WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to microbe.
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…
Aeromonas is a genus of Gram-negative, facultatively anaerobic bacteria found in aquatic environments and, increasingly recognized as an opportunistic gut pathogen. Several species — particularly Aeromonas hydrophila, A. veronii, and A. caviae — are associated with gast…
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…
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 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.…
A class of Gram-negative bacteria within the phylum Proteobacteria that has emerged as a causal risk factor for schizophrenia and bipolar disorder through Mendelian randomization studies. Betaproteobacteria includes genera with notable metal tolerance -- particularly wi…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
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…
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…
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…
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, …
Enterobacter is a genus of Gram-negative, facultatively anaerobic bacteria in the enterobacteriaceae family. Key species include enterobacter cloacae (the most clinically relevant) and E. hormaechei. Like other Enterobacteriaceae, Enterobacter possesses iron-dependent s…
A family of Gram-negative, facultative anaerobic Gammaproteobacteria that includes many of the most important human pathogens: escherichia coli, klebsiella pneumoniae, salmonella typhimurium, shigella flexneri, yersinia pestis, proteus mirabilis, Morganella, and Serrati…
Escherichia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species E. coli is simultaneously the most studied bacterium in biology and one of the most consistently enriched organisms in disease-associated micr…
The most abundant bacterium in the healthy human colon (5-15% of total fecal microbiota), F. prausnitzii is the premier butyrate producer in the gut and a cornerstone of anti-inflammatory intestinal homeostasis. Its depletion is one of the most consistent microbiome sig…
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…
Klebsiella is a genus of Gram-negative, encapsulated, facultatively anaerobic bacteria in the Enterobacteriaceae family. With 141 file mentions across the vault, Klebsiella is one of the most frequently referenced opportunistic pathogens. The dominant species is klebsie…
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…
This page serves as the family-level hub for Lachnospiraceae, connecting the individual genus and species pages (roseburia, blautia, anaerostipes, eubacterium rectale) with the overarching ecological and metabolic framework that defines the family. For the primary entit…
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…
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…
A genus of lipophilic basidiomycete yeasts that is the dominant fungus on human skin and has recently been recognized as a significant component of the gut mycobiome. M. restricta, M. globosa, and M. furfur are the primary species. Originally studied as the cause of dan…
Methylobacterium is a genus of methylotrophic alpha-Proteobacteria (phylum Pseudomonadota) predominantly found in soil, water, plant surfaces, and air environments. It is a methylotroph — capable of using one-carbon compounds such as methanol as a carbon and energy sour…
Oscillibacter is a genus of Gram-negative, strictly anaerobic, motile bacteria within the family Oscillospiraceae (phylum Firmicutes). The type species, Oscillibacter valericigenes, was first isolated from the alimentary tract of a Japanese freshwater fish and named for…
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…
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-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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A filamentous fungus in the order Hypocreales (family Ophiocordycipitaceae), historically studied as an insect and nematode pathogen (P. lilacinum, formerly Paecilomyces lilacinus), now emerging as a clinically significant protective member of the gut mycobiome — and it…
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…
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…
Shigella is a genus of Gram-negative, facultatively anaerobic bacteria in the family Enterobacteriaceae, closely related to Escherichia coli — so closely that many 16S rRNA-based studies report them as the Escherichia/Shigella complex, unable to distinguish the two gene…
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 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 Gram-negative, obligate anaerobic genus within the Firmicutes phylum (class Negativicutes, family Veillonellaceae). The primary species V. parvula is a specialized lactate utilizer that occupies a unique metabolic niche by cross-feeding with lactate-producing bacteria…
A family of Gram-negative, obligate anaerobic bacteria within the Firmicutes phylum (class Negativicutes) that occupies a unique metabolic niche as specialized lactate utilizers. Veillonellaceae cannot ferment sugars directly -- instead, they cross-feed on lactate produ…