WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
A large, polyphyletic genus of Gram-positive, obligate anaerobic, spore-forming bacteria encompassing both critical beneficial commensals and dangerous pathogens. Former Clostridium clusters IV and XIVa are now reclassified into ruminococcus-family Ruminococcaceae and l…
Clostridium butyricum is a spore-forming, obligate anaerobic, Gram-positive bacterium and one of the leading next-generation probiotic candidates. The MIYAIRI 588 strain (CBM 588) is approved as a pharmaceutical probiotic in Japan and has expanding clinical evidence acr…
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…
Clostridium symbiosum is a Gram-positive, obligately anaerobic bacterium within the Clostridium cluster XIVa — a taxonomic group enriched for short-chain fatty acid (SCFA) producers and specialized bile acid metabolizers. Despite its ambiguous name (suggesting symbiotic…
Lachnoclostridium is a genus of obligate anaerobic, Gram-positive bacteria in the lachnospiraceae family. It is a butyrate-producing commensal with emerging clinical significance as a treatment response biomarker and diagnostic marker.
A genus of Gram-positive obligate anaerobes in the family Lachnospiraceae (Clostridium cluster XIVa) that occupy a critical metabolic relay position in gut ecosystem stability: converting lactate to butyrate. Anaerostipes is one of the most consistently depleted genera …
Beta-glucuronidase (β-glucuronidase, EC 3.2.1.31) is an enzyme that catalyzes the hydrolysis of glucuronidated compounds, cleaving the β-1,4-glycosidic bond between a sugar and a glucuronic acid group. In the microbiome, beta-glucuronidase is the key enzyme of the estro…
Bile salt hydrolase (BSH) is the microbial enzyme that deconjugates primary bile acids (taurocholate, glycocholate) by cleaving the amino acid (taurine or glycine) from the steroid core. This is the first and rate-limiting step in microbial bile acid transformation — wi…
Cadaverine (1,5-diaminopentane) is a biogenic amine produced by bacterial lysine decarboxylase — primarily by Enterobacteriaceae, Fusobacterium, and Clostridium — during proteolytic fermentation of undigested protein in the distal colon. It is a product of putrefaction …
A class of Gram-positive, obligate anaerobic bacteria within the phylum Firmicutes that represents the most functionally diverse and clinically significant taxonomic class in the human gut microbiome. Clostridia encompasses the dominant butyrate producers sustaining col…
Clostridioides difficile is the current NCBI name for NCBITaxon:1496 and the correct, medically recommended combination recorded by LPSN. Both records retain Clostridium difficile as a validly published homotypic synonym of the same organism rather than a separate speci…
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…
Hidradenitis suppurativa (HS) is a chronic, relapsing inflammatory skin disease characterized by painful nodules, abscesses, and sinus tracts in apocrine gland-bearing skin (axillae, groin, inframammary folds). Long classified as a purely dermatological condition, emerg…
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 family within the Firmicutes phylum (order Clostridiales, formerly Clostridium cluster XIVa) that serves as a sentinel indicator of gut health -- its depletion is the single most consistent microbiome signature across nearly every disease represented in this wiki. The…
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…
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…
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…
Tryptamine is a microbial decarboxylation product of tryptophan, produced by bacterial tryptophan decarboxylase (found in ruminococcus gnavus, Clostridium sporogenes, and others). It is a serotonin receptor agonist (particularly 5-HT4) that stimulates gut motility and f…
Tyzzerella is a genus of Gram-positive, strictly anaerobic bacteria within the family Lachnospiraceae (order Clostridiales, phylum Firmicutes). It was recently reclassified from Clostridium cluster XIVa and remains poorly characterized at the species level. The genus in…