WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
An analysis of which microbial taxa appear across multiple disease signatures in this knowledge base, what metal dependencies they share, and what the taxonomic overlap reveals about shared pathogenic mechanisms. This analysis covers the 13 disease signatures currently …
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…
Actinobacteria (reclassified as Actinomycetota in 2021) is a major Gram-positive, high-GC-content bacterial phylum with remarkable ecological breadth. In the gut, it typically comprises 1-10% of the community -- a distant third behind firmicutes and bacteroidetes -- but…
A genus of Gram-positive, facultatively anaerobic, filamentous bacteria that are among the most abundant colonizers of the human oral cavity. Actinomyces species, particularly A. naeslundii, play dual roles as early dental plaque colonizers and as opportunistic pathogen…
A pathotype of escherichia coli that adheres to and invades intestinal epithelial cells, survives and replicates within macrophages, and is strongly associated with ileal Crohn's disease. Unlike classical diarrheagenic E. coli pathotypes (EPEC, ETEC, EHEC), AIEC does no…
A ubiquitous filamentous fungal genus that is both an environmental saprophyte and an opportunistic human pathogen. A. fumigatus is the primary cause of invasive aspergillosis in immunocompromised patients, while A. niger is relevant to food contamination. The genus is …
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…
A Gram-negative obligate anaerobe and the most clinically significant member of the Bacteroides genus. B. fragilis occupies a unique dual position in gut microbiology: as a non-toxigenic commensal (NTBF), it produces polysaccharide A (PSA) that shapes immune tolerance; …
A Gram-negative obligate anaerobe that exemplifies the commensal-pathobiont spectrum. B. vulgatus is a common component of the healthy gut microbiota, yet is significantly enriched in colorectal cancer and depression, suggesting a context-dependent pathogenic potential.…
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…
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…
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, …
Clostridium perfringens is a Gram-positive, strictly anaerobic, spore-forming bacterium infamous for causing gas gangrene, food poisoning, and necrotizing enterocolitis (NEC) in premature infants. It is one of the most widely distributed pathogenic bacteria in nature, f…
A genus of Gram-positive, obligate anaerobic bacteria within the Actinobacteria phylum (family Coriobacteriaceae) that has emerged as a consistent pathobiont enriched in cardiometabolic and autoimmune diseases. C. aerofaciens is the most studied species, with establishe…
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…
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…
A genus of Gram-negative, obligate anaerobic, sulfate-reducing bacteria (SRB) that produces hydrogen sulfide (H2S) as its primary metabolic end-product. H2S is a potent cytotoxin that disrupts colonocyte energy metabolism, damages the gut barrier, and promotes chronic i…
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…
A Gram-negative, obligate anaerobic bacterium that has emerged as the most consistently CRC-associated microorganism in human gut microbiome studies. F. nucleatum is the primary species of concern, originally a commensal of the oral cavity that translocates to colorecta…
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 …
Gardnerella vaginalis is a Gram-variable, facultatively anaerobic bacterium that is the key organism in bacterial vaginosis (BV), the most common vaginal infection in women of reproductive age. Its sialidase production, biofilm-forming capacity, and associations with he…
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 community of trillions of microorganisms — bacteria, archaea, fungi (mycobiome), viruses, and bacteriophages — inhabiting the human gastrointestinal tract, with the highest density in the colon (~10¹¹ cells/g). The gut microbiome encodes 100–150 times more genes tha…
Hungatella hathewayi is a Gram-positive, obligate anaerobic bacterium within the Firmicutes phylum (family Clostridiaceae) that has rapidly emerged as a multi-disease cancer-associated pathobiont. A recently reclassified genus (from Clostridium hathewayi), it is now rec…
A Gram-negative obligate anaerobe traditionally considered an oral commensal, but increasingly recognized as an opportunistic pathobiont with the ability to translocate from oral biofilms to the gastrointestinal tract and bloodstream. Leptotrichia species are prominentl…
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…
