WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
Bacteremia is the presence of viable bacteria in the bloodstream. In the WikiBiome framework, bacteremia results from bacterial translocation across compromised barriers — the gut epithelium (→ portal bacteremia) or the oral mucosa (→ systemic bacteremia during dental p…
Endotoxemia is the presence of bacterial endotoxin (lipopolysaccharide, LPS) in the bloodstream. Metabolic endotoxemia — chronic, low-grade LPS translocation from the gut — is a central mechanism linking dysbiosis to systemic disease across dozens of conditions in this …
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A Gram-negative, aerobic, non-fermenting coccobacillus and a member of the ESKAPE group of priority pathogens (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter). Acinetobacter baumannii is among the most problematic nosocomial pathogens…
WHO Priority 1: Critical. A Gram-negative, strictly aerobic coccobacillus and one of the most dangerous nosocomial pathogens on the planet. A. baumannii belongs to the ESKAPE group and causes ventilator-associated pneumonia, wound infections, and bloodstream infections …
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…
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…
Candidozyma auris is the current name for NCBITaxon:498019. Liu and colleagues established the combination in 2024 as MycoBank MB 848169; Candida auris Satoh & Makimura 2009 is its basionym, not a separate species ncbi taxonomy candidozyma auris index fungorum candidozy…
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…
A progressive loss of kidney function affecting approximately 850 million people worldwide (10–14% of adults), causing 1.2 million deaths annually. CKD is unique among diseases in this wiki because it occupies both sides of the metal-disease equation: heavy metals (Cd, …
Cirrhosis is end-stage liver fibrosis characterized by nodular regeneration, portal hypertension, and progressive hepatic failure. The gut-liver axis is central: portal venous blood delivers gut-derived LPS, bacterial DNA, and viable bacteria directly to the liver, and …
Coronary artery disease (CAD) -- the progressive narrowing of coronary arteries by atherosclerotic plaque -- is the single leading cause of death globally, responsible for approximately 9 million deaths annually. CAD encompasses stable angina, unstable angina, and myoca…
Diabetic kidney disease (DKD), also known as diabetic nephropathy, is the leading cause of end-stage renal disease (ESRD) worldwide, affecting 30-40% of patients with type 2 diabetes and type 1 diabetes. DKD is defined by progressive albuminuria, declining glomerular fi…
Dysmenorrhea -- painful menstruation -- is the most common gynecological complaint, affecting 50-90% of reproductive-age women. It is classified as primary (no identifiable pelvic pathology) or secondary (caused by conditions such as endometriosis, adenomyosis, or fibro…
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…
Endothelial dysfunction is the impairment of the vascular endothelium's ability to produce nitric oxide (NO), regulate vascular tone, and prevent thrombosis. It is the earliest detectable stage of atherosclerosis and the mechanistic link between gut dysbiosis, systemic …
Enterobacter is a genus of Gram-negative, facultatively anaerobic bacteria in the enterobacteriaceae family. Key species include enterobacter cloacae (the most clinically relevant) and E. hormaechei. Like other Enterobacteriaceae, Enterobacter possesses iron-dependent s…
Enterobacter cloacae is a Gram-negative, facultatively anaerobic member of the Enterobacteriaceae. Ubiquitous in soil, water, and the mammalian gut, it is a leading cause of nosocomial infections and carries clinically significant antibiotic resistance through inducible…
Enterococcus faecalis is a Gram-positive, facultatively anaerobic coccus that inhabits the gastrointestinal tract, oral cavity, and genitourinary tract of humans. It is a commensal in the healthy gut at low abundance but is one of the most clinically significant opportu…
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 gut-kidney axis describes the bidirectional relationship between the gut microbiome and kidney function. As kidney disease progresses, the resulting biochemical changes (uremia, altered pH, fluid shifts) reshape the gut microbiome. The dysbiotic microbiome, in turn,…
The gut-prostate axis describes the bidirectional communication between the gut microbiome and the prostate gland. Gut-derived microbial metabolites, inflammatory mediators, and immune signals influence prostatic health, while prostatic disease states alter systemic inf…
The master regulator of systemic iron homeostasis. Hepcidin is a 25-amino-acid peptide hormone produced primarily by hepatocytes that controls iron absorption, recycling, and distribution by binding to and degrading ferroportin (SLC40A1/FPN) -- the only known cellular i…
Homocysteine is a sulfur-containing amino acid intermediate in the methionine cycle. Elevated plasma homocysteine (hyperhomocysteinemia) is an established risk factor for cardiovascular disease, endothelial dysfunction, and neurodegenerative disease. The gut microbiome …
The most abundant transition metal in the human body and arguably the most consequential metal in biology. Iron sits at the center of a paradox that drives pathology across virtually every disease domain: organisms need it for oxygen transport, energy metabolism, DNA sy…
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.
