WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
arsenic (As) is unique among dietary heavy metals because it exists in two fundamentally different forms with dramatically different toxicities: inorganic arsenic (iAs, the dangerous form) and organic arsenic (arsenobetaine, arsenosugars — largely non-toxic). Understand…
cadmium (Cd) enters the human body primarily through food. Unlike nickel, which has high-concentration food categories that can be avoided, cadmium contamination is diffuse — embedded in staple crops, leafy greens, and grains that form the basis of most dietary patterns…
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.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
High dietary fiber intake as a preventive strategy against ovarian cancer. This is the strongest epidemiological evidence for any dietary intervention in OC, with meta-analytic dose-response data from 13 studies and 142,189 participants.
Dietary fiber supplementation (resistant starch, inulin, arabinoxlan oligosaccharides, or whole-food fiber) to shift gut fermentation from proteolytic to saccharolytic, reducing the two key protein-bound uremic toxins (indoxyl sulfate and p-cresyl sulfate) that drive CK…
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 …
lead (Pb) has no safe level of exposure. Unlike most dietary metals, lead does not play any known biological role — every atom absorbed represents toxic burden. While environmental lead exposure (paint, soil, air) has decreased dramatically since leaded gasoline phase-o…
A synthesis of how dietary heavy metal exposure varies across the human lifespan, highlighting that the same metals present different risks at different developmental stages due to changing absorption rates, detoxification capacity, dietary patterns, and organ vulnerabi…
This page identifies the contradictions and clinical dilemmas that become visible only when the 236 source pages in this wiki are read together. Each paradox describes a situation where evidence-based dietary or supplementation advice -- advice that is correct for most …
Every meal delivers metals to the gut lumen — essential minerals, trace elements, and contaminants alike. These metals do not passively transit the GI tract. They actively reshape the microbial ecosystem, selecting for metal-tolerant organisms, enabling virulence in met…
Food is the primary source of nickel exposure for the general (non-occupational) population. While food nickel poses minimal risk to most adults, children and nickel-sensitized individuals are high-risk groups.
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 Autoimmune Protocol (AIP) diet is an elimination diet that removes foods associated with increased intestinal permeability and autoimmune activation. In Hashimoto's thyroiditis, it targets the gut-thyroid connection by reducing antigenic triggers that drive molecula…
Gluten-Free Diet is discussed across 7 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.
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.
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.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Low-carbohydrate diets reduce esophageal acid exposure time from 5.1% to 2.5% (P=0.022) by decreasing gastric distension and transient lower esophageal sphincter relaxations (TLESRs). Critically, benefits are independent of weight loss.
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.
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.
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.
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.
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.
The Mediterranean diet improves glycemic control and cardiovascular risk in T1D youth while promoting butyrate-producing taxa depleted in T1D, particularly F. prausnitzii. Combination with L. johnsonii N6.2 supplementation has been proposed.
