WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to microbe.
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…
Aerococcus is a genus of Gram-positive, alpha-hemolytic, catalase-negative cocci. The primary species of clinical relevance are A. urinae (a cause of urinary tract infections, particularly in elderly men) and A. christensenii (a vaginal commensal). In the WikiBiome vaul…
Alishewanella is a genus of Gram-negative, facultative anaerobic bacteria within the class Gammaproteobacteria. Primarily known as environmental organisms, Alishewanella species have been identified in the microbiome of deep endometriosis — both in vaginal samples and w…
Alloscardovia is a genus of anaerobic, Gram-positive bacteria in the family Bifidobacteriaceae (phylum Actinobacteria). The primary species is A. omnicolens, which colonizes the human urogenital tract. In the WikiBiome vault, Alloscardovia appears exclusively in endomet…
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 …
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…
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…
Burkholderiales is an order of Gram-negative Betaproteobacteria that includes environmentally versatile genera such as Ralstonia, Burkholderia, and Sutterella. Many members are notable for their metal resistance mechanisms, which enable survival in heavy metal-contamina…
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…
Butyrivibrio is a genus of Gram-positive, obligate anaerobic bacteria within the family Lachnospiraceae (phylum Firmicutes). Originally characterized as a dominant fiber-fermenting genus in the rumen, Butyrivibrio species are also found in the human colon where they con…
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…
A genus of Gram-negative, obligate anaerobic, sulfate-reducing bacteria (SRB) that produces hydrogen sulfide (H2S) as its primary metabolic end-product. H2S is a potent cytotoxin that disrupts colonocyte energy metabolism, damages the gut barrier, and promotes chronic i…
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, …
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, …
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…
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…
Gordonibacter is a genus of Gram-positive, strictly anaerobic gut bacteria within the phylum Actinobacteria. It is recognized as a key participant in polyphenol metabolism, producing bioactive metabolites including equol (from dietary isoflavones) and urolithins (from e…
Lachnobacterium is a genus of Gram-positive, obligate anaerobic bacteria within the family Lachnospiraceae (phylum Firmicutes). It is a commensal member of the healthy human gut microbiota, though relatively understudied compared to other Lachnospiraceae genera. Lachnob…
Lachnospira is a genus of Gram-positive, obligate anaerobic bacteria within the lachnospiraceae family (Firmicutes phylum). L. pectinoschiza, the type species, is a specialist pectin fermenter that produces short chain fatty acids from plant-derived polysaccharides. The…
Lactobacillaceae is the family containing the genus lactobacillus and related genera. It is the dominant family in the healthy vaginal microbiome and a significant family in the gut. Family-level depletion is reported across schizophrenia szeligowski 2020 gut microbiome…
Lactobacillus gasseri is a vaginal and gut commensal that defines Community State Type II (CST-II) in the vaginal microbiome. It is a common probiotic species with anti-obesity properties in clinical trials.
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…
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…
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…
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 …
Parasutterella excrementihominis is a Gram-negative, obligate anaerobic bacterium within the Betaproteobacteria class that has gained attention as an emerging biomarker across metabolic, inflammatory, and endocrine conditions. Despite its relatively recent characterizat…
A Gram-negative, obligate anaerobic genus within the Firmicutes phylum (family Acidaminococcaceae, class Negativicutes). The primary species P. faecium and the recently characterized P. succinatutens are specialized propionate producers that utilize succinate as their m…
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…
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…
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…
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…
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…
Ureaplasma is a genus of wall-less bacteria in the class Mollicutes, comprising two species pathogenic to humans: U. urealyticum and U. parvum. The genus is named for its defining characteristic — obligate urease activity — which hydrolyzes urea to ammonia and CO2, prov…