Host defenses11 sources
Pathogen Metal Acquisition Systems
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Search: “pathogen”
Ranked matches across titles, topics, categories, and article introductions.
80 records in this view
Microorganisms9 sources
Acinetobacter
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…
Microorganisms6 sources
Acinetobacter baumannii
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 …
Microorganisms10 sources
Actinobacteria (Actinomycetota)
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Microorganisms8 sources
Actinomyces
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…
Microorganisms0 sources
Aeromonas
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…
Mechanisms7 sources
Alpha-Synuclein
A 140-amino-acid presynaptic protein whose misfolding into insoluble fibrils and their deposition in Lewy bodies is the defining neuropathological hallmark of parkinsons disease and the broader family of synucleinopathies (including Lewy body dementia and multiple syste…
Mechanisms7 sources
Amyloid-Beta
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…
Microorganisms3 sources
Anaerococcus
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 …
Microorganisms8 sources
Anaerostipes
A genus of Gram-positive obligate anaerobes in the family Lachnospiraceae (Clostridium cluster XIVa) that occupy a critical metabolic relay position in gut ecosystem stability: converting lactate to butyrate. Anaerostipes is one of the most consistently depleted genera …
Mechanisms7 sources
Antimicrobial Resistance
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…
Microorganisms7 sources
Aspergillus
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 …
Other0 sources
Author Outreach — First Touch (Template)
Purpose: Introduce WikiBiome to cited authors. Build the relationship. No money ask. When to send: After a source page is published on WikiBiome. Subject line options (test which performs best): - Your research on [TOPIC] is now part of WikiBiome - We cited your [YEAR] …
Other0 sources
Author Outreach — Follow-Up Submission + Donation (Template)
Purpose: Introduce the paper submission pathway with suggested donation. Sent only to authors who engaged with the first email (replied, visited their source page, or submitted corrections). When to send: 2–3 weeks after first-touch, only if the author engaged. Subject …
Mechanisms8 sources
Autophagy
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…
Microorganisms6 sources
Bacillus
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…
Mechanisms3 sources
Bacterial Vaginosis
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…
Microorganisms4 sources
Bacteroides vulgatus
A Gram-negative obligate anaerobe that exemplifies the commensal-pathobiont spectrum. B. vulgatus is a common component of the healthy gut microbiota, yet is significantly enriched in colorectal cancer and depression, suggesting a context-dependent pathogenic potential.…
Microorganisms3 sources
Barnesiella
Barnesiella is a genus of Gram-negative, obligate anaerobic bacteria within the phylum Bacteroidetes. It is a commensal member of the healthy human gut microbiota, recognized for its role in colonization resistance — the ability of the resident microbiome to prevent est…
Microorganisms5 sources
Bifidobacterium infantis
Bifidobacterium longum subsp. infantis (commonly called B. infantis) is the premier human milk oligosaccharide (HMO)-utilizing bacterium and the dominant species in the breastfed infant gut. It drives immune maturation, Treg induction, and pathogen exclusion in early li…
Mechanisms3 sources
Blood-Brain Barrier
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…
Microorganisms1 sources
Brucella
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…
Host defenses4 sources
Calprotectin (S100A8/A9)
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…
Microorganisms5 sources
Campylobacter jejuni
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…
Microorganisms13 sources
Candida albicans
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 …
Microorganisms3 sources
Candida auris
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…
Microorganisms3 sources
Candida glabrata
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…
Microorganisms5 sources
Candida tropicalis
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Diseases8 sources
Celiac Disease
Celiac disease is a chronic autoimmune condition triggered by dietary gluten (gliadin proteins from wheat, barley, and rye) in genetically susceptible individuals (HLA-DQ2/DQ8, carried by ~30-40% of Europeans but penetrant in only ~1% of carriers). Gluten exposure cause…
Mechanisms4 sources
Chitotriosidase
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…
Microorganisms6 sources
Chlamydia
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…
Microorganisms12 sources
Citrobacter
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 …
Microorganisms8 sources
Clostridia
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…
Microorganisms8 sources
Clostridiales
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…
Microorganisms3 sources
Clostridioides difficile
A Gram-positive, spore-forming, obligate anaerobic bacterium that is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in healthcare settings. In the metallomics framework, C. difficile sits at the intersection of metal-antibiotic co-selec…
Microorganisms5 sources
Clostridium
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…
Microorganisms6 sources
Clostridium perfringens
Clostridium perfringens is a Gram-positive, strictly anaerobic, spore-forming bacterium infamous for causing gas gangrene, food poisoning, and necrotizing enterocolitis (NEC) in premature infants. It is one of the most widely distributed pathogenic bacteria in nature, f…
Microorganisms7 sources
Clostridium symbiosum
Clostridium symbiosum is a Gram-positive, obligately anaerobic bacterium within the Clostridium cluster XIVa — a taxonomic group enriched for short-chain fatty acid (SCFA) producers and specialized bile acid metabolizers. Despite its ambiguous name (suggesting symbiotic…
Microorganisms5 sources
Collinsella
A genus of Gram-positive, obligate anaerobic bacteria within the Actinobacteria phylum (family Coriobacteriaceae) that has emerged as a consistent pathobiont enriched in cardiometabolic and autoimmune diseases. C. aerofaciens is the most studied species, with establishe…
