Table 1 Published relationships among microbial clades, pathways, and human genes and pathways involved in autoimmune diseases
From: Functional profiling of the gut microbiome in disease-associated inflammation
| Disease | Microbes | Microbial pathways | Host pathways | Representative host genes | References |
|---|---|---|---|---|---|
| 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] |