WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum (family Rikenellaceae). Alistipes occupies a complex and context-dependent role in the gut ecosystem — some species carry well-documented anti-inflammatory properties, while the genus is paradoxic…
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…
Arachidonic acid (AA) is a 20-carbon omega-6 polyunsaturated fatty acid (20:4n-6) that serves as the primary substrate for prostaglandin and leukotriene synthesis via COX-2 and 5-LOX pathways. It is the dominant pro-inflammatory lipid mediator — and its balance with ant…
Aspirin (acetylsalicylic acid) is a non-steroidal anti-inflammatory drug (NSAID) that irreversibly inhibits cyclooxygenase (COX) enzymes, suppressing prostaglandin synthesis. While widely used as an antiplatelet and anti-inflammatory agent, aspirin carries significant i…
A Gram-negative, obligate anaerobic bacterium within the phylum Bacteroidetes and a common member of the healthy human gut microbiota. B. uniformis is a versatile polysaccharide degrader with emerging significance as an anti-inflammatory commensal whose depletion appear…
Berberine is an isoquinoline alkaloid from traditional Chinese medicine (Coptis chinensis, Berberis species) that acts as a prebiotic microbiome modulator rather than a direct antimicrobial at gut-relevant concentrations. It is discussed across 16+ sources in the WikiBi…
Bifidobacterium bifidum is an obligate anaerobic, Gram-positive species that specializes in human milk oligosaccharide (HMO) and mucin glycan degradation. It is one of the earliest colonizers of the infant gut and a widely used probiotic species.
Bifidobacterium breve is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria, predominantly found in the infant gut and breast milk. It is among the earliest colonizers of the neonatal intestine and plays a key role in human milk oligosaccharide…
Butyrate is a four-carbon short-chain fatty acid produced when anaerobic gut microorganisms ferment dietary substrates. In the colon, it participates in epithelial energy metabolism, barrier maintenance, immune signaling, and gene regulation. Its effects depend on conce…
A genus of Gram-positive, strictly anaerobic, butyrate-producing bacteria in the order Clostridiales (phylum Firmicutes). The type species, Butyricicoccus pullicaecorum, was originally isolated from chicken caecal content but has since been identified as a significant m…
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…
Butyrivibrio is a genus of Gram-positive, obligate anaerobic bacteria within the family Lachnospiraceae (phylum Firmicutes). Originally characterized as a dominant fiber-fermenting genus in the rumen, Butyrivibrio species are also found in the human colon where they con…
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.
Curcumin is discussed across 4 sources in the WikiBiome vault as a potential intervention. Triangle evidence linking this intervention to specific conditions needs to be populated from the source literature.
A genus of Gram-positive, obligate anaerobic bacteria within the Firmicutes phylum that includes several of the most important butyrate producers in the human colon. Key species are E. rectale, E. hallii (now reclassified as Anaerobutyricum hallii), and E. limosum. Cons…
Faecalibacterium is a genus of obligate anaerobic, Gram-positive bacteria in the family Ruminococcaceae (phylum Firmicutes). It is the most abundant genus in the healthy human colon (5–15% of fecal bacteria) and its depletion is the single most reproducible microbiome f…
The most abundant bacterium in the healthy human colon (5-15% of total fecal microbiota), F. prausnitzii is the premier butyrate producer in the gut and a cornerstone of anti-inflammatory intestinal homeostasis. Its depletion is one of the most consistent microbiome sig…
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.
