WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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…
The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that functions as a master sensor at the intersection of gut microbial metabolism, environmental chemical exposure, and immune regulation. It is expressed broadly across immune cells, intesti…
A Gram-negative, obligate anaerobic, mucin-degrading bacterium first isolated from human feces and formally described as a second species within the genus Akkermansia. Like its well-studied sister species akkermansia muciniphila, A. mucinicola colonizes the intestinal m…
A Gram-negative, obligate anaerobic, mucin-degrading bacterium that colonizes the intestinal mucus layer and has emerged as one of the most important next-generation probiotics. A. muciniphila is consistently depleted in disease states associated with metal dyshomeostas…
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…
A Gram-negative obligate anaerobe identified as a histamine-producing bacterium enriched in dysbiotic microbiota associated with obesity, metabolic syndrome, and metabolic endotoxemia. Allisonella is a minor but functionally significant genus whose primary clinical rele…
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…
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 …
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…
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 …
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…
Purpose: Introduce the paper submission pathway with suggested donation. Sent only to authors who engaged with the first email (replied, visited their source page, or submitted corrections). When to send: 2–3 weeks after first-touch, only if the author engaged. Subject …
Bacteroidaceae is a family of obligate anaerobic, Gram-negative bacteria in the order bacteroidales. The dominant genus is bacteroides, which includes B. fragilis, B. vulgatus, B. thetaiotaomicron, and B. uniformis. Bacteroidaceae are among the most abundant gut bacteri…
Bacteroidales is an order of obligate anaerobic, Gram-negative bacteria within the phylum Bacteroidetes. It includes the families Bacteroidaceae (bacteroides), Prevotellaceae (prevotella), Rikenellaceae, and Porphyromonadaceae (porphyromonas). Bacteroidales are among th…
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 anaerobic bacterium within the phylum Bacteroidetes and a common member of the healthy human gut microbiota. B. uniformis is a versatile polysaccharide degrader with emerging significance as an anti-inflammatory commensal whose depletion appear…
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.…
Barnesella is a genus of obligate anaerobic, Gram-negative bacteria in the phylum Bacteroidetes. It is a relatively understudied gut commensal that appears in the WikiBiome vault primarily in the context of endometriosis microbiome studies, where it is part of the compl…
Barnesiella is a genus of Gram-negative, obligate anaerobic bacteria within the phylum Bacteroidetes. It is a commensal member of the healthy human gut microbiota, recognized for its role in colonization resistance — the ability of the resident microbiome to prevent est…
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…
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 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 Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum (family Odoribacteraceae). Despite its relatively recent characterization, Butyricimonas has gained significant attention as a member of the protective butyrate-producing consortium that is consis…
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…
The most abundant mineral in the human body, with ~99% stored in bones and teeth. Calcium's biological significance extends far beyond structural support -- it is the universal second messenger in cell signaling, controlling neurotransmitter release, muscle contraction,…
Chlamydia is a genus of obligate intracellular, Gram-negative bacteria with a unique biphasic developmental cycle. The genus includes three species pathogenic to humans: chlamydia trachomatis (STI and trachoma), C. pneumoniae (respiratory infections, atherosclerosis ass…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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 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…
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 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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
Dialister is a genus of Gram-negative, obligate anaerobic bacteria within the family Veillonellaceae that represents one of the strongest protective associations in gut-brain-axis research. Dialister depletion is a consistent and independent biomarker of depression, anx…
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 …
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…
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, …
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 Gram-negative bacterium that spans the commensal-pathogen spectrum, with pathogenic variants (UPEC, STEC, EHEC) deploying nickel-dependent enzymes as virulence factors. E. coli is the model organism for nickel transport biology -- the NikABCDE system was first charact…
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…
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…
The transfer of processed stool from a healthy donor into a recipient's gastrointestinal tract to restore a disrupted microbial community. FMT is the most direct form of microbiome intervention -- replacing the entire community rather than supplementing individual strai…
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…
An order of Gram-negative, obligate anaerobic bacteria within the phylum Fusobacteriota (formerly Fusobacteria). This order-level page covers the broader taxonomic group that includes the well-characterized genus fusobacterium and its key species fusobacterium nucleatum…
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 has emerged as a major pathogen in colorectal cancer (CRC) and inflammatory bowel disease. F. nucleatum is significantly enriched in CRC tissue and tumors compared to healthy mucosa, making it one of the strongest microbe-cancer as…
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 …
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…
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…
--- 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…
Microbial tryptophan metabolites produced by gut bacteria through the third branch of tryptophan metabolism -- the indole pathway. Unlike the host-dominated kynurenine pathway (~95% of Trp) and the serotonin pathway (~1-2%), the indole pathway is exclusively microbial a…
--- 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…
A fundamental ordering of divalent transition metal ion binding affinities, established by Harry Irving and Robert Williams in 1953: Mg2+ < Mn2+ < Fe2+ < Co2+ < Ni2+ < Cu2+ Zn2+ This series holds for virtually all ligands and biological chelators. It means that copper b…
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 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…
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…
Megasphaera is a genus of obligate anaerobic, Gram-negative bacteria in the family Veillonellaceae (class Negativicutes, phylum Firmicutes). The genus occupies two distinct ecological niches — the vaginal microbiome (where it is a hallmark of bacterial vaginosis) and th…
Methanobrevibacter smithii is the dominant methanogenic archaeon in the human gut, responsible for consuming hydrogen gas produced by fermentative bacteria and converting it to methane. Despite being an archaeon rather than a bacterium, it represents 0–15% of gut microb…
Odoribacter splanchnicus is a Gram-negative, obligate anaerobic bacterium belonging to the family Odoribacteraceae within the phylum Bacteroidota (formerly Bacteroidetes). It is a commensal resident of the human colon recognized primarily as a producer of short chain fa…
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: Oxalobacter type: entity subtype: microbe created: 2026-04-10 updated: 2026-04-16 lastsubstantiveupdate: 2026-04-16 sources: [duan-2020-gut-microbiota-heavy-metal-probiotic-strategy, zhang-2022-causal-gut-microbiome-cvd-mr, dai-2024-gut-microbiota-cvd-bidirec…
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum, closely related to bacteroides fragilis. The best-characterized species, P. distasonis, has emerged as a key anti-inflammatory commensal with significant roles in bile acid metabolism and metabol…
Paraprevotella is a genus of obligate anaerobic, Gram-negative bacteria in the family Prevotellaceae, related to prevotella. It is a gut commensal with emerging associations across neuropsychiatric and reproductive conditions. - Schizophrenia: Altered in gut-brain axis …
Parasutterella excrementihominis is a Gram-negative, obligate anaerobic bacterium within the Betaproteobacteria class that has gained attention as an emerging biomarker across metabolic, inflammatory, and endocrine conditions. Despite its relatively recent characterizat…
--- 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…