A Gram-positive, obligate anaerobic genus that has emerged as one of the most consistently enriched taxa in colorectal cancer. The key pathogenic species P. anaerobius promotes colorectal carcinogenesis through multiple mechanisms including cholesterol biosynthesis indu…
Peptostreptococcus stomatis is a Gram-positive, obligately anaerobic coccus originally isolated from the human oral cavity (oral streptococcal species) that has emerged as a carcinogenic oral pathobiont enriched in colorectal cancer, particularly in advanced stages. Unl…
Phage therapy uses bacteriophages — viruses that infect and lyse specific bacteria — as precision antimicrobials. Unlike broad-spectrum antibiotics, phages target specific bacterial species or strains, sparing the commensal microbiome. In the WikiBiome framework, phage …
A Gram-negative, obligate anaerobic genus with the keystone pathogen P. gingivalis at its center. Named for its porphyrin (heme) requirement, Porphyromonas is the prototypical periodontal pathogen and one of the most important organisms connecting oral health to systemi…
A Gram-negative obligate anaerobe and keystone pathogen of the oral microbiome that causes chronic periodontitis and is increasingly implicated in systemic diseases including alzheimers disease and cardiovascular disease. P. gingivalis virulence is fundamentally depende…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum that exemplifies context-dependent microbiome effects -- beneficial in some settings, pathogenic in others. P. copri is the dominant species in the human gut and a hallmark of plant-rich, fiber-ri…
A Gram-negative obligate anaerobe that occupies a unique context-dependent niche in the human gut microbiome. P. copri is significantly enriched in rheumatoid arthritis patients and is associated with metabolic syndrome and obesity, yet in other contexts it can function…
A Gram-negative, obligately anaerobic, black-pigmented bacterium and one of the classical periodontopathogens. P. intermedia belongs to the "orange complex" of periodontal pathogens (Socransky classification) and is distinguished by its iron and heme dependency -- the c…
Proteobacteria (recently reclassified as Pseudomonadota) is the phylum that signals trouble. In a healthy adult gut, Proteobacteria comprise less than 1% of the community. When they bloom to 10-50% of the microbiome, it marks a fundamental ecological shift -- the collap…
A genus of Gram-positive, obligate anaerobic cocci within the Firmicutes phylum that exemplifies dual-nature microbiology — containing both keystone beneficial species and disease-associated pathobionts within the same genus. The genus spans multiple former taxonomic gr…
A Gram-positive obligate anaerobe that has emerged as a pro-inflammatory pathobiont enriched across multiple disease states including crohns disease, depression, and multiple sclerosis. R. gnavus produces a species-specific inflammatory polysaccharide that activates int…
A genus of ascomycete yeasts that includes both a proven therapeutic probiotic (S. boulardii) and species associated with disease states (S. cerevisiae enriched in CRC mycobiome). This dual nature -- commensal/probiotic versus disease-associated -- parallels the bacteri…
Saccharomyces cerevisiae is a unicellular budding fungus (ascomycete) ubiquitous in fermentation, brewing, bread-making, and increasingly used as a pharmaceutical probiotic (Hatoum et al. 2012). The strain S. boulardii (also called S. cerevisiae var. boulardii) is the m…
Research summary -- not medical advice. This page synthesizes published research on why broad-spectrum antibiotics may worsen gut dysbiosis rather than correct it. This does NOT apply to life-threatening infections requiring antibiotic treatment. Consult a qualified hea…
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.
Harm potential: YELLOW — True iron deficiency anemia requires supplementation.
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive, facultatively anaerobic coccus that exists in two clinical contexts: (1) as a major neonatal pathogen causing life-threatening meningitis and sepsis in newborns, and (2) as an enric…
A Gram-negative, microaerophilic genus within the Proteobacteria phylum (family Sutterellaceae). The primary species S. wadsworthensis is classified as a pathobiont due to its IgA-degrading capacity and associations with neurodevelopmental and inflammatory conditions. H…
A genus of ascomycete yeasts (formerly classified as Zygosaccharomyces) found in fermentation environments (bread, wine, kombucha) and increasingly detected as a component of the human gut mycobiome. While typically at low abundance in healthy individuals, Torulaspora d…
A chronic inflammatory bowel disease characterized by continuous mucosal inflammation of the colon, extending proximally from the rectum. Unlike crohns disease, UC is limited to the colon, affects only the mucosa/submucosa (not transmural), produces no skip lesions, and…