A Gram-positive obligate anaerobe in the family Ruminococcaceae (Clostridium cluster IV) whose defining metabolic activity is the degradation of dietary flavonoids — the very polyphenols that serve as anti-inflammatory, antioxidant, and antimicrobial agents. When Flavon…
Fusicatenibacter is a Gram-positive obligate anaerobic genus within the Lachnospiraceae (Firmicutes). The primary species, F. saccharivorans, was isolated from human feces and is recognized as a beneficial commensal that produces butyrate and modulates intestinal immune…
A Gram-negative obligate anaerobe that occupies a paradoxical niche in the gut microbiota: as a weak butyrate producer (short-chain fatty acid), it has anti-inflammatory potential; as a virulent invasive pathobiont in inflammatory bowel disease (particularly ulcerative …
Gordonibacter is a genus of Gram-positive, strictly anaerobic gut bacteria within the phylum Actinobacteria. It is recognized as a key participant in polyphenol metabolism, producing bioactive metabolites including equol (from dietary isoflavones) and urolithins (from e…
Gordonibacter urolithinfaciens is a Gram-positive, obligate anaerobic bacterium belonging to the family Eggerthellaceae that plays a specialized and critical role in polyphenol metabolism and conversion of ellagic acid to urolithin A. This microbial conversion is one of…
Interleukin-10 is the primary anti-inflammatory cytokine, produced by Treg cells, macrophages, dendritic cells, and B cells. It suppresses pro-inflammatory cytokine production (IL-6, TNF-alpha, IL-1β), inhibits antigen presentation, and maintains immune tolerance. IL-10…
The immune system is not a monolith but a dynamic equilibrium between pro-inflammatory effector responses (Th1, Th2, Th17) and anti-inflammatory regulatory responses (Treg, IL-10, TGF-beta). Metals and the microbiome are two of the most potent environmental modulators o…
Isoflavones (genistein, daidzein, glycitein) are phytoestrogens found primarily in soy products. They bind estrogen receptors (ERα and ERβ) with weak agonist/antagonist activity and are among the most microbiome-dependent dietary bioactives — their clinical effects depe…
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.
Ketone bodies (beta-hydroxybutyrate [BHB], acetoacetate, acetone) are produced by hepatic fatty acid oxidation during carbohydrate restriction, fasting, or ketogenic diet consumption. BHB is the most abundant and is structurally and functionally analogous to butyrate — …
A genus of Gram-positive, facultatively anaerobic lactic acid bacteria (LAB) that are among the most extensively studied probiotics. In the metallomics context, Lactobacillus species are critical for two reasons: they actively detoxify heavy metals through binding and s…
Lactobacillus reuteri is one of the most extensively studied probiotic species, notable for its production of neuroactive metabolites (GABA, histamine) and its effects on the hypothalamic-pituitary-gonadal axis (testosterone, oxytocin).
An anti-inflammatory dietary pattern characterized by high consumption of extra-virgin olive oil, fruits, vegetables, legumes, whole grains, nuts, and fish, with limited red meat, processed food, and added sugars. The Mediterranean diet (MD) has evidence across multiple…
The Mediterranean diet demonstrated broad symptomatic improvement in fibromyalgia across multiple domains in an RCT (n=84), including pain, disability, fatigue, anxiety, and depression at 2 months.
The Mediterranean diet is associated with a 47% reduction in GERD odds (OR=0.53) at the highest adherence level. Multiple complementary mechanisms contribute to symptom relief beyond simple acid suppression.
Adherence to the Alternate Mediterranean Diet (AMED) pattern — high in fiber, polyphenols, omega-3 fatty acids, and plant-based foods — as both a preventive and post-diagnosis survival strategy. This is the only dietary pattern with direct overall survival data in OC.
Omega-3 fatty acids — eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) — are anti-inflammatory polyunsaturated fatty acids that counterbalance the pro-inflammatory effects of omega-6 arachidonic acid. They act through multiple mechanisms: competitive COX-2/5-L…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum, closely related to bacteroides fragilis. The best-characterized species, P. distasonis, has emerged as a key anti-inflammatory commensal with significant roles in bile acid metabolism and metabol…
Parabacteroides distasonis is a Gram-negative obligate anaerobe formerly classified within Bacteroides. It is a core member of the healthy human gut microbiome, typically found in the colon where it contributes to polysaccharide degradation and bile acid metabolism.
