WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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…
Aerococcus is a genus of Gram-positive, alpha-hemolytic, catalase-negative cocci. The primary species of clinical relevance are A. urinae (a cause of urinary tract infections, particularly in elderly men) and A. christensenii (a vaginal commensal). In the WikiBiome vaul…
Alloscardovia is a genus of anaerobic, Gram-positive bacteria in the family Bifidobacteriaceae (phylum Actinobacteria). The primary species is A. omnicolens, which colonizes the human urogenital tract. In the WikiBiome vault, Alloscardovia appears exclusively in endomet…
Anaerococcus is a genus of Gram-positive, obligate anaerobic cocci within the phylum Firmicutes. It is a normal inhabitant of the human vaginal, skin, and gastrointestinal microbiota, but is recognized as an opportunistic pathogen in dysbiotic states, particularly when …
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 …
Atopobium is a genus of obligate anaerobic, Gram-positive bacteria in the phylum Actinobacteria. The primary species of clinical relevance is A. vaginae (recently reclassified as Fannyhessea vaginae), which is one of the hallmark organisms of bacterial vaginosis (BV) an…
A Gram-positive, aerobic to facultatively anaerobic, spore-forming genus that bridges environmental and human microbiology. The genus encompasses both beneficial species (B. subtilis, B. coagulans as probiotics) and pathogens (B. cereus causing food poisoning, B. anthra…
A genus of Gram-positive, obligate anaerobic bacteria that dominate the infant gut microbiome and remain important commensals throughout life. Bifidobacterium species are distinctive in the metallomics context because some species possess Ni-dependent urease -- an unusu…
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…
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…
A genus of Gram-positive, obligate anaerobic bacteria within the lachnospiraceae family that produces short chain fatty acids and plays a significant role in bile acid metabolism. Key species include B. obeum, B. wexlerae, B. hydrogenotrophica, and B. producta. While pr…
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…
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…
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…
An order of Gram-positive, obligate anaerobic bacteria within the class clostridia (phylum Firmicutes) that represents the single most functionally important taxonomic group in the human gut. Clostridiales encompasses the major butyrate-producing families (lachnospirace…
A Gram-positive, spore-forming, obligate anaerobic bacterium that is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in healthcare settings. In the metallomics framework, C. difficile sits at the intersection of metal-antibiotic co-selec…
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…
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…
A Gram-positive, obligate anaerobic genus within the lachnospiraceae family (Firmicutes phylum). Coprococcus is one of the most important butyrate-producing commensals in the human gut and has gained particular attention as the "happiness bug" -- one of very few taxa di…
Corynebacterium is a large genus of Gram-positive, club-shaped bacteria with over 130 species spanning commensals, opportunistic pathogens, and the classic pathogen C. diphtheriae. In the WikiBiome context, Corynebacterium is most notable for its dominance in the male r…
A Gram-positive, obligate anaerobic genus within the lachnospiraceae family (Firmicutes phylum). Dorea occupies a mixed role in the gut ecosystem -- while it is a core member of the healthy human microbiome, several species are consistently enriched in autoimmune and ne…
Eggerthella is a genus of Gram-positive, strictly anaerobic, non-spore-forming bacteria in the family Eggerthellaceae (phylum Actinobacteria). The most studied species, Eggerthella lenta, was originally classified as Eubacterium lentum before reclassification. It is a n…
A Gram-positive obligate anaerobe and key estrobolome member that links metabolic dysbiosis to hormone-driven diseases, particularly endometriosis. E. lenta is remarkable for its ability to inactivate cardiac glycosides (like digoxin) and to produce beta-glucuronidase, …
A genus of Gram-positive bacteria (primarily E. faecalis and E. faecium) that exemplifies the metal-antibiotic resistance co-selection crisis. Enterococci carry diverse metal tolerance genes for mercury, arsenic, copper, and cadmium on the same mobile genetic elements a…
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…
Erysipelotrichaceae is a family within the phylum Firmicutes that has drawn increasing attention for its consistent enrichment in metabolic disorders. Members of this family are Gram-positive, obligate anaerobes found throughout the mammalian gastrointestinal tract, whe…
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…
Eubacterium rectale (recently reclassified as Agathobacter rectalis) is a Gram-positive, strictly anaerobic, non-spore-forming bacterium that belongs to Clostridium cluster XIVa within the lachnospiraceae family. It is one of the most abundant butyrate producers in the …
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…
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…
Gemella is a genus of Gram-positive, facultatively anaerobic cocci that are normal commensals of the oral cavity. Species include G. morbillorum, G. haemolysans, and G. sanguinis. In the WikiBiome context, Gemella is notable for its oral-gut translocation pattern — an o…
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…
A genus of Gram-positive, strictly anaerobic bacteria in the family Erysipelotrichaceae (phylum Firmicutes) that is emerging as one of the most consistently protective gut commensals in human disease. Holdemanella is depleted across a striking range of conditions -- inf…
--- title: Hungatella type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [altinok-dindar-2023-gut-microbiota-breast-cancer-diet, qin-2024-consistent-microbiome-signatures-old-young-onset-crc, zhang-2025-gut-v…
--- title: Intestinibacter type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [dai-2024-gut-microbiota-cvd-bidirectional-mr, xiang-2023-host-gene-microbiome-crc-mr, wu-2017-metformin-gut-microbiome-t2d-nature…
A Gram-positive, obligate anaerobic genus within the Firmicutes phylum (family Oscillospiraceae or Ruminococcaceae depending on classification) that possesses a unique metabolic capability: butyrate production from lysine fermentation rather than from dietary fiber. Thi…
Lachnobacterium is a genus of Gram-positive, obligate anaerobic bacteria within the family Lachnospiraceae (phylum Firmicutes). It is a commensal member of the healthy human gut microbiota, though relatively understudied compared to other Lachnospiraceae genera. Lachnob…
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.
