WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to mechanism.
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Tryptophan (Trp) is an essential amino acid metabolized via three competing pathways: the kynurenine pathway, the serotonin pathway, and the microbial indole pathway. The balance among these pathways is profoundly influenced by the gut microbiome, inflammation, and meta…
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Histidine is a semi-essential amino acid with a unique property that makes it central to metal biology: its imidazole side chain is one of the strongest biological metal-binding groups, coordinating zinc, nickel, copper, iron, and other transition metals in enzymes and …
[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…
Hyperparathyroidism is the overproduction of parathyroid hormone (PTH), a master regulator of calcium homeostasis. While primary hyperparathyroidism (from parathyroid adenoma) is well described, the WikiBiome framework highlights secondary hyperparathyroidism -- the com…
Microbial tryptophan metabolites produced by gut bacteria through the third branch of tryptophan metabolism -- the indole pathway. Unlike the host-dominated kynurenine pathway (~95% of Trp) and the serotonin pathway (~1-2%), the indole pathway is exclusively microbial a…
Interleukin-6 is a pleiotropic cytokine that sits at the crossroads of innate immunity, adaptive immunity, and metabolism. It is one of the most frequently elevated inflammatory mediators across conditions in this wiki — appearing in disease signatures spanning IBD, aut…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mitochondrial dysfunction refers to the impairment of mitochondrial energy production, redox balance, and signaling functions. Mitochondria are the primary targets of heavy metal toxicity in human cells, and they are also the organelles most dependent on metal cofactors…
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 …
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Oxalate (ethanedioic acid, C2O4^2-) is a small dicarboxylic acid found in many plant foods that has outsized significance for mineral metabolism and kidney health. In the gut, oxalate's fate is determined by a single specialist bacterium -- Oxalobacter formigenes -- who…
A microbial metabolite produced by gut bacteria through tyrosine fermentation that has emerged as one of the most consistent biomarkers linking gut dysbiosis to neurological and renal disease. p-Cresol (4-methylphenol) is a simple aromatic compound, but its effects are …
Pharmacomicrobiomics is the study of bidirectional interactions between drugs and the microbiome. The gut microbiome is not a passive bystander in pharmacology -- it actively metabolizes drugs, alters their bioavailability, and modulates therapeutic efficacy. Conversely…
Phenylalanine is an essential aromatic amino acid that sits at a metabolic crossroads: it is the precursor to tyrosine (and through it to dopamine, norepinephrine, and epinephrine), a substrate for microbial conversion to cardiovascular risk metabolites, and a participa…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Premenstrual syndrome (PMS) affects an estimated 20-40% of women of reproductive age, characterized by cyclical physical and psychological symptoms in the luteal phase (post-ovulation, pre-menstruation). While PMS has traditionally been attributed solely to hormonal flu…
A gut microbiome-derived metabolite that has emerged as one of the strongest microbial biomarkers for cardiovascular disease risk. TMAO exemplifies how microbial metabolism of dietary nutrients can generate systemically toxic products -- a fundamentally different paradi…
Uremic toxins are metabolic waste products that accumulate in the blood when kidney function declines. A striking proportion of the most clinically significant uremic toxins are produced not by human metabolism but by the gut microbiome -- making the gut-kidney axis a c…