Mechanisms3 sources
Colonization Resistance
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…
Diseases18 sources
Colorectal Cancer
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Metals56 sources
Copper
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…
Microorganisms14 sources
Corynebacterium
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…
Microorganisms3 sources
Cryptococcus neoformans
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 …
Microorganisms4 sources
Debaryomyces
Debaryomyces is a genus of ascomycetous fungi, with D. hansenii being the most clinically relevant species, that represents a prominent opportunistic pathobiont enriched in inflammatory bowel disease, particularly crohns disease. Unlike many commensal fungi, Debaryomyce…
Analyses31 sources
Dietary Metal Paradoxes: When Healthy Foods and Good Intentions Backfire
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 …
Mechanisms8 sources
Dietary Metal-Microbiome Interactions
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…
Mechanisms3 sources
Dimethylglyoxime (DMG)
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Microorganisms8 sources
Eggerthella lenta
A Gram-positive obligate anaerobe and key estrobolome member that links metabolic dysbiosis to hormone-driven diseases, particularly endometriosis. E. lenta is remarkable for its ability to inactivate cardiac glycosides (like digoxin) and to produce beta-glucuronidase, …
Microorganisms5 sources
Enterobacter
Enterobacter is a genus of Gram-negative, facultatively anaerobic bacteria in the enterobacteriaceae family. Key species include enterobacter cloacae (the most clinically relevant) and E. hormaechei. Like other Enterobacteriaceae, Enterobacter possesses iron-dependent s…
Microorganisms3 sources
Enterobacter cloacae
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Microorganisms5 sources
Enterobacteriaceae
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…
Microorganisms3 sources
Enterococcus
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…
Microorganisms9 sources
Enterococcus faecalis
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…
Microorganisms4 sources
Erysipelotrichaceae
Erysipelotrichaceae is a family within the phylum Firmicutes that has drawn increasing attention for its consistent enrichment in metabolic disorders. Members of this family are Gram-positive, obligate anaerobes found throughout the mammalian gastrointestinal tract, whe…
Microorganisms8 sources
Escherichia
Escherichia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species E. coli is simultaneously the most studied bacterium in biology and one of the most consistently enriched organisms in disease-associated micr…
Microorganisms6 sources
Escherichia coli
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…
Microorganisms7 sources
Fusobacterium nucleatum
A Gram-negative obligate anaerobe that has emerged as a major pathogen in colorectal cancer (CRC) and inflammatory bowel disease. F. nucleatum is significantly enriched in CRC tissue and tumors compared to healthy mucosa, making it one of the strongest microbe-cancer as…
Microorganisms8 sources
Fusobacterium varium
A Gram-negative obligate anaerobe that occupies a paradoxical niche in the gut microbiota: as a weak butyrate producer (short-chain fatty acid), it has anti-inflammatory potential; as a virulent invasive pathobiont in inflammatory bowel disease (particularly ulcerative …
Microorganisms4 sources
Gardnerella
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…
Microorganisms10 sources
Gardnerella vaginalis
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…
Diseases6 sources
Gastric Cancer
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, …
Reference0 sources
Glossary
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…
Mechanisms6 sources
Glyoxalase I
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…
Microorganisms9 sources
Haemophilus
Haemophilus is a genus of small, Gram-negative, facultatively anaerobic coccobacilli that inhabit the upper respiratory tract, oral cavity, and gastrointestinal tract. The genus name literally means "blood-loving" -- a direct reference to its absolute requirement for he…
Microorganisms8 sources
Helicobacter hepaticus
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…
Microorganisms5 sources
Helicobacter pylori
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…
Other0 sources
Hungatella
--- title: Hungatella type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [altinok-dindar-2023-gut-microbiota-breast-cancer-diet, qin-2024-consistent-microbiome-signatures-old-young-onset-crc, zhang-2025-gut-v…
Mechanisms4 sources
Hydrogenase
[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…
Host defenses5 sources
IFN-gamma (Interferon Gamma)
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Other0 sources
Intestinibacter
--- title: Intestinibacter type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [dai-2024-gut-microbiota-cvd-bidirectional-mr, xiang-2023-host-gene-microbiome-crc-mr, wu-2017-metformin-gut-microbiome-t2d-nature…
Metals55 sources
Iron
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…
Microorganisms7 sources
Klebsiella
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…
Microorganisms3 sources
Klebsiella pneumoniae
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…
Microorganisms9 sources
Lactobacillus
A genus of Gram-positive, facultatively anaerobic lactic acid bacteria (LAB) that are among the most extensively studied probiotics. In the metallomics context, Lactobacillus species are critical for two reasons: they actively detoxify heavy metals through binding and s…
Microorganisms6 sources
Lactobacillus crispatus
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…
Microorganisms5 sources
Lactobacillus iners
Lactobacillus iners is a Gram-positive, facultatively anaerobic bacterium that dominates the vaginal microbiome of many women worldwide, defining Community State Type III (CST-III) in vaginal microbiome classification. For decades, all vaginal Lactobacillus species were…
Microorganisms5 sources
Lactobacillus jensenii
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).
Host defenses5 sources
Lactoferrin
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…
Interventions0 sources
Lactoferrin Supplementation (Cross-Condition)
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.