WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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…
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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…
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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 aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that functions as a master sensor at the intersection of gut microbial metabolism, environmental chemical exposure, and immune regulation. It is expressed broadly across immune cells, intesti…
A Gram-negative, obligate anaerobic, mucin-degrading bacterium that colonizes the intestinal mucus layer and has emerged as one of the most important next-generation probiotics. A. muciniphila is consistently depleted in disease states associated with metal dyshomeostas…
A Gram-negative obligate anaerobe identified as a histamine-producing bacterium enriched in dysbiotic microbiota associated with obesity, metabolic syndrome, and metabolic endotoxemia. Allisonella is a minor but functionally significant genus whose primary clinical rele…
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Alloprevotella is a genus of Gram-negative, obligate anaerobic bacteria within the family Prevotellaceae that represents a distinct clade from prevotella with specific protective roles in type 2 diabetes prevention and metabolic health. Alloprevotella depletion is one o…
An anti-aging protein that has emerged as a critical mediator between heavy metal exposure and chronic kidney disease progression. Originally discovered as a gene whose mutation caused premature aging in mice, alpha-klotho is now understood to be a multifunctional prote…
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…
A non-essential metal and the most abundant metallic element in the Earth's crust. Unlike manganese, iron, or selenium, aluminum has no known biological function in humans. Its significance in metal toxicology stems from two major concerns: proven neurotoxicity at eleva…
The most common form of dementia, affecting an estimated 55 million people worldwide and projected to triple by 2050 zhang 2024 recent advances alzheimers mechanisms trials. Characterized by progressive memory loss, cognitive decline, amyloid-beta plaques, and neurofibr…
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 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 …
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…
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This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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 …
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A neurodevelopmental condition affecting approximately 1 in 36 children (US CDC 2023 estimate), characterized by differences in social communication, restricted interests, and repetitive behaviors. From a metallomics perspective, ASD presents a compelling convergence of…
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…
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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…
Viruses that exclusively infect bacteria. Bacteriophages -- phages for short -- are the most abundant biological entities on Earth, outnumbering bacteria in most environments by ratios of 1:1 to 10:1. In the human gut, the phageome represents a powerful but underexplore…
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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.…
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A class of Gram-negative bacteria within the phylum Proteobacteria that has emerged as a causal risk factor for schizophrenia and bipolar disorder through Mendelian randomization studies. Betaproteobacteria includes genera with notable metal tolerance -- particularly wi…
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…
Bile acids are cholesterol-derived amphipathic molecules synthesized in the liver, secreted into the duodenum, and extensively modified by gut bacteria. The host-microbe co-metabolism of bile acids creates a signaling network with profound effects on lipid metabolism, g…
Bilophila wadsworthia is a Gram-negative, obligate anaerobic, sulfite-reducing bacterium that has emerged as a key pathobiont linking high-fat diets, taurine metabolism, hydrogen sulfide production, and inflammatory disease. Its unique metabolic niche -- using taurine-c…
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,…
Measurable indicators of biological state, exposure, or disease. In the metallomics context, biomarkers span three interconnected domains: metal biomarkers (quantifying exposure and body burden), microbiome biomarkers (reflecting microbial community disruption), and met…
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A genus of Gram-positive, obligate anaerobic bacteria within the lachnospiraceae family that produces short chain fatty acids and plays a significant role in bile acid metabolism. Key species include B. obeum, B. wexlerae, B. hydrogenotrophica, and B. producta. While pr…
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…
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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 biologically potent short-chain fatty acid (C4). Butyrate is the primary energy source for colonocytes, a histone deacetylase (HDAC) inhibitor with broad epigenetic effects, and a key anti-inflammatory mediator. Its depletion -- driven by loss of butyrate-produ…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum (family Odoribacteraceae). Despite its relatively recent characterization, Butyricimonas has gained significant attention as a member of the protective butyrate-producing consortium that is consis…
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…
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 …
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Cerebral palsy (CP) is the most common motor disability in childhood, affecting 2-3 per 1,000 live births allen 2021 multi organ dysfunction cerebral palsy. Characterized by non-progressive disturbances in movement and posture arising from injury to the developing brain…
The major copper-carrying protein in human blood, binding approximately 95% of circulating copper. Ceruloplasmin is far more than a passive transport vehicle -- it is a multicopper oxidase with ferroxidase activity, an acute-phase reactant that rises with inflammation, …
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…
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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, …
Cirrhosis is end-stage liver fibrosis characterized by nodular regeneration, portal hypertension, and progressive hepatic failure. The gut-liver axis is central: portal venous blood delivers gut-derived LPS, bacterial DNA, and viable bacteria directly to the liver, and …
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 …
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…
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…
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…
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…
A transition metal that is essential to human health exclusively as a component of cobalamin (vitamin B12), but toxic at higher levels of exposure. Cobalt occupies a distinctive position in metal biology: it is the only metal whose essential biological function in mamma…
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…
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…
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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…
A Gram-positive, obligate anaerobic genus within the lachnospiraceae family (Firmicutes phylum). Coprococcus is one of the most important butyrate-producing commensals in the human gut and has gained particular attention as the "happiness bug" -- one of very few taxa di…
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This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A chronic, relapsing-remitting inflammatory bowel disease (IBD) characterized by transmural inflammation of the gastrointestinal tract, most commonly affecting the terminal ileum and colon but capable of involving any segment from mouth to anus zhang 2017 intestinal mic…
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 …
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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…
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Depression is the most prevalent mental health disorder globally, affecting over 280 million people zhu 2025 microbiota gut brain axis depression review, and one of the most metal-sensitive conditions in this wiki. It sits at the convergence of nearly every pathway cata…
A genus of Gram-negative, obligate anaerobic, sulfate-reducing bacteria (SRB) that produces hydrogen sulfide (H2S) as its primary metabolic end-product. H2S is a potent cytotoxin that disrupts colonocyte energy metabolism, damages the gut barrier, and promotes chronic i…
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…
Dialister is a genus of Gram-negative, obligate anaerobic bacteria within the family Veillonellaceae that represents one of the strongest protective associations in gut-brain-axis research. Dialister depletion is a consistent and independent biomarker of depression, anx…
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…