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Table 1 Overview of select gut bacterial genera and species commonly affected by diet

From: Influence of diet on the gut microbiome and implications for human health

Bacteria Basic features Associated physiologic changes Associated disease states References
Bifidobacterium spp. Gram positive obligate anaerobe branched; nonmotile SCFA production; improve gut mucosal barrier; lower intestinal LPS levels Reduced abundance in obesity [166, 167]
Lactobacillus spp. Gram positive facultative anaerobe rod-shaped SCFA production; anti-inflammatory and anti-cancer activities Attenuate IBD [168, 169]
Bacteroides spp. Gram negative obligate anaerobe rod-shaped; variable motility Activate CD4 + T cells Increased abundance in IBD [170173]
Alistipes spp. Gram negative obligate anaerobe rod-shaped; bile-resistant and pigment-producinga   Reported in tissue from acute appendicitis and perirectal and brain abscesses [174]
Bilophila spp. Gram negative obligate anaerobe urease-positive, bile resistant, catalase-positive Promote pro-inflammatory TH1 immunity B. wadsworthia observed in colitis, perforated and gangrenous appendicitis, liver and soft tissue abscesses, cholecystitis, FG, empyema, osteomyelitis, and HS [175, 176]
Clostridium spp. Gram positive obligate anaerobe rod-shaped; spore-forming Promote generation of TH17 cells Several spp. are pathogenic causing tetanus, botulism, gas gangrene, or pseudomembranous colitis [177, 178]
Roseburia spp. Gram variable obligate anaerobe curved rod-shaped; motile SCFA production Reduced abundance in IBD [179]
Eubacterium spp. Gram positive obligate anaerobe rod-shaped SCFA production; form beneficial phenolic acids Reduced abundance in IBD [180, 181]
Enterococcus spp. Gram positive facultative anaerobe cocci   Several spp. are pathogenic causing UTI, endocarditis, or bacteremia [182]
Faecalibacterium prausnitzii Gram positive obligate anaerobe rod-shaped; nonmotile SCFA production; anti-inflammatory effects Reduced abundance in IBD and obesity [183, 184]
Akkermansia muciniphila Gram negative obligate anaerobe oval-shaped; nonmotile Anti-inflammatory effects Reduced abundance in IBD, obesity, and psoriatic arthritis [53, 133, 185]
Escherichia coli Gram negative facultative anaerobe rod-shaped TLR-activation Increased abundance in IBD gastroenteritis, UTI, and meningitis [186188]
Helicobacter pylori Gram negative microaerophilic helix-shaped; motile   Gastritis; ulcers; MALT cancers [189, 190]
Streptococcus spp. Gram positive facultative anaerobe cocci   Some spp. are pathogenic causing meningitis, pneumonia, and endocarditis [191]
  1. spp species, SCFA short chain fatty acid, LPS lipopolysaccharide, IBD inflammatory bowel disease, T H T helper, FG Fournier’s gangrene, HS hidradenitis suppurativa, UTI urinary tract infection(s), TLR toll-like receptor, MALT mucosa-associated lymphoid tissue
  2. a A. putredinis does not produce pigment and is susceptible to bile