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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]
  1. SFV, segmented filamentous bacteria.
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