Fig. 3: Diversity and microbiome-derived age of the infant’s gut.

Shannon diversity index of a 3-month samples for one or more atopic or allergic diagnoses (1+, n = 344), two or more allergic diagnoses (2+, n = 130), and individual clinical diagnoses at 5 years, i.e., atopic dermatitis (AD, n = 211), food allergy (FA, n = 73), asthma (As, n = 100), or allergic rhinitis (AR, n = 108), at 5 years, and healthy control (HC, n = 244) participants, as well as b 1-year samples for 1+ (n = 353, p = 0.039), 2+ (n = 82), and individual clinical diagnoses at 5 years, i.e., AD (n = 212, p = 0.021), FA (n = 75, p = 0.043), As (An = 103, p = 0.0097), or AR (n = 113), at 5 years, and HC (n = 236) participants, c Scatterplot between chronological age and microbiome-derived age with linear regression line of best fit (Pearson R = 0.89, p < 2.2e-16). d Predicted age and chronological age for aggregate and individual clinical diagnoses as compared to no diagnoses at 5 years. e Predicted age of 1-year samples for 1+ (n = 353, p = 0.000036), 2+ (n = 82, p = 0.0023), and individual clinical diagnoses at 5 years, i.e., AD (n = 212, p = 0.000014), FA (n = 75, p = 0.00083), As (n = 103, p = 0.0073), or AR (n = 113, p = 0.0021), at 5 years, and HC (n = 236) participants. P values are from Wilcoxon tests between HC and each allergic diagnosis (b, c, e). For box plots, data are presented as box plots (center line at the median, upper bound at 75th percentile, lower bound at 25th percentile) with whiskers at minimum and maximum values. (*) p < 0.05.