Table 1 Published relationships among microbial clades, pathways, and human genes and pathways involved in autoimmune diseases

Inflammatory bowel disease

Enterobacteriaceae, Roseburia,

Ruminococcaceae

Glutathione metabolism and transport,

riboflavin metabolism,

short-chain fatty acid metabolism

Autophagy,

Th17, T-cell responses and cytokines, JAK-STAT, NF-kB, microbial sensing

ATG16L1, CARD9, DUOX2, IL10, IL23R, IRGM, FUT2, MHC, NCF4, NOD2

[3, 25, 31, 32, 86, 87, 107, 109]

Type 1 diabetes

Akkermansia,

Bacteroidales,

Lactobacillaceae

Amino acid metabolism,

secondary metabolite biosynthesis,

butyrate production,

carbohydrate metabolism,

glycan biosynthesis and metabolism,

lactate production,

lipid metabolism,

nucleotide metabolism

Innate immune signaling,

mucin,

MyD88,

Toll-like receptors

CTLA4, IL2RA, IFIH1, INS, MYD88, MHC, PTPN22, TLR

[5, 91, 110–116]

Rheumatoid arthritis

Bacteroides fragilis,

Bacteroides vulgatus,

Clostridium coccoides,

Eubacterium rectale,

Klebsiella,

Lactobacillus,

Porphyromonas,

Prevotella,

SFB

-

CD40,

IL-2,

NF-kB activation,

SAA or CCL5 signaling,

T-cell activation and response

CD40, CCL21, HLA-DRB1, IL2, IL17, IFNG, KIF5A,

MHC, TLR2, TLR4, TNF, TNFAIP3, PRKCQ

[38, 117, 118]

Multiple sclerosis

Epstein-Barr virus,

Mycobacteria

Vitamin D metabolism

Vitamin D,

CD4⁺ T cells

DRB1, IL2, IL7, HLA, MHC

[56, 57, 119–121]

Allergy, atopy

Aerobes,

Bifidobacteria,

Enterococci,

Staphylococcus aureus,

Escherichia coli, Clostridium difficile

-

IgE antibody regulation,

vitamin D

ADAM33, ADRB2, CD14TNF, IL10, IL4, IL13, IL4RA, IFNG, FLG, FCER1B, HLA-DRB1, HLA-DQB1, MHC

[17, 18, 45, 46, 122–128]