WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
A Gram-negative, obligate anaerobic, mucin-degrading bacterium that colonizes the intestinal mucus layer and has emerged as one of the most important next-generation probiotics. A. muciniphila is consistently depleted in disease states associated with metal dyshomeostas…
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 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…
Bifidobacteriaceae is the family containing bifidobacterium and related genera (alloscardovia). It is the dominant family in the healthy infant gut and a significant commensal family in adults. Family-level depletion is documented in ASD (marked reduction of Actinobacte…
A genus of Gram-positive, obligate anaerobic bacteria that dominate the infant gut microbiome and remain important commensals throughout life. Bifidobacterium species are distinctive in the metallomics context because some species possess Ni-dependent urease -- an unusu…
Christensenellaceae is a family of Gram-negative, strictly anaerobic bacteria within the order Clostridiales (phylum Firmicutes) that has emerged as one of the most consistently health-associated and heritable members of the human gut microbiome. First formally describe…
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…
A genus of Gram-positive, obligate anaerobic bacteria within the Firmicutes phylum that includes several of the most important butyrate producers in the human colon. Key species are E. rectale, E. hallii (now reclassified as Anaerobutyricum hallii), and E. limosum. Cons…
Eubacterium rectale (recently reclassified as Agathobacter rectalis) is a Gram-positive, strictly anaerobic, non-spore-forming bacterium that belongs to Clostridium cluster XIVa within the lachnospiraceae family. It is one of the most abundant butyrate producers in the …
Faecalibacterium is a genus of obligate anaerobic, Gram-positive bacteria in the family Ruminococcaceae (phylum Firmicutes). It is the most abundant genus in the healthy human colon (5–15% of fecal bacteria) and its depletion is the single most reproducible microbiome f…
The most abundant bacterium in the healthy human colon (5-15% of total fecal microbiota), F. prausnitzii is the premier butyrate producer in the gut and a cornerstone of anti-inflammatory intestinal homeostasis. Its depletion is one of the most consistent microbiome sig…
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…
A family within the Firmicutes phylum (order Clostridiales, formerly Clostridium cluster XIVa) that serves as a sentinel indicator of gut health -- its depletion is the single most consistent microbiome signature across nearly every disease represented in this wiki. The…
This page serves as the family-level hub for Lachnospiraceae, connecting the individual genus and species pages (roseburia, blautia, anaerostipes, eubacterium rectale) with the overarching ecological and metabolic framework that defines the family. For the primary entit…
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…
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…
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…
A genus of Gram-positive, obligate anaerobic, flagellated bacteria within the lachnospiraceae family that ranks among the most important butyrate producers in the human gut. Key species include R. intestinalis and R. hominis. Roseburia is consistently depleted across in…
Ruminococcaceae is a family of obligate anaerobic, Gram-positive bacteria in the order Clostridiales (phylum Firmicutes) that represents one of the most important butyrate-producing and fiber-degrading families in the human gut. Key genera include faecalibacterium (incl…
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 …