WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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-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; …
Bacteroides thetaiotaomicron is one of the most abundant and metabolically versatile commensals of the human gut, routinely cited as a model organism for studying host-microbe symbiosis. Its genome was one of the first human gut bacterial genomes fully sequenced, and su…
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.…
Barnesiella is a validly published genus of Gram-negative, obligately anaerobic bacteria in the phylum Bacteroidota and family Barnesiellaceae. NCBI Taxonomy assigns the genus NCBITaxon:397864, and LPSN lists Barnesiella Sakamoto et al. 2007 as the correct name ncbi tax…
Barrett's esophagus (BE) is a premalignant condition in which the normal squamous epithelium of the distal esophagus is replaced by intestinal-type columnar epithelium (intestinal metaplasia). It is the primary risk factor for esophageal adenocarcinoma (EAC), a cancer w…
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…
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…
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…
An order of Gram-negative, strictly anaerobic sulfate-reducing bacteria (SRB) within the class Deltaproteobacteria. The defining metabolic feature of Desulfovibrionales is dissimilatory sulfate reduction -- using sulfate as a terminal electron acceptor and producing hyd…
Dialister histaminiformans is the current name for the species originally described as Allisonella histaminiformans. NCBI Taxonomy assigns the species NCBITaxon:209880, and LPSN treats A. histaminiformans as its validly published homotypic synonym and basionym ncbi taxo…
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, …
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…
Finegoldia is a genus of Gram-positive, strictly anaerobic cocci, with Finegoldia magna as the primary species of clinical relevance. Formerly classified within Peptostreptococcus, this organism inhabits mucosal surfaces including the vaginal, skin, and gastrointestinal…
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 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 …
Gastroesophageal reflux disease (GERD) is a chronic condition in which stomach acid or bile flows back into the esophagus, causing mucosal damage and symptoms such as heartburn and regurgitation. Affecting approximately 20% of Western populations, GERD is conventionally…
Haemophilus is a genus of small, Gram-negative, facultatively anaerobic coccobacilli that inhabit the upper respiratory tract, oral cavity, and gastrointestinal tract. The genus name literally means "blood-loving" -- a direct reference to its absolute requirement for he…
Research summary — not medical advice. This page synthesizes published research on a mechanism-level intervention. It is not a clinical recommendation.
Hypoxia refers to a state of low oxygen tension (partial pressure of O₂ < 5% in tissue, vs. ~21% in air). In the context of microbiome metallomics, hypoxia is a critical ecological determinant that reshapes bacterial community structure by favoring obligate and facultat…
Lancefieldella parvula is the current name for NCBITaxon:1382. Atopobium parvulum is a validly published historical homotypic synonym rather than the current canonical name ncbi taxonomy lancefieldella parvula lpsn lancefieldella parvula.
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…
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…
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…
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…
Oxygen state is a master ecological variable in the gut that determines which microorganisms thrive and which are excluded. The healthy colon maintains a steep oxygen gradient — oxygenated tissue at the epithelial surface drops to near-anaerobic conditions in the lumen,…
Parabacteroides distasonis is a Gram-negative obligate anaerobe formerly classified within Bacteroides. It is a core member of the healthy human gut microbiome, typically found in the colon where it contributes to polysaccharide degradation and bile acid metabolism.
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 …
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…
See also: porphyromonas (genus page), porphyromonas gingivalis (species page) Porphyromonas bennonis is an obligate anaerobic, Gram-negative bacterium related to the periodontal pathogen porphyromonas gingivalis. Unlike its oral relative, P. bennonis is primarily associ…
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 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…
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…
Rikenella is a genus of obligate anaerobic, Gram-negative bacteria in the family Rikenellaceae (phylum Bacteroidetes). The primary species is R. microfusus. In the WikiBiome vault, Rikenella is consistently depleted across disease states — a protective commensal whose l…
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…
Sneathia is a genus of obligate anaerobic, Gram-negative bacteria in the phylum Fusobacteriota (formerly Fusobacteria). The primary species is S. sanguinegens (formerly Leptotrichia sanguinegens), with S. amnii also clinically significant. Sneathia is a member of the BV…
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…
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 …