WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
A pathotype of escherichia coli that adheres to and invades intestinal epithelial cells, survives and replicates within macrophages, and is strongly associated with ileal Crohn's disease. Unlike classical diarrheagenic E. coli pathotypes (EPEC, ETEC, EHEC), AIEC does no…
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 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…
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…
Chlamydia trachomatis is a Gram-negative, obligate intracellular bacterium and the most common bacterial sexually transmitted infection worldwide. Its biphasic developmental cycle — alternating between the infectious elementary body (EB) and the replicative reticulate b…
Chromium is a transition metal (atomic number 24) whose toxicology is defined by a stark oxidation-state divide. Hexavalent chromium, Cr(VI), is an IARC Group 1 human carcinogen that causes DNA damage through a unique mechanism of intracellular reduction and ternary add…
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…
A distinct form of regulated cell death caused by excess intracellular copper binding to lipoylated proteins in the TCA cycle, first characterized by Tsvetkov et al. in Science (2022). Unlike ferroptosis (iron-dependent lipid peroxidation) or apoptosis (caspase-dependen…
Cysteine is a sulfur-containing amino acid whose thiol (-SH) group makes it the primary metal-binding residue in biology. It is the rate-limiting precursor for glutathione (the master intracellular antioxidant), a key residue in metallothioneins (metal-binding proteins)…
The primary intracellular iron storage protein, capable of sequestering up to 4,500 iron atoms in a single molecule as a mineralized ferric oxyhydroxide core. Ferritin is one of the most elegant solutions evolution has produced for the iron paradox: iron is essential fo…
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 most abundant intracellular thiol and the master antioxidant of mammalian cells. Glutathione is a tripeptide (gamma-glutamyl-cysteinyl-glycine) whose sulfhydryl (-SH) group makes it both a critical antioxidant and a primary target for heavy metal binding. GSH deplet…
[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…
Interferon gamma (IFN-γ) is the signature Th1 cytokine and the primary activator of macrophage antimicrobial functions. In the WikiBiome framework, IFN-γ is critical for two reasons: it drives nutritional immunity (iron restriction against intracellular pathogens) and i…
Iron-sulfur (Fe-S) clusters are among the most ancient and ubiquitous metal cofactors in biology, present in all domains of life. These inorganic prosthetic groups -- typically [2Fe-2S] or [4Fe-4S] configurations -- mediate electron transfer, enzymatic catalysis, and re…
The labile metal pool (LMP) is the fraction of intracellular metal that is bioavailable -- loosely coordinated with small molecules, transiently protein-bound, or truly "free" in solution. This pool is vanishingly small (often <1 free atom per cell for zinc and copper) …
Manganese is an essential trace element with a narrow therapeutic window: required as a cofactor for critical enzymes including Mn-SOD (SOD2), pyruvate carboxylase, arginase, and ribonucleotide reductase, yet profoundly neurotoxic at elevated levels martin 2022 manganes…
The biological processes by which organisms maintain proper intracellular and systemic concentrations of essential metals -- importing what is needed, storing excess safely, and exporting or sequestering surplus. Both host and microbial systems have evolved elaborate me…
Metal sensing is the set of regulatory mechanisms bacteria use to detect intracellular metal concentrations and adjust gene expression accordingly. Because metal ions cannot be synthesized or degraded -- only imported, exported, sequestered, or trafficked -- sensing and…
Protein-based transcription factors that sense intracellular metal concentrations and regulate gene expression accordingly. Metalloregulators are the decision-making layer of bacterial metal homeostasis -- they read the labile metal pool, determine whether a specific me…
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…
N-acetylcysteine (NAC) is the acetylated form of the amino acid L-cysteine and serves as the rate-limiting precursor for glutathione synthesis — the body's primary intracellular antioxidant and a critical cofactor for phase II detoxification of heavy metals. In the micr…
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…
Phosphodiesterases (PDEs) are a family of enzymes that hydrolyze cyclic nucleotides (cAMP and cGMP), regulating intracellular signaling cascades. PDE5, the isoform targeted by sildenafil and tadalafil, is best known for its role in erectile dysfunction pharmacotherapy, …
Salmonella is a genus of Gram-negative, facultatively anaerobic bacteria in the family Enterobacteriaceae. The two species — S. enterica (with 2,500 serovars including Typhimurium and Typhi) and S. bongori — cause a spectrum of disease from self-limiting gastroenteritis…
A Gram-negative enteric pathogen that possesses four distinct hydrogenases of the [NiFe] class -- the most of any well-characterized human pathogen. These hydrogenases are critical for intracellular survival within macrophages, and a triple hydrogenase mutant is 100% av…
A Gram-negative intracellular pathogen causing bacillary dysentery (shigellosis), responsible for approximately 165 million illness episodes and over 1 million deaths annually, predominantly in children under 5 in developing countries. S. flexneri relies on nickel-depen…
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive, facultatively anaerobic coccus that exists in two clinical contexts: (1) as a major neonatal pathogen causing life-threatening meningitis and sepsis in newborns, and (2) as an enric…
Copper is elevated in the blood/serum of nearly every disease state examined in this wiki: | Disease | Cu Direction | Evidence | |---|---|---| | PCOS | Elevated | SMD = 0.51, p < 0.0001 (meta-analysis of 9 studies) | | Breast cancer | Elevated | SMD 2.44 in plasma/serum…
Tuberculosis is caused by mycobacterium tuberculosis, an intracellular pathogen that survives inside macrophage phagosomes. In the WikiBiome framework, TB exemplifies the intracellular metal battleground: M. tuberculosis deploys mycobactins (lipophilic siderophores) and…
Zinc is the most widely utilized transition metal cofactor in biology. Approximately 9-10% of the eukaryotic proteome and 5-6% of the bacterial proteome consists of zinc-binding proteins capdevila 2024 bacterial metallostasis sensing trafficking. An estimated one-third …