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

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

[170–173]

Alistipes spp.

Gram negative obligate anaerobe rod-shaped; bile-resistant and pigment-producing^a

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 T_H1 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 T_H17 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

[186–188]

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]