WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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 …
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A genus of Gram-positive, facultatively anaerobic, filamentous bacteria that are among the most abundant colonizers of the human oral cavity. Actinomyces species, particularly A. naeslundii, play dual roles as early dental plaque colonizers and as opportunistic pathogen…
The ability of microorganisms to survive and replicate in the presence of antimicrobial agents — antibiotics, antifungals, antivirals, antiparasitic drugs — at concentrations that would normally inhibit or kill them. Antimicrobial resistance (AMR) is designated by the W…
Autophagy (from Greek, "self-eating") is the cellular process of degrading and recycling damaged organelles, misfolded proteins, and intracellular pathogens through lysosomal digestion. It is the cell's primary quality control mechanism -- a housekeeping system that bec…
A Gram-positive, aerobic to facultatively anaerobic, spore-forming genus that bridges environmental and human microbiology. The genus encompasses both beneficial species (B. subtilis, B. coagulans as probiotics) and pathogens (B. cereus causing food poisoning, B. anthra…
A selective semipermeable border formed by brain endothelial cells connected by tight junctions, pericytes, and astrocytic end-feet. The BBB restricts passage of most molecules from blood to brain, protecting the CNS from toxins, pathogens, and inflammatory mediators. M…
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…
An opportunistic fungal pathogen whose relationship with metals is multifaceted: C. albicans can biosorb heavy metals from its environment, heavy metal exposure promotes its virulence in immunocompromised hosts, and metal nanoparticles are being developed as antifungal …
Candida auris is an emerging multidrug-resistant fungal pathogen first identified in 2009 (Satoh et al. 2009, from a Japanese patient's ear canal) and now classified as a critical-priority pathogen by the WHO (WHO Fungal Priority Pathogens List 2022) and CDC (CDC 2019 A…
Chitotriosidase (CHIT1) is a human chitinase that degrades chitin — the structural polysaccharide of fungal cell walls, insect exoskeletons, and parasitic helminths. It is the most abundant chitinase in human serum and represents a direct arm of innate nutritional immun…
A class of Gram-positive, obligate anaerobic bacteria within the phylum Firmicutes that represents the most functionally diverse and clinically significant taxonomic class in the human gut microbiome. Clostridia encompasses the dominant butyrate producers sustaining col…
An order of Gram-positive, obligate anaerobic bacteria within the class clostridia (phylum Firmicutes) that represents the single most functionally important taxonomic group in the human gut. Clostridiales encompasses the major butyrate-producing families (lachnospirace…
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 collective ability of the resident gut microbiome to prevent colonization by exogenous pathogens and suppress expansion of resident pathobionts. Colonization resistance is not a property of any single organism but an emergent function of the whole microbial communit…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
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…
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 …
Every meal delivers metals to the gut lumen — essential minerals, trace elements, and contaminants alike. These metals do not passively transit the GI tract. They actively reshape the microbial ecosystem, selecting for metal-tolerant organisms, enabling virulence in met…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A family of Gram-negative, facultative anaerobic Gammaproteobacteria that includes many of the most important human pathogens: escherichia coli, klebsiella pneumoniae, salmonella typhimurium, shigella flexneri, yersinia pestis, proteus mirabilis, Morganella, and Serrati…
A genus of Gram-positive bacteria (primarily E. faecalis and E. faecium) that exemplifies the metal-antibiotic resistance co-selection crisis. Enterococci carry diverse metal tolerance genes for mercury, arsenic, copper, and cadmium on the same mobile genetic elements a…
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…
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 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…
[NiFe] hydrogenases are the second major nickel-dependent virulence factor class in human pathogens. Less widespread than urease but critical for energy metabolism in gastric, enteric, and intracellular pathogens. The discovery that H. pylori hydrogenase powers CagA tra…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
Klebsiella is a genus of Gram-negative, encapsulated, facultatively anaerobic bacteria in the Enterobacteriaceae family. With 141 file mentions across the vault, Klebsiella is one of the most frequently referenced opportunistic pathogens. The dominant species is klebsie…
A Gram-negative opportunistic pathogen and member of the ESKAPE group of antibiotic-resistant priority pathogens. K. pneumoniae deploys multiple nickel-dependent enzymes for virulence and relies on the dual-function metallophore yersiniabactin for both iron and nickel s…
Lactobacillus jensenii defines Community State Type V (CST-V) in the vaginal microbiome. It produces hydrogen peroxide and lactic acid, contributing to vaginal defense against pathogens, though less dominant than lactobacillus crispatus (CST-I).
An iron-binding glycoprotein of the transferrin family that sequesters iron (and potentially other metals) from pathogens at mucosal surfaces and sites of inflammation. Lactoferrin is a key effector of nutritional immunity, complementing calprotectin's role in metal res…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
Inflammation is a broad concept, but in the metallomics context it has a specific character: heavy metals and pathogens activate overlapping inflammatory pathways, creating convergent pathology where distinguishing the metal contribution from the microbial contribution …
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
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.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Hyperaccumulation is the ability of certain plant species to concentrate metals in their tissues at levels 10-100x higher than the surrounding soil. This is a genetically determined trait that evolved as a defense mechanism — metal-loaded tissues are toxic to herbivores…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum that exemplifies context-dependent microbiome effects -- beneficial in some settings, pathogenic in others. P. copri is the dominant species in the human gut and a hallmark of plant-rich, fiber-ri…
A Gram-negative, obligately anaerobic, black-pigmented bacterium and one of the classical periodontopathogens. P. intermedia belongs to the "orange complex" of periodontal pathogens (Socransky classification) and is distinguished by its iron and heme dependency -- the c…
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…
Shigella is a genus of Gram-negative, facultatively anaerobic bacteria in the family Enterobacteriaceae, closely related to Escherichia coli — so closely that many 16S rRNA-based studies report them as the Escherichia/Shigella complex, unable to distinguish the two gene…
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…
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 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…
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…
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…
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…
The most widespread nickel-dependent virulence factor across human pathogens. Urease is found in at least 40 prokaryotic and 9 eukaryotic pathogenic species, making it the single most important enzyme linking dietary/environmental nickel to infectious disease.