Polyamines -- putrescine, spermidine, spermine, and cadaverine -- are small polycationic molecules produced by both the host and the gut microbiome. They regulate cell growth, differentiation, apoptosis, and immune function. In the gut ecosystem, polyamines are metaboli…
Polyphenols are a diverse class of plant-derived compounds characterized by multiple phenol structural units. They are among the most abundant antioxidants in the human diet, found in fruits, vegetables, tea, coffee, wine, chocolate, and spices. What makes polyphenols p…
Polyunsaturated fatty acids (PUFAs) are fatty acids with multiple double bonds, divided into omega-3 (EPA, DHA, ALA) and omega-6 (arachidonic acid, linoleic acid) families. The omega-6:omega-3 ratio determines inflammatory tone — Western diets (~15:1) favor pro-inflamma…
Postpartum depression (PPD) affects 10-20% of women after delivery, with profound consequences for maternal health, infant bonding, and child neurodevelopment chao 2025 microbiota gut brain perinatal depression. The standard framing centers on hormonal withdrawal (estro…
Multi-strain probiotic supplementation with L. acidophilus, B. longum, and B. bifidum has shown promise in slowing CKD progression through anti-inflammatory mechanisms, though its effect on uremic toxins remains unconfirmed.
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.
Resveratrol is discussed across 5 sources in the WikiBiome vault as a potential intervention. Triangle evidence linking this intervention to specific conditions needs to be populated from the source literature.
A genus of Gram-positive, obligate anaerobic, flagellated bacteria within the lachnospiraceae family that ranks among the most important butyrate producers in the human gut. Key species include R. intestinalis and R. hominis. Roseburia is consistently depleted across in…
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…
See also: saccharomyces (genus page) Saccharomyces boulardii is a non-pathogenic yeast strain used as a probiotic across a wide range of gastrointestinal and inflammatory conditions. Taxonomically a strain of S. cerevisiae, it is phenotypically distinct — optimally acti…
Statin Therapy is discussed across 18 sources in the WikiBiome vault as a potential intervention. Triangle evidence linking this intervention to specific conditions needs to be populated from the source literature.
Statins (HMG-CoA reductase inhibitors) are the most widely prescribed drug class globally, used primarily for cholesterol lowering and cardiovascular risk reduction. Over 200 million people take statins worldwide. Beyond their canonical mechanism of inhibiting cholester…
Statins (HMG-CoA reductase inhibitors) are the most prescribed drug class worldwide for cholesterol lowering. In the WikiBiome framework, statins are notable for their microbiome-modulating effects and drug repurposing potential beyond cardiovascular disease — including…
Streptococcus thermophilus is a Gram-positive, facultative anaerobic coccus that is the primary probiotic species used in commercial yogurt fermentation and thermophilic dairy fermentation worldwide. Distinct from pathogenic Streptococcus species, S. thermophilus produc…
Systemic inflammation is the state in which inflammatory mediators — IL-6, TNF-alpha, CRP, IL-1beta — circulate throughout the body rather than remaining confined to a local injury site. In the WikiBiome framework, systemic inflammation is the final common pathway throu…
The Th17/Treg balance is the immunological equilibrium between pro-inflammatory T helper 17 (Th17) cells and anti-inflammatory regulatory T (Treg) cells. This balance is the master switch between immune tolerance and autoimmune/inflammatory pathology — and the gut micro…
Fish is the primary dietary source of methylmercury (MeHg) -- a potent neurotoxin that crosses the blood-brain barrier, depletes glutathione, and can increase amyloid-beta production and tau phosphorylation mercury. MeHg is 95-100% absorbed in the intestinal tract. An e…
Anti-inflammatory and plant-forward diets are the standard nutritional recommendation for endometriosis, PCOS, rheumatoid arthritis, and IBD. These diets emphasize legumes, whole grains, nuts, seeds, dark chocolate, and cruciferous vegetables -- precisely the foods with…
Ursodeoxycholic acid is a hydrophilic secondary bile acid used therapeutically for primary biliary cholangitis (PBC), gallstone dissolution, and cholestatic liver disease. It is also a microbial metabolite — gut bacteria (7α/β-hydroxysteroid dehydrogenases) convert chen…