WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
The bacterial contamination hypothesis proposes that bacterial endotoxin (LPS) contamination of menstrual blood and endometrial tissue is a key driver of endometriosis pathogenesis. First formalized by Khan et al. (2018), this hypothesis shifts endometriosis from a pure…
Catalase is a heme-iron enzyme that decomposes hydrogen peroxide into water and oxygen. In microbial peroxide defense, it acts downstream of superoxide dismutase: superoxide dismutase converts superoxide to hydrogen peroxide, and catalase removes that hydrogen peroxide …
iron occupies a unique position among dietary metals: it is both an essential nutrient and a selective pressure that shapes the gut microbial ecosystem. The form, quantity, and bioavailability of dietary iron determines which microbes thrive and which are competitively …
Direct DNA damage is the primary carcinogenic mechanism for chromium but is notably absent or minor for nickel and arsenic. This distinction is fundamental to understanding why these three metals cause cancer through such different pathways.
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…
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…
Kynurenine is the primary metabolite of the kynurenine pathway, which handles ~95% of tryptophan catabolism in the body. While serotonin gets more attention, the kynurenine pathway is quantitatively dominant -- and its downstream metabolites span the range from neuropro…
The kynurenine pathway (KP) is the dominant route of tryptophan catabolism, accounting for approximately 95% of dietary tryptophan degradation. It produces a cascade of neuroactive, immunomodulatory, and potentially neurotoxic metabolites whose balance determines whethe…
Lead is a purely toxic heavy metal with no known biological function. It is the most extensively studied metal in relation to neurodevelopmental harm and is increasingly recognized as a contributor to chronic disease across virtually every organ system, even at levels o…
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.
The ability of certain metals to cause cancer has been known since the 19th century. The three metals covered in this wiki — nickel, arsenic, and chromium — represent distinct mechanistic paradigms that collectively illustrate the diversity of metal-induced carcinogenes…
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…
Pathogens deploy dedicated cellular machinery to import, store, regulate, and when necessary export transition metals. These systems complement the extracellular siderophores metallophores that scavenge metals from the host environment by providing the membrane transpor…
Periodontitis is a chronic inflammatory disease of the periodontal tissues (gingiva, periodontal ligament, alveolar bone) driven by a dysbiotic polymicrobial biofilm in the subgingival pocket. The keystone pathogen is porphyromonas gingivalis, whose zinc-dependent gingi…
A Gram-negative, obligate anaerobic genus with the keystone pathogen P. gingivalis at its center. Named for its porphyrin (heme) requirement, Porphyromonas is the prototypical periodontal pathogen and one of the most important organisms connecting oral health to systemi…
A Gram-negative obligate anaerobe and keystone pathogen of the oral microbiome that causes chronic periodontitis and is increasingly implicated in systemic diseases including alzheimers disease and cardiovascular disease. P. gingivalis virulence is fundamentally depende…
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…
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. Iron-deficiency anemia in colorectal can…
Tryptophan (Trp) is an essential amino acid that the human body cannot synthesize and must obtain from diet. It occupies a uniquely important position at the intersection of neuroscience, immunology, and microbial ecology because it is the sole precursor to serotonin, a…