Plant-based diets shift the gut microbiome from proteolytic to saccharolytic fermentation, reducing production of the uremic toxins indoxyl sulfate (IS) and p-cresyl sulfate (PCS) that accelerate CKD progression. Plant protein has lower bioavailability, which reduces gl…
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. Evidence quality ratings reflect the str…
Celiac patients achieve serological remission on a gluten-free diet (GFD), confirming that the diet is working at the immunological level. Yet a subset develops NEW or WORSENING gastrointestinal and extraintestinal symptoms on prolonged GFD. The cause: gluten-free subst…
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…
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 Gram-negative, obligate anaerobic genus within the family veillonellaceae (class Negativicutes, phylum Firmicutes) defined by its specialized amino acid fermentation -- the genus name literally means "acid from amino acids." Acidaminococcus ferments glutamate as its p…
Adlercreutzia is a genus of Gram-positive, strictly anaerobic gut bacteria within the phylum Actinobacteria, named after Finnish researcher Herman Adlercreutz who pioneered phytoestrogen research. The genus is best known for producing equol, a potent bioactive metabolit…
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…
Alloprevotella is a genus of Gram-negative, obligate anaerobic bacteria within the family Prevotellaceae that represents a distinct clade from prevotella with specific protective roles in type 2 diabetes prevention and metabolic health. Alloprevotella depletion is one o…
A non-essential metal and the most abundant metallic element in the Earth's crust. Unlike manganese, iron, or selenium, aluminum has no known biological function in humans. Its significance in metal toxicology stems from two major concerns: proven neurotoxicity at eleva…
The most common form of dementia, affecting an estimated 55 million people worldwide and projected to triple by 2050 zhang 2024 recent advances alzheimers mechanisms trials. Characterized by progressive memory loss, cognitive decline, amyloid-beta plaques, and neurofibr…
The ability of microorganisms to survive and replicate in the presence of antimicrobial agents — antibiotics, antifungals, antivirals, antiparasitic drugs — at concentrations that would normally inhibit or kill them. Antimicrobial resistance (AMR) is designated by the W…
Arsenic is a metalloid and potent carcinogen (IARC Group 1) that ranks among the most widespread environmental toxicants affecting human health. An estimated 225 million people worldwide are chronically exposed through contaminated drinking water alone ghosh 2023 heavy …
This page serves as a cross-reference point for the existing ahr concept page, which provides comprehensive coverage of AhR signaling, microbiome-derived ligands, and immune regulation. The aryl hydrocarbon receptor is a ligand-activated transcription factor that integr…
Atherosclerosis is a chronic inflammatory disease of arterial walls characterized by lipid-laden plaque formation, endothelial dysfunction, and progressive vascular occlusion. It is the pathological substrate underlying coronary artery disease, stroke, and peripheral ar…
Bacteroides is the most abundant genus in the Western adult gut and a cornerstone of intestinal polysaccharide metabolism. As members of the bacteroidetes phylum, Bacteroides species encode enormous repertoires of carbohydrate-active enzymes (CAZymes) organized into pol…
Bacteroidetes (recently reclassified as Bacteroidota) is one of the two dominant bacterial phyla in the human gut, together with firmicutes typically comprising 90% of the intestinal microbiota. Bacteroidetes are Gram-negative, obligately anaerobic, non-spore-forming ro…
Bifidobacterium adolescentis is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria and the dominant Bifidobacterium species in the adult human gut. It is a specialist degrader of resistant starch and dietary fiber, producing acetate and lactate…
Bilophila wadsworthia is a Gram-negative, obligate anaerobic, sulfite-reducing bacterium that has emerged as a key pathobiont linking high-fat diets, taurine metabolism, hydrogen sulfide production, and inflammatory disease. Its unique metabolic niche -- using taurine-c…
A heavy metal traditionally considered safe enough for over-the-counter gastrointestinal remedies (Pepto-Bismol, De-Nol), bismuth is re-emerging as a potent antimicrobial synergist. Its key property: Bi3+ competes with Fe3+ for binding sites on siderophores and bacteria…
Breast cancer is the most common cancer in women worldwide, with approximately 2.3 million new cases annually. While genetic, hormonal, and lifestyle factors are well-established risk determinants, the metallomic dimension reveals a consistent pattern of trace element d…
Breast milk is the most effective single intervention for NEC prevention. Human milk oligosaccharides (HMOs) — the third most abundant component of breast milk — are selectively metabolized by Bifidobacteria, establishing the protective neonatal microbiome. Formula-fed …
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…
Cadmium is a toxic non-essential heavy metal (IARC Group 1 carcinogen) with a biological half-life of 17--30 years in mammals, primarily accumulating in the renal cortex via proximal tubular reabsorption of the Cd-metallothionein complex rasin 2025 cadmium exposure heal…
