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…
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…
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 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 …
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…
An opportunistic fungal pathogen whose relationship with metals is multifaceted: C. albicans can biosorb heavy metals from its environment, heavy metal exposure promotes its virulence in immunocompromised hosts, and metal nanoparticles are being developed as antifungal …
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Citrobacter is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family, named for its ability to utilize citrate as a sole carbon source. Species include C. freundii, C. koseri, and C. rodentium (a mouse model for EHEC infection). In …
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…
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…
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…
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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…
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 Gram-negative opportunistic pathogen and member of the ESKAPE group of antibiotic-resistant priority pathogens. K. pneumoniae deploys multiple nickel-dependent enzymes for virulence and relies on the dual-function metallophore yersiniabactin for both iron and nickel s…
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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<!-- Auto-created stub from Rule 13 scope discovery. 6 source pages mention this taxon. Awaiting content expansion. --
An opportunistic Gram-negative pathogen with a unique dual-use siderophore system: its pyoverdine and pyochelin serve not only as iron scavengers but as extracellular chelators of toxic metals including nickel, copper, and cadmium. This makes P. aeruginosa unusually wel…
Serratia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species is S. marcescens, famous for its red pigment prodigiosin and its role as a nosocomial opportunistic pathogen. In the WikiBiome vault, Serratia ap…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.