WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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 auris is an emerging multidrug-resistant fungal pathogen first identified in 2009 (Satoh et al. 2009, from a Japanese patient's ear canal) and now classified as a critical-priority pathogen by the WHO (WHO Fungal Priority Pathogens List 2022) and CDC (CDC 2019 A…
A haploid, asexual yeast and the second most common cause of invasive candidiasis after Candida albicans. Recently reclassified into the genus Nakaseomyces (as N. glabratus), though the name C. glabrata remains in widespread clinical use. Unlike C. albicans, C. glabrata…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
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 …
Structured microbial communities encased in a self-produced extracellular polymeric substance (EPS) matrix. Biofilms are the predominant mode of bacterial and fungal growth in chronic infections, device-associated infections, and the gut. From a metallomics perspective,…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
A genus of Gram-positive, strictly anaerobic, butyrate-producing bacteria in the order Clostridiales (phylum Firmicutes). The type species, Butyricicoccus pullicaecorum, was originally isolated from chicken caecal content but has since been identified as a significant m…
Clostridium butyricum is a spore-forming, obligate anaerobic, Gram-positive bacterium and one of the leading next-generation probiotic candidates. The MIYAIRI 588 strain (CBM 588) is approved as a pharmaceutical probiotic in Japan and has expanding clinical evidence acr…
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…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
HIV (Human Immunodeficiency Virus) causes progressive CD4+ T cell depletion leading to AIDS. In the WikiBiome framework, HIV is notable for the gut-centric model of disease progression: HIV preferentially destroys gut-associated lymphoid tissue (GALT) early in infection…
A genus of Gram-positive, strictly anaerobic bacteria in the family Erysipelotrichaceae (phylum Firmicutes) that is emerging as one of the most consistently protective gut commensals in human disease. Holdemanella is depleted across a striking range of conditions -- inf…
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
This knowledge-base record is being expanded from WikiBiome’s evidence graph.
Mortierella is a genus of soil-dwelling fungi in the phylum Mortierellomycota (formerly placed in Zygomycota). While primarily known as environmental saprotrophs, Mortierella species have recently been identified as residents of the human gut mycobiome -- the fungal com…
The fungal component of the human microbiome, comprising ~0.1-1% of the total gut microbial community by abundance but disproportionately active in immune signaling and cross-kingdom interactions. While bacterial communities dominate microbiome research, emerging eviden…
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…
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…
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…
Harm potential: GREEN — PPIs remain appropriate first-line therapy; this STOP recommends co-administration of probiotics, not PPI avoidance.
Research summary -- not medical advice. This page synthesizes published research on why a commonly recommended intervention may be counterproductive in this specific clinical context. Consult a qualified healthcare provider before making any changes to treatment.
Verrucomicrobia is a bacterial phylum represented in the human gut almost exclusively by a single genus — Akkermansia — which comprises 1–5% of the healthy gut microbiota. Despite being a low-diversity phylum, Verrucomicrobia's importance is outsized: A. muciniphila is …