WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
Urea is the substrate of urease. In the microbial systems covered by WikiBiome, urease hydrolyzes urea to ammonia and bicarbonate; those products can supply microbial nitrogen and help neutralize acidic environments maier 2019 nickel microbial pathogenesis. At a glance,…
Ureaplasma is a genus of wall-less bacteria in the class Mollicutes, comprising two species pathogenic to humans: U. urealyticum and U. parvum. The genus is named for its defining characteristic — obligate urease activity — which hydrolyzes urea to ammonia and CO2, prov…
See also: ureaplasma (genus page with full biology and metal dependency profile) Ureaplasma urealyticum is one of two human-pathogenic Ureaplasma species (alongside U. parvum). Like all Ureaplasma, it depends on nickel-dependent urease for energy generation.
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.
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…
Actinobacteria (reclassified as Actinomycetota in 2021) is a major Gram-positive, high-GC-content bacterial phylum with remarkable ecological breadth. In the gut, it typically comprises 1-10% of the community -- a distant third behind firmicutes and bacteroidetes -- but…
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…
Ammonia is a nitrogen-containing product of microbial urease activity. When urease hydrolyzes urea, ammonia and bicarbonate are produced; in the microbial systems covered by WikiBiome, those products can provide nitrogen and raise local pH maier 2019 nickel microbial pa…
A genus of Gram-positive, obligate anaerobic bacteria that dominate the infant gut microbiome and remain important commensals throughout life. Bifidobacterium species are distinctive in the metallomics context because some species possess Ni-dependent urease -- an unusu…
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 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 leading bacterial cause of diarrheal disease worldwide, with an estimated 400-500 million cases annually. C. jejuni is notable in the metallomics context for possessing a nickel-dependent [NiFe] hydrogenase essential for colonization but lacking urease -- a striking…
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 …
A progressive loss of kidney function affecting approximately 850 million people worldwide (10–14% of adults), causing 1.2 million deaths annually. CKD is unique among diseases in this wiki because it occupies both sides of the metal-disease equation: heavy metals (Cd, …
An encapsulated basidiomycete yeast that causes cryptococcal meningitis -- the leading cause of meningitis in HIV/AIDS patients and responsible for an estimated 180,000 deaths annually. Its nickel-dependent urease has been called the organism's "Achilles' heel" because …
Dimethylglyoxime (DMG) is a high-affinity, nickel-specific chelator — two DMG molecules coordinate one Ni²⁺ ion to form a characteristic red complex (Tschugaeff reaction). Unlike broad-spectrum chelation agents (EDTA, DMSA) that bind multiple divalent cations indiscrimi…
A Gram-negative bacterium that spans the commensal-pathogen spectrum, with pathogenic variants (UPEC, STEC, EHEC) deploying nickel-dependent enzymes as virulence factors. E. coli is the model organism for nickel transport biology -- the NikABCDE system was first charact…
The fifth most common cancer worldwide and third leading cause of cancer death, with over 1 million new cases annually. Gastric cancer stands unique in this wiki as the disease where a single microorganism -- helicobacter pylori -- provides the dominant causal pathway, …
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 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…
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…
[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…
Microbial communities do not acquire and use metals in isolation. Within biofilms, polymicrobial infections, and the gut microbiome, microbes engage in complex cooperative and competitive relationships mediated by metals -- sharing metallophores, concentrating metals in…
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…
Transition metals serve as essential cofactors for pathogen virulence factors across virtually all domains of microbial life. The dependence of pathogens on metals they must scavenge from the host environment creates a fundamental tension at the heart of infectious dise…
A class of bacteria within the phylum Tenericutes defined by the complete absence of a cell wall -- the smallest self-replicating organisms known, with minimal genomes (580 kb-1.4 Mb). While Mollicutes are best known through their pathogenic members (Mycoplasma pneumoni…
Morganella morganii is a Gram-negative, facultatively anaerobic rod belonging to the family Morganellaceae (formerly classified within Enterobacteriaceae). It inhabits the human gastrointestinal tract as a low-abundance commensal but becomes an opportunistic pathogen in…
The causative agent of tuberculosis (TB), the leading infectious disease killer worldwide (~1.3 million deaths annually). M. tuberculosis has an exceptionally complex metal biology: it deploys nickel-dependent hydrogenase and urease for intracellular survival, species-s…
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…
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 …
A chronic metabolic condition affecting over 1 billion people globally, characterized by excess adipose tissue accumulation, systemic low-grade inflammation, and gut microbiome disruption pendergrass 2026 heavy metals obesity epidemic. From a metallomics perspective, ob…
Oxidative stress is the imbalance between the production of reactive oxygen and nitrogen species (ROS/RNS) and the capacity of biological antioxidant defense systems to detoxify them. It is the single most commonly invoked mechanism across metal toxicology in this wiki,…
The second most common neurodegenerative disease, affecting over 10 million people worldwide dorsey 2018 parkinsons incidence meta analysis. Characterized by progressive loss of dopaminergic neurons in the substantia nigra, alpha-synuclein aggregation (Lewy bodies), and…
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A Gram-negative uropathogen whose Ni-dependent urease is the central driver of catheter-associated urinary tract infection (CAUTI) pathogenesis. Urease-mediated urea hydrolysis produces ammonia and alkalinizes urine, triggering precipitation of struvite (magnesium ammon…
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 …
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…
Virulence factors are the molecular tools that enable a microorganism to colonize, invade, evade immune defenses, and cause damage to the host. They include toxins, adhesins, invasins, immune evasion molecules, and metabolic enzymes that provide competitive advantages i…