WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to microbe.
A Gram-negative, aerobic, non-fermenting coccobacillus and a member of the ESKAPE group of priority pathogens (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, Enterobacter). Acinetobacter baumannii is among the most problematic nosocomial pathogens…
WHO Priority 1: Critical. A Gram-negative, strictly aerobic coccobacillus and one of the most dangerous nosocomial pathogens on the planet. A. baumannii belongs to the ESKAPE group and causes ventilator-associated pneumonia, wound infections, and bloodstream infections …
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 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…
Alternaria is a ubiquitous environmental mold genus comprising over 300 species, with A. alternata as the most common human-associated species. Primarily recognized as an outdoor allergen and plant pathogen, Alternaria is increasingly documented as a component of the hu…
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 …
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 …
A Gram-positive, aerobic to facultatively anaerobic, spore-forming genus that bridges environmental and human microbiology. The genus encompasses both beneficial species (B. subtilis, B. coagulans as probiotics) and pathogens (B. cereus causing food poisoning, B. anthra…
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…
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.…
Bifidobacteriales is an order of Gram-positive, strictly anaerobic bacteria within the phylum Actinobacteria. The order contains the family Bifidobacteriaceae, which includes the genus Bifidobacterium — among the most widely studied probiotic organisms and a hallmark of…
A genus of Gram-negative intracellular pathogens causing brucellosis, the most common bacterial zoonosis worldwide. Brucella species depend on nickel-activated urease for gastrointestinal survival during the initial phase of infection, and urease immunization has been s…
The leading bacterial cause of diarrheal disease worldwide, with an estimated 400-500 million cases annually. C. jejuni is notable in the metallomics context for possessing a nickel-dependent [NiFe] hydrogenase essential for colonization but lacking urease -- a striking…
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 …
Candida tropicalis is an opportunistic fungal pathogen and occasional gut commensal, increasingly recognized as one of the most clinically significant non-albicans Candida (NAC) species. Once considered a distant runner-up to C. albicans, it has emerged as a major drive…
Candidozyma auris is the current name for NCBITaxon:498019. Liu and colleagues established the combination in 2024 as MycoBank MB 848169; Candida auris Satoh & Makimura 2009 is its basionym, not a separate species ncbi taxonomy candidozyma auris index fungorum candidozy…
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…
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 …
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…
Clostridioides difficile is the current NCBI name for NCBITaxon:1496 and the correct, medically recommended combination recorded by LPSN. Both records retain Clostridium difficile as a validly published homotypic synonym of the same organism rather than a separate speci…
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 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…
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…
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…
An encapsulated basidiomycete yeast that causes cryptococcal meningitis -- the leading cause of meningitis in HIV/AIDS patients and responsible for an estimated 180,000 deaths annually. Its nickel-dependent urease has been called the organism's "Achilles' heel" because …
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…
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…
Enterobacter cloacae is a Gram-negative, facultatively anaerobic member of the Enterobacteriaceae. Ubiquitous in soil, water, and the mammalian gut, it is a leading cause of nosocomial infections and carries clinically significant antibiotic resistance through inducible…
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…
A genus of Gram-positive bacteria (primarily E. faecalis and E. faecium) that exemplifies the metal-antibiotic resistance co-selection crisis. Enterococci carry diverse metal tolerance genes for mercury, arsenic, copper, and cadmium on the same mobile genetic elements a…
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…
Enterococcus faecium is a Gram-positive, facultatively anaerobic bacterium that epitomizes the metal-antibiotic co selection problem in modern medicine. As one of the six ESKAPE pathogens (the group responsible for the majority of hospital-acquired infections that fail …
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…
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…
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 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 …
Gardnerella vaginalis is a Gram-variable, facultatively anaerobic bacterium that is the key organism in bacterial vaginosis (BV), the most common vaginal infection in women of reproductive age. Its sialidase production, biofilm-forming capacity, and associations with he…
See also the genus page: gardnerella Gardnerella vaginalis is the primary causative agent of bacterial vaginosis (BV), the most common vaginal infection worldwide. This species page focuses on the species-level biology — particularly the vaginolysin cytotoxin and biofil…
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…
A Gram-negative, microaerophilic bacterium within the Epsilonproteobacteria (family Helicobacteraceae) that is the primary murine model of hepatobiliary and intestinal disease. Unlike its more famous relative helicobacter pylori, which colonizes the stomach, H. hepaticu…
A gastric pathogen that is arguably the most nickel-dependent human pathogen known. Two of its key virulence factors — urease and [NiFe] hydrogenase — require nickel, and the bacterium has evolved an elaborate nickel trafficking, storage, and regulation system to suppor…
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 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…
A Gram-positive, facultatively anaerobic bacterium that is the dominant species in the healthy human vaginal microbiome and a defining member of Community State Type I (CST-I). L. crispatus dominance is associated with reproductive health, pathogen resistance, and reduc…
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…
Lactobacillus jensenii defines Community State Type V (CST-V) in the vaginal microbiome. It produces hydrogen peroxide and lactic acid, contributing to vaginal defense against pathogens, though less dominant than lactobacillus crispatus (CST-I).