Lachnospira is a genus of Gram-positive, obligate anaerobic bacteria within the lachnospiraceae family (Firmicutes phylum). L. pectinoschiza, the type species, is a specialist pectin fermenter that produces short chain fatty acids from plant-derived polysaccharides. The…
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…
A Gram-positive, facultatively anaerobic bacterium that is the dominant species in the healthy human vaginal microbiome and a defining member of Community State Type I (CST-I). L. crispatus dominance is associated with reproductive health, pathogen resistance, and reduc…
Lactobacillus iners is a Gram-positive, facultatively anaerobic bacterium that dominates the vaginal microbiome of many women worldwide, defining Community State Type III (CST-III) in vaginal microbiome classification. For decades, all vaginal Lactobacillus species were…
Lactococcus lactis is a Gram-positive, facultatively anaerobic, lactic acid bacterium best known as the workhorse of the dairy fermentation industry. It holds GRAS (Generally Recognized As Safe) status and has emerged as a versatile platform for probiotic and therapeuti…
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A Gram-positive, obligate anaerobic genus within the family lachnospiraceae (phylum Firmicutes) that was recently reclassified from Ruminococcus based on phylogenomic evidence. The key species Mediterraneibacter faecis (formerly Ruminococcus gnavus clade relatives) is a…
A family of Gram-positive obligate anaerobes (formerly classified as the genus Oscillospira, now reclassified into Oscillibacter and related genera within Oscillospiraceae) that serve as keystone butyrate producers in the healthy human distal colonic microbiota (Konikof…
An order of Gram-positive, obligate anaerobic bacteria within the class Clostridia (phylum Firmicutes) that has emerged as one of the most consistent markers of a healthy gut ecosystem. Oscillospirales members are butyrate producers associated with leanness and metaboli…
--- title: Parvimonas type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [qin-2024-consistent-microbiome-signatures-old-young-onset-crc, saito-2019-metagenomic-gut-microbiota-colorectal-adenoma, wu-2021-micro…
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…
A Gram-positive, obligate anaerobic bacterium within the Firmicutes phylum (family Peptostreptococcaceae) that has emerged as a consistently enriched organism in the colorectal cancer tumor microenvironment. While fusobacterium nucleatum receives the most attention as a…
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…
Propionibacterium (largely reclassified as Cutibacterium for skin species) is a genus of Gram-positive, anaerobic to aerotolerant bacteria that produce propionic acid as their primary fermentation product. P. acnes (now Cutibacterium acnes) is the dominant skin commensa…
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…
Rothia is a genus of Gram-positive, facultatively anaerobic bacteria in the family Micrococcaceae (phylum Actinobacteria). The most commonly identified species in microbiome studies are Rothia dentocariosa and Rothia mucilaginosa, both of which are primary inhabitants o…
Ruminococcaceae is a family of obligate anaerobic, Gram-positive bacteria in the order Clostridiales (phylum Firmicutes) that represents one of the most important butyrate-producing and fiber-degrading families in the human gut. Key genera include faecalibacterium (incl…
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…
Ruminococcus albus is a Gram-positive, obligate anaerobic bacterium that represents one of the primary cellulolytic (fiber-degrading) specialists in the human gut microbiota. This species constructs cellulosomes — extraordinary multi-enzyme complexes organized on bacter…
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 Gram-positive, obligate anaerobic genus within the phylum Actinobacteria (family Coriobacteriaceae) that has emerged as one of the most frequently identified taxa in Mendelian randomization studies across disparate conditions -- erectile dysfunction, chronic kidney di…
A genus of Gram-positive, facultative anaerobic cocci that includes some of the most clinically significant human pathogens. Staphylococci are defined by their exceptionally comprehensive metal acquisition arsenal -- arguably the most thoroughly characterized of any bac…
A versatile Gram-positive pathogen with one of the best-characterized nutritional immunity evasion systems known. S. aureus requires nickel, iron, zinc, and manganese for virulence and has evolved dedicated acquisition systems for each, including the novel metallophore …
A genus of Gram-positive facultative anaerobes that occupy niches ranging from benign commensals (dental plaque, skin) to acute pathogens (pharyngitis, impetigo, invasive disease). Streptococci are uniquely manganese-dependent for catalytic scavenging of reactive oxygen…
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-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…
The primary architect of dental caries -- the most prevalent chronic infectious disease worldwide. S. mutans is a Gram-positive, facultative anaerobe that colonizes tooth surfaces and produces the acid-rich, metal-managed biofilms known as dental plaque. What sets this …
A Gram-positive pathogen (the "pneumococcus") that depends on iron, manganese, and zinc for virulence and has evolved dedicated transport systems for each. Iron is required for viability itself, manganese powers the superoxide dismutase needed to survive the oxidative b…
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…
A Gram-positive, facultatively anaerobic genus within the class Erysipelotrichia (phylum Firmicutes) that has become one of the most frequently identified taxa in gut-brain and gut-immune Mendelian randomization studies. Turicibacter sanguinis, the type species, possess…
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…
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