WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
Bacteroidetes (recently reclassified as Bacteroidota) is one of the two dominant bacterial phyla in the human gut, together with firmicutes typically comprising 90% of the intestinal microbiota. Bacteroidetes are Gram-negative, obligately anaerobic, non-spore-forming ro…
Actinobacteria (reclassified as Actinomycetota in 2021) is a major Gram-positive, high-GC-content bacterial phylum with remarkable ecological breadth. In the gut, it typically comprises 1-10% of the community -- a distant third behind firmicutes and bacteroidetes -- but…
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…
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…
Bacteroides is the most abundant genus in the Western adult gut and a cornerstone of intestinal polysaccharide metabolism. As members of the bacteroidetes phylum, Bacteroides species encode enormous repertoires of carbohydrate-active enzymes (CAZymes) organized into pol…
Bacteroides caccae is a Gram-negative, obligate anaerobic member of the bacteroidetes phylum and a common fiber-degrading commensal in the human colon. While less individually prominent than bacteroides fragilis or bacteroides thetaiotaomicron, B. caccae has emerged as …
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 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…
Disruption of the normal composition and metabolic function of microbial communities, particularly the gut microbiome. In the metallomics context, dysbiosis is both a consequence of metal toxicity and an amplifier of further disease -- creating vicious cycles where meta…
Firmicutes (recently reclassified as Bacillota) is the dominant bacterial phylum in the Western adult gut, comprising the core community of short-chain fatty acid (SCFA) producers that maintain intestinal barrier integrity, regulate immune function, and influence system…
Flavobacterium is a genus of Gram-negative, aerobic bacteria within the phylum Bacteroidetes. Primarily environmental organisms found in soil and freshwater, Flavobacterium species have been identified in human microbiome studies of the cervical and reproductive tract, …
The community of trillions of microorganisms — bacteria, archaea, fungi (mycobiome), viruses, and bacteriophages — inhabiting the human gastrointestinal tract, with the highest density in the colon (~10¹¹ cells/g). The gut microbiome encodes 100–150 times more genes tha…
A chronic metabolic condition affecting over 1 billion people globally, characterized by excess adipose tissue accumulation, systemic low-grade inflammation, and gut microbiome disruption pendergrass 2026 heavy metals obesity epidemic. From a metallomics perspective, ob…
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 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…
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.
A Gram-negative, obligate anaerobic genus within the phylum Bacteroidota (formerly Bacteroidetes) that was recently reclassified from Bacteroides based on phylogenomic evidence (Garcia-Lopez et al., 2019). The key species -- Phocaeicola vulgatus (formerly Bacteroides vu…
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…
Premenstrual Dysphoric Disorder (PMDD) affects 3-8% of menstruating individuals Epperson et al. 2012, causing severe mood disturbances, irritability, anxiety, and physical symptoms during the luteal phase of the menstrual cycle. Distinguished from premenstrual syndrome …
A Gram-negative, obligate anaerobic genus within the Bacteroidetes phylum that exemplifies context-dependent microbiome effects -- beneficial in some settings, pathogenic in others. P. copri is the dominant species in the human gut and a hallmark of plant-rich, fiber-ri…
A family of Gram-negative, obligate anaerobic bacteria within the phylum Bacteroidota (formerly Bacteroidetes) that includes the genus prevotella and the recently described alloprevotella. Prevotellaceae are specialist fiber fermenters producing short-chain fatty acids,…
A three-carbon short-chain fatty acid (SCFA) produced primarily by Bacteroidetes and certain Firmicutes through anaerobic fermentation of dietary substrates. At physiological concentrations in healthy gut microbiomes, propionic acid (PPA) is a normal fermentation produc…
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…
Type 1 diabetes is an autoimmune disease in which immune-mediated destruction of insulin-producing beta cells in the pancreatic islets of Langerhans leads to lifelong insulin dependence. T1D is fundamentally distinct from type 2 diabetes, which is characterized by insul…