citrate as a sole carbon source. Species include C. freundii, C. koseri, and C. rodentium (a mouse model for EHEC infection). In …
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…
Enterococcus faecalis is a Gram-positive, facultatively anaerobic coccus that inhabits the gastrointestinal tract, oral cavity, and genitourinary tract of humans. It is a commensal in the healthy gut at low abundance but is one of the most clinically significant opportu…
The transfer of processed stool from a healthy donor into a recipient's gastrointestinal tract to restore a disrupted microbial community. FMT is the most direct form of microbiome intervention -- replacing the entire community rather than supplementing individual strai…
The primary intracellular iron storage protein, capable of sequestering up to 4,500 iron atoms in a single molecule as a mineralized ferric oxyhydroxide core. Ferritin is one of the most elegant solutions evolution has produced for the iron paradox: iron is essential fo…
Gardnerella vaginalis is a Gram-variable, facultatively anaerobic bacterium that is the key organism in bacterial vaginosis (BV), the most common vaginal infection in women of reproductive age. Its sialidase production, biofilm-forming capacity, and associations with he…
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…
The most common malignancy of the stomach, accounting for over 95% of gastric cancers. helicobacter pylori infection is the strongest known risk factor, classified as a Group 1 carcinogen by IARC. In the metallomics framework, gastric adenocarcinoma reveals a striking d…
A breach in the gastric mucosal lining extending through the muscularis mucosae, most commonly caused by helicobacter pylori infection or chronic NSAID use. Gastric ulceration represents a critical node in the upper GI disease continuum, linking gerd, chronic gastritis,…
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…
The master regulator of systemic iron homeostasis. Hepcidin is a 25-amino-acid peptide hormone produced primarily by hepatocytes that controls iron absorption, recycling, and distribution by binding to and degrading ferroportin (SLC40A1/FPN) -- the only known cellular i…
HIV (Human Immunodeficiency Virus) causes progressive CD4+ T cell depletion leading to AIDS. In the WikiBiome framework, HIV is notable for the gut-centric model of disease progression: HIV preferentially destroys gut-associated lymphoid tissue (GALT) early in infection…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Interleukin-6 is a pleiotropic cytokine that sits at the crossroads of innate immunity, adaptive immunity, and metabolism. It is one of the most frequently elevated inflammatory mediators across conditions in this wiki — appearing in disease signatures spanning IBD, aut…
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…
A Gram-positive, facultatively anaerobic bacterium that is the dominant species in the healthy human vaginal microbiome and a defining member of Community State Type I (CST-I). L. crispatus dominance is associated with reproductive health, pathogen resistance, and reduc…
Post-acute sequelae of SARS-CoV-2 infection (PASC), affecting an estimated 10-30% of COVID-19 survivors (WHO and CDC post-acute surveillance estimates) with symptoms persisting 12 weeks. Characterized by fatigue, cognitive dysfunction ("brain fog"), exercise intolerance…
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.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
The biological processes by which organisms maintain proper intracellular and systemic concentrations of essential metals -- importing what is needed, storing excess safely, and exporting or sequestering surplus. Both host and microbial systems have evolved elaborate me…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mycoplasma is a genus of wall-less bacteria in the class Mollicutes, characterized by the smallest genomes of any self-replicating organisms (~580–1,350 kb). The lack of a cell wall makes them intrinsically resistant to beta-lactam antibiotics and undetectable by Gram s…
See also: mycoplasma (genus page) Mycoplasma hominis is a wall-less bacterium in the class Mollicutes that colonizes the urogenital tract. It is associated with bacterial vaginosis, pelvic inflammatory disease, and neonatal infections.
--- title: Neisseria meningitidis type: entity subtype: microbe created: 2026-04-09 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [maier-2019-nickel-microbial-pathogenesis, patil-2021-infection-metallomics-critical-care, patil-2021-infection-metallomics…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
--- title: Parvimonas type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [qin-2024-consistent-microbiome-signatures-old-young-onset-crc, saito-2019-metagenomic-gut-microbiota-colorectal-adenoma, wu-2021-micro…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Pneumonia is infection of the lung parenchyma, most commonly caused by streptococcus pneumoniae, Klebsiella pneumoniae, Haemophilus influenzae, and viruses (influenza, SARS-CoV-2). In the WikiBiome framework, pneumonia exemplifies the metal battleground at the host-path…
A Gram-negative uropathogen whose Ni-dependent urease is the central driver of catheter-associated urinary tract infection (CAUTI) pathogenesis. Urease-mediated urea hydrolysis alkalinizes urine, triggering precipitation of struvite (magnesium ammonium phosphate) and ap…
An opportunistic Gram-negative pathogen with a unique dual-use siderophore system: its pyoverdine and pyochelin serve not only as iron scavengers but as extracellular chelators of toxic metals including nickel, copper, and cadmium. This makes P. aeruginosa unusually wel…
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…
Sepsis is life-threatening organ dysfunction caused by a dysregulated host response to infection. In the WikiBiome framework, sepsis represents the catastrophic failure of both colonization resistance (pathogen invasion) and nutritional immunity (metal restriction). Inf…
Siderophores are small, high-affinity iron-chelating molecules secreted by bacteria, fungi, and some plants to scavenge ferric iron (Fe3+) from their environment. In the context of infection, siderophores are the molecular weapons pathogens deploy to break through nutri…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Small regulatory RNAs (sRNAs) are non-coding RNA molecules, typically 50-500 nucleotides long, that regulate gene expression post-transcriptionally in bacteria. In the context of metal biology and microbial pathogenesis, sRNAs serve as rapid-response coordinators that h…
A versatile Gram-positive pathogen with one of the best-characterized nutritional immunity evasion systems known. S. aureus requires nickel, iron, zinc, and manganese for virulence and has evolved dedicated acquisition systems for each, including the novel metallophore …
Research summary -- not medical advice. This page synthesizes published research on why broad-spectrum antibiotics may worsen gut dysbiosis rather than correct it. This does NOT apply to life-threatening infections requiring antibiotic treatment. Consult a qualified hea…
Warning: Clinical Disclaimer: This STOP page represents a hypothesis based on mechanistic evidence and should NOT replace clinical judgment. Always consult with a qualified healthcare provider before modifying any treatment plan. Evidence quality ratings reflect the str…
A genus of Gram-positive facultative anaerobes that occupy niches ranging from benign commensals (dental plaque, skin) to acute pathogens (pharyngitis, impetigo, invasive disease). Streptococci are uniquely manganese-dependent for catalytic scavenging of reactive oxygen…
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive, facultatively anaerobic coccus that exists in two clinical contexts: (1) as a major neonatal pathogen causing life-threatening meningitis and sepsis in newborns, and (2) as an enric…
A Gram-positive pathogen (the "pneumococcus") that depends on iron, manganese, and zinc for virulence and has evolved dedicated transport systems for each. Iron is required for viability itself, manganese powers the superoxide dismutase needed to survive the oxidative b…
Tuberculosis is caused by mycobacterium tuberculosis, an intracellular pathogen that survives inside macrophage phagosomes. In the WikiBiome framework, TB exemplifies the intracellular metal battleground: M. tuberculosis deploys mycobactins (lipophilic siderophores) and…