WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to mechanism.
The most extensively referenced missing concept in this wiki. SCFAs -- acetate (C2), propionate (C3), and butyrate (C4) -- are the primary metabolic products of anaerobic bacterial fermentation of dietary fiber in the colon. They serve as the critical molecular link bet…
Acetate (acetic acid, C2) is the most abundant SCFA in the colon (~60% of total SCFAs) and the primary cross-feeding substrate for butyrate production. Produced by Bacteroides, Bifidobacterium, Prevotella, and acetogens from dietary fiber fermentation, acetate reaches p…
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…
Disruption of the normal composition and metabolic function of microbial communities, particularly the gut microbiome. In the metallomics context, dysbiosis is both a consequence of metal toxicity and an amplifier of further disease -- creating vicious cycles where meta…
Fermentative metabolism is the set of anaerobic metabolic pathways by which bacteria break down carbohydrates and amino acids in the absence of oxygen, producing short-chain fatty acids (SCFAs) (primarily butyrate, propionate, acetate), gases (H₂, CO₂, CH₄), and organic…
Bidirectional communication between the gut microbiota and the central nervous system, mediated by neural (vagus nerve, enteric nervous system), immune (cytokines, microglia), endocrine (HPA axis), and metabolic (SCFAs, neurotransmitter precursors, tryptophan metabolite…
The gut-gonadal axis describes the bidirectional communication between the intestinal microbiome and the reproductive endocrine system. Gut bacteria modulate sex hormone levels through enzymatic activity (particularly beta glucuronidase-mediated estrogen deconjugation),…
The relationship between heavy metals and the gut microbiota is bidirectional: metals reshape microbial community composition and metabolic output, while the microbiota modulates metal absorption, speciation, and toxicity. The gut microbiota serves as the first line of …
The gut-thyroid axis describes the bidirectional communication between the gut microbiome and the thyroid gland. The thyroid regulates metabolism, energy homeostasis, and immune function -- and the microbiome influences thyroid physiology at every level: mineral absorpt…
Immunotherapy harnesses the patient's own immune system to fight disease, most notably cancer. Immune checkpoint inhibitors (ICIs) -- antibodies that block PD-1, PD-L1, or CTLA-4 -- have revolutionized oncology since their introduction in the 2010s, producing durable re…
Interleukin-22 (IL-22) is an immune signaling protein that helps coordinate host responses at epithelial surfaces. In the gut evidence represented by WikiBiome, group 3 innate lymphoid cells (ILC3s) are a prominent source, while Th17-associated responses can also includ…
Microbiome-derived metabolites are small molecules made, consumed, or chemically transformed through activity in the gut microbiome and other host-associated communities. They connect community function to host biology, but the phrase covers several kinds of provenance:…
Oxygen state is a master ecological variable in the gut that determines which microorganisms thrive and which are excluded. The healthy colon maintains a steep oxygen gradient — oxygenated tissue at the epithelial surface drops to near-anaerobic conditions in the lumen,…
Postbiotics are defined by ISAPP (2021) as "preparations of inanimate microorganisms and/or their components that confer a health benefit on the host." They include heat-killed bacteria, cell-free supernatants, bacterial lysates, and purified microbial metabolites (SCFA…
Saccharolytic fermentation is the microbial breakdown of carbohydrates (dietary fiber, resistant starch, host glycans) to produce short chain fatty acids (acetate, propionate, butyrate) and gases (H₂, CO₂, CH₄). It is the beneficial fermentation mode — the metabolic act…