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…
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Lodderomyces elongisporus is an ascomycetous yeast and the closest known phylogenetic relative of Candida parapsilosis. Originally considered non-pathogenic, it has emerged as a rare but clinically significant cause of fungemia, particularly in patients with indwelling …
A class of bacteria within the phylum Tenericutes defined by the complete absence of a cell wall -- the smallest self-replicating organisms known, with minimal genomes (580 kb-1.4 Mb). While Mollicutes are best known through their pathogenic members (Mycoplasma pneumoni…
Morganella morganii is a Gram-negative, facultatively anaerobic rod belonging to the family Morganellaceae (formerly classified within Enterobacteriaceae). It inhabits the human gastrointestinal tract as a low-abundance commensal but becomes an opportunistic pathogen in…
The causative agent of tuberculosis (TB), the leading infectious disease killer worldwide (~1.3 million deaths annually). M. tuberculosis has an exceptionally complex metal biology: it deploys nickel-dependent hydrogenase and urease for intracellular survival, species-s…
Mycoplasma is a genus of wall-less bacteria in the class Mollicutes, characterized by the smallest genomes of any self-replicating organisms (~580–1,350 kb). The lack of a cell wall makes them intrinsically resistant to beta-lactam antibiotics and undetectable by Gram s…
Nakaseomyces glabratus is the current name for NCBITaxon:5478. Takashima and Sugita established the current combination in 2022 as MycoBank MB 843854; Candida glabrata is a homotypic synonym and former combination, while Cryptococcus glabratus H.W. Anderson 1917 is the …
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…
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…
A Gram-negative, obligate anaerobic genus with the keystone pathogen P. gingivalis at its center. Named for its porphyrin (heme) requirement, Porphyromonas is the prototypical periodontal pathogen and one of the most important organisms connecting oral health to systemi…
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 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 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…
A Gram-negative, obligately anaerobic, black-pigmented bacterium and one of the classical periodontopathogens. P. intermedia belongs to the "orange complex" of periodontal pathogens (Socransky classification) and is distinguished by its iron and heme dependency -- the c…
Propionibacterium (largely reclassified as Cutibacterium for skin species) is a genus of Gram-positive, anaerobic to aerotolerant bacteria that produce propionic acid as their primary fermentation product. P. acnes (now Cutibacterium acnes) is the dominant skin commensa…
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A Gram-negative uropathogen whose Ni-dependent urease is the central driver of catheter-associated urinary tract infection (CAUTI) pathogenesis. Urease-mediated urea hydrolysis produces ammonia and alkalinizes urine, triggering precipitation of struvite (magnesium ammon…
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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…
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…
Ralstonia is a genus of Gram-negative, aerobic bacteria in the class Betaproteobacteria. While Wikipedia focuses on R. solanacearum (a plant pathogen), the WikiBiome-relevant species are R. pickettii and R. metallidurans (now Cupriavidus metallidurans) — organisms with …
Rothia is a genus of Gram-positive, facultatively anaerobic bacteria in the family Micrococcaceae (phylum Actinobacteria). The most commonly identified species in microbiome studies are Rothia dentocariosa and Rothia mucilaginosa, both of which are primary inhabitants o…
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…
See also: saccharomyces (genus page) Saccharomyces boulardii is a non-pathogenic yeast strain used as a probiotic across a wide range of gastrointestinal and inflammatory conditions. Taxonomically a strain of S. cerevisiae, it is phenotypically distinct — optimally acti…
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…