Cardiovascular disease (CVD) -- encompassing atherosclerosis, coronary artery disease, hypertension, myocardial infarction, heart failure, and stroke -- is the leading cause of death globally. The gut-heart axis has emerged as a central paradigm linking microbial metabo…
Celiac disease is a chronic autoimmune condition triggered by dietary gluten (gliadin proteins from wheat, barley, and rye) in genetically susceptible individuals (HLA-DQ2/DQ8, carried by ~30-40% of Europeans but penetrant in only ~1% of carriers). Gluten exposure cause…
Cerebral palsy (CP) is the most common motor disability in childhood, affecting 2-3 per 1,000 live births allen 2021 multi organ dysfunction cerebral palsy. Characterized by non-progressive disturbances in movement and posture arising from injury to the developing brain…
Chelation therapy uses high-affinity metal-binding molecules to form stable, excretable complexes with toxic metals, removing them from the body. The term derives from Greek "chele" (claw) -- the chelator grips the metal ion at multiple coordination sites. While chelati…
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…
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 transition metal that is essential to human health exclusively as a component of cobalamin (vitamin B12), but toxic at higher levels of exposure. Cobalt occupies a distinctive position in metal biology: it is the only metal whose essential biological function in mamma…
The collective ability of the resident gut microbiome to prevent colonization by exogenous pathogens and suppress expansion of resident pathobionts. Colonization resistance is not a property of any single organism but an emergent function of the whole microbial communit…
Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer death. Over 90% of cases are sporadic, driven by a complex interplay between genetic predisposition, dietary habits, gut microbiome composition, and environmental ex…
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 chronic, relapsing-remitting inflammatory bowel disease (IBD) characterized by transmural inflammation of the gastrointestinal tract, most commonly affecting the terminal ileum and colon but capable of involving any segment from mouth to anus zhang 2017 intestinal mic…
Debaryomyces is a genus of ascomycetous fungi, with D. hansenii being the most clinically relevant species, that represents a prominent opportunistic pathobiont enriched in inflammatory bowel disease, particularly crohns disease. Unlike many commensal fungi, Debaryomyce…
Depression is the most prevalent mental health disorder globally, affecting over 280 million people zhu 2025 microbiota gut brain axis depression review, and one of the most metal-sensitive conditions in this wiki. It sits at the convergence of nearly every pathway cata…
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…
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.
Endometriosis is a chronic estrogen-dependent inflammatory condition affecting approximately 10% of reproductive-age women, characterized by the growth of endometrial-like tissue outside the uterus colonetti 2023 gut vaginal microbiota endometriosis meta analysis. The c…
This page addresses the practical question: how do toxic metals get into people? Metal toxicology research identifies the mechanisms of harm, but understanding exposure routes -- dietary, occupational, environmental, and consumer product-mediated -- is essential for pre…
Epilepsy is a chronic neurological disorder characterized by recurrent unprovoked seizures, affecting ~50 million people worldwide. Approximately 30% of patients have drug-resistant epilepsy -- a population where microbiome-targeted interventions (particularly the ketog…
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.
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.
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 only known cellular iron exporter in mammals. Encoded by the SLC40A1 gene, ferroportin (FPN) sits on the basolateral membrane of enterocytes, the surface of macrophages, and the membrane of hepatocytes, controlling the flow of iron from these cells into the bloodstr…
Fibromyalgia (FM) is a chronic pain syndrome affecting 2-4% of the global population Heidari et al. 2017, characterized by widespread musculoskeletal pain, fatigue, cognitive dysfunction ("fibro fog"), and sleep disturbances. Conventionally attributed to central sensiti…
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…
Gamma-aminobutyric acid (GABA) is the primary inhibitory neurotransmitter in the central nervous system. In the WikiBiome context, GABA is notable because gut bacteria produce it — certain Lactobacillus and Bifidobacterium species possess glutamate decarboxylase (GAD) e…
The fifth most common cancer worldwide and third leading cause of cancer death, with over 1 million new cases annually. Gastric cancer stands unique in this wiki as the disease where a single microorganism -- helicobacter pylori -- provides the dominant causal pathway, …
Gastroesophageal reflux disease (GERD) is a chronic condition in which stomach acid or bile flows back into the esophagus, causing mucosal damage and symptoms such as heartburn and regurgitation. Affecting approximately 20% of Western populations, GERD is conventionally…