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Children with higher fungal abundance at 2years were more likely to develop asthma and AR by 6years, odds ratios 1.70 (95% CI 1.06-2.75) and 1.41 (1.03-1.93), respectively. We explored causal connections, and children with eczema at 1-2years appeared to have more mature bacterial microbiota, as well as being depleted of genus. Although LBP and FABP2 did not correlate with eczema, increased bacterial abundance was associated with increased serum FABP2. We observed positive associations between gut fungal abundance and allergy-related dise