Leptin is an adipokine (hormone produced by adipose tissue) that signals satiety to the hypothalamus — suppressing appetite and increasing energy expenditure. Leptin resistance (elevated leptin with impaired signaling) is a hallmark of obesity, paralleling insulin resis…
Lipopolysaccharide (LPS), also called endotoxin, is a major structural component of the outer membrane of Gram-negative bacteria. When released into circulation through a compromised gut barrier, LPS triggers potent inflammatory signaling via Toll-like receptor 4 (TLR4)…
Lodderomyces elongisporus is an ascomycetous yeast and the closest known phylogenetic relative of Candida parapsilosis. Originally considered non-pathogenic, it has emerged as a rare but clinically significant cause of fungemia, particularly in patients with indwelling …
Post-acute sequelae of SARS-CoV-2 infection (PASC), affecting an estimated 10-30% of COVID-19 survivors (WHO and CDC post-acute surveillance estimates) with symptoms persisting 12 weeks. Characterized by fatigue, cognitive dysfunction ("brain fog"), exercise intolerance…
Major depressive disorder (MDD) is a psychiatric condition characterized by persistent depressed mood, anhedonia, and cognitive/somatic symptoms. In the WikiBiome framework, MDD is a paradigm case for the gut brain axis: gut dysbiosis drives systemic inflammation and ne…
Maternal immune activation (MIA) describes the phenomenon in which infection or inflammatory stimulation during pregnancy produces persistent neurological and microbiome alterations in offspring, increasing risk for autism spectrum disorder, schizophrenia, and other neu…
Methylobacterium is a genus of methylotrophic alpha-Proteobacteria (phylum Pseudomonadota) predominantly found in soil, water, plant surfaces, and air environments. It is a methylotroph — capable of using one-carbon compounds such as methanol as a carbon and energy sour…
Nakaseomyces glabratus is the current name for NCBITaxon:5478. Takashima and Sugita established the current combination in 2022 as MycoBank MB 843854; Candida glabrata is a homotypic synonym and former combination, while Cryptococcus glabratus H.W. Anderson 1917 is the …
A Gram-negative diplococcus that is simultaneously a nasopharyngeal commensal (carried asymptomatically by 10–35% of the population) and a devastating invasive pathogen causing bacterial meningitis and meningococcal septicemia. The transition from harmless carriage to l…
Non-alcoholic fatty liver disease (NAFLD), recently reclassified as metabolic dysfunction-associated steatotic liver disease (MASLD), encompasses a spectrum from simple hepatic steatosis to metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH), fibrosis…
Parvimonas micra is a small (0.5–1.0 µm), Gram-positive, obligately anaerobic coccus originally isolated from the human oral cavity that has emerged as one of the most consistent and universally enriched pathobionts in colorectal cancer across all geographic regions, ag…
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…
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…
Sepsis is life-threatening organ dysfunction caused by a dysregulated host response to infection. In the WikiBiome framework, sepsis represents the catastrophic failure of both colonization resistance (pathogen invasion) and nutritional immunity (metal restriction). Inf…
Serratia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species is S. marcescens, famous for its red pigment prodigiosin and its role as a nosocomial opportunistic pathogen. In the WikiBiome vault, Serratia ap…
Serratia marcescens is a Gram-negative, facultatively anaerobic member of the Enterobacteriaceae, historically recognized by its distinctive red pigment prodigiosin. Once considered a harmless environmental saprophyte, S. marcescens is now recognized as a significant op…
Staphylococcus epidermidis is a Gram-positive, facultative anaerobic coagulase-negative staphylococcus and one of the most abundant commensals of human skin and mucosal surfaces. While generally benign, it is a leading cause of nosocomial infections associated with indw…
Research summary -- not medical advice. This page synthesizes published research on why a commonly prescribed intervention may be counterproductive in this specific clinical context. Consult a qualified healthcare provider before making any changes to treatment.
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. Iron-deficiency anemia in colorectal can…
Harm potential: YELLOW — True iron deficiency anemia requires supplementation regardless of inflammatory state.
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…
Harm potential: YELLOW — True iron deficiency anemia requires supplementation.
A Gram-positive, facultatively anaerobic bacterium formerly classified as Streptococcus bovis biotype I that holds a unique position in clinical medicine as a sentinel organism for colorectal cancer. The detection of S. gallolyticus in blood cultures (bacteremia or endo…
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…
Iron deficiency is common and clinically significant across multiple conditions: postpartum anemia increases PPD risk 1.89-fold (RR = 1.887), low ferritin (<1 ug) increases PPD risk 3.98-fold azami 2019 anemia ppd meta analysis, iron deficiency impairs thyroid peroxidas…
Tight junctions are the multiprotein complexes that seal the paracellular space between intestinal epithelial cells, forming the physical barrier that separates the gut lumen (with its ~10^13 bacteria, LPS, and dietary antigens) from the underlying lamina propria and sy…
Type 2 diabetes (T2D) is a metabolic disease characterized by insulin resistance and progressive beta-cell dysfunction, affecting over 500 million people worldwide (IDF Diabetes Atlas 2021). The conventional framing centers on caloric excess and sedentary behavior. The …