Table1:

Summary of the main findings of the studies included in this review except for the genomic studies, which we have reviewed in a complementary article¹¹.

Microbiome/gut metabolomics	Transcriptomics	Epigenomics (methylomics)	Multi-omics
Food allergy/sensitization	Acute response to peanut	Differential DNA methylation in FA	Transcriptomics/metabolomics response to profilin
Lachnospiraceae ↑28 Streptococcaceae ↑28 Ruminococcaceae ↑28 Citrobacter ↓27 Oscillospira ↓27 Lactococcus ↓27 Haemophilus ↓27 Dialister ↓27 Clostridium↓27 Leuconostoc ↓28 De novo sphingolipid synthesis ↓30	Acute-phase inflammatory response ↑42 Positive regulation of NK cell chemotaxis ↑42 Key drivers: LTB4R, PADI4, IL1R2, PP1R3D, KLHL2, ECHDC342 Macrophages ↑42 Neutrophils ↑42 CD4+ Tcells (naïve) ↓42	MAPK signalling pathway genes53 Butirosin and neomycin biosynthesis54 Starch & sucrose metabolism54 Fructose & mannose metabolism54 Th1-Th2 balance genes54	Platelet function genes ↓65 Protein synthesis genes ↓65 Histone modification genes ↓65 Fatty acid metabolism genes ↓65 Carbohydrates, pyruvate ↓65 Lactate ↑65 Carnitine ↓ (with severity)65
		Allergy resolution/tolerance development
	IgE clonal response in peanut allergy	Th2 cytokine methylation ↑55 Th1 cytokine methylation ↓55 FOXP3 methylation ↓56,57
	Convergence of IgE gene rearrangements43 IgEs cross-reactivity for Ara h2 – Ara h343		Transcriptomics/epigenomics TCR activation in FA
			E2F/MYC TF network genes ↓66 Diff methylation metabolic genes66 Diff methylation inflammatory genes66 Diff methylation TCR cascade genes66
Allergy resolution
Firmicutes ↑25 Clostridia ↑25 Fatty acid metabolism 25	T cell clonal expansion signature	Biomarkers of FA
	CD154, CD69, TNFRSA, GATA3 ↑44 CCR7, LEF1, SELL ↓44 Th2 signature enrichment44	96 CpG signature: 79.2% accuracy66
		FA and biological age
		DNA methylation age ↑62 DNA meth. age acceleration ↑62	Transcriptomics/epigenomics of reaction severity
Therapeutic potential	Reactive vs hyporeactive T cell response
Clostridiales (several genera)33 Bacteroidales (several genera)33 Subdoligranulum variabile33	Macrophages ↑45 Th2 and Th17 cell genes ↑45 Treg and immune regulation genes ↓45		Neutrophil immunity involvement67 NFKBIA and ARG1 are hub genes67 PHACTR1/ZNF121 expression mediate CpG associations67