WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions, filtered to microbe.
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…
Alloprevotella is a genus of Gram-negative, obligate anaerobic bacteria within the family Prevotellaceae that represents a distinct clade from prevotella with specific protective roles in type 2 diabetes prevention and metabolic health. Alloprevotella depletion is one o…
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 …
Bacteroidales is an order of obligate anaerobic, Gram-negative bacteria within the phylum Bacteroidetes. It includes the families Bacteroidaceae (bacteroides), Prevotellaceae (prevotella), Rikenellaceae, and Porphyromonadaceae (porphyromonas). Bacteroidales are among th…
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.…
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…
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-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…
Bifidobacterium adolescentis is a Gram-positive, obligate anaerobic species within the phylum Actinobacteria and the dominant Bifidobacterium species in the adult human gut. It is a specialist degrader of resistant starch and dietary fiber, producing acetate and lactate…
Bifidobacterium bifidum is an obligate anaerobic, Gram-positive species that specializes in human milk oligosaccharide (HMO) and mucin glycan degradation. It is one of the earliest colonizers of the infant gut and a widely used probiotic species.
A genus of Gram-positive, obligate anaerobic bacteria within the lachnospiraceae family that produces short chain fatty acids and plays a significant role in bile acid metabolism. Key species include B. obeum, B. wexlerae, B. hydrogenotrophica, and B. producta. While pr…
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…
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 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…
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…
Eubacteriales Buchanan 1917 (Approved Lists 1980) is the current correct name for NCBITaxon:186802. LPSN records Clostridiales Prévot 1953 (Approved Lists 1980) as a validly published heterotypic synonym, not a separate current order ncbi taxonomy eubacteriales lpsn eub…
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…
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…
Firmicutes (recently reclassified as Bacillota) is the dominant bacterial phylum in the Western adult gut, comprising the core community of short-chain fatty acid (SCFA) producers that maintain intestinal barrier integrity, regulate immune function, and influence system…
Lachnoclostridium is a genus of obligate anaerobic, Gram-positive bacteria in the lachnospiraceae family. It is a butyrate-producing commensal with emerging clinical significance as a treatment response biomarker and diagnostic marker.
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, agathobacter rectalis) with the overarching ecological and metabolic framework that defines the family. For the primary ent…
Lactobacillus rhamnosus is a Gram-positive, facultatively anaerobic lactic acid bacterium and one of the most extensively studied probiotic species. The GG strain (ATCC 53103), isolated from a healthy human intestinal tract by Gorbach and Goldin in 1983, is the single m…
Megamonas is a genus of obligate anaerobic, Gram-negative bacteria in the family Veillonellaceae (class Negativicutes, phylum Firmicutes). The type species is Megamonas hypermegale, with M. funiformis also well-characterized. It is a common member of the human gut micro…
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…
Odoribacter splanchnicus is a Gram-negative, obligate anaerobic bacterium belonging to the family Odoribacteraceae within the phylum Bacteroidota (formerly Bacteroidetes). It is a commensal resident of the human colon recognized primarily as a producer of short chain fa…
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…
An order of Gram-positive, obligate anaerobic bacteria within the class Clostridia (phylum Firmicutes) that has emerged as one of the most consistent markers of a healthy gut ecosystem. Oscillospirales members are butyrate producers associated with leanness and metaboli…
A family of Gram-negative, obligate anaerobic bacteria within the phylum Bacteroidota (formerly Bacteroidetes) that includes the genus prevotella and the recently described alloprevotella. Prevotellaceae are specialist fiber fermenters producing short-chain fatty acids,…
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…
Ruminococcus albus is a Gram-positive, obligate anaerobic bacterium that represents one of the primary cellulolytic (fiber-degrading) specialists in the human gut microbiota. This species constructs cellulosomes — extraordinary multi-enzyme complexes organized on bacter…
Ruminococcus bromii is a Gram-positive, obligate anaerobic bacterium within the ruminococcaceae family and the primary keystone degrader of resistant starch in the human gut. Without R. bromii, the microbial community cannot efficiently access resistant starch types RS2…
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…
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A family of Gram-negative, obligate anaerobic bacteria within the Firmicutes phylum (class Negativicutes) that occupies a unique metabolic niche as specialized lactate utilizers. Veillonellaceae cannot ferment sugars directly -- instead, they cross-feed on lactate produ…