Table 1.

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

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]

SFV, segmented filamentous bacteria.