WikiBiomeThe human microbiome encyclopediaRanked matches across titles, topics, categories, and article introductions.
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…
Cadaverine (1,5-diaminopentane) is a biogenic amine produced by bacterial lysine decarboxylase — primarily by Enterobacteriaceae, Fusobacterium, and Clostridium — during proteolytic fermentation of undigested protein in the distal colon. It is a product of putrefaction …
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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 …
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…
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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…
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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…
An umbrella term for chronic relapsing-remitting inflammatory conditions of the gastrointestinal tract, principally crohns disease (CD; transmural, any GI segment) and ulcerative colitis (UC; mucosal, colon only). Approximately 6 million patients worldwide. IBD represen…
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…
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Necrotizing enterocolitis (NEC) is the most common and lethal gastrointestinal emergency in premature infants, affecting 5-12% of very low birth weight neonates (<1500 g) with mortality rates of 20-30%. Characterized by intestinal inflammation, necrosis, and perforation…
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Salmonella is a genus of Gram-negative, facultatively anaerobic bacteria in the family Enterobacteriaceae. The two species — S. enterica (with 2,500 serovars including Typhimurium and Typhi) and S. bongori — cause a spectrum of disease from self-limiting gastroenteritis…
Serratia is a genus of Gram-negative, facultatively anaerobic bacteria in the Enterobacteriaceae family. The primary species is S. marcescens, famous for its red pigment prodigiosin and its role as a nosocomial opportunistic pathogen. In the WikiBiome vault, Serratia ap…
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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…
A Gram-negative intracellular pathogen causing bacillary dysentery (shigellosis), responsible for approximately 165 million illness episodes and over 1 million deaths annually, predominantly in children under 5 in developing countries. S. flexneri relies on nickel-depen…
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Harm potential: GREEN — PPIs remain appropriate first-line therapy; this STOP recommends co-administration of probiotics, not PPI avoidance.