Fig. 2. Compositionally distinct, age-independent bacterial gut microbiota–states (NGMs) exist in neonates, exhibit significant differences in fungal taxonomy and are related to relative risk of atopy at age–2 years.

(a) NGM designation significantly explains observed variation (n = 130; PERMANOVA with unweighted UniFrac R² = 0.09; P < 0.001) in bacterial β–diversity. (b) NGM participants do not differ significantly in age (n = 130; Kruskal–Wallis; P = 0.256). Boxplots are defined by the 25^th and 75^th percentiles with the center line representing the median (50^th percentile). Lines that extend from the box are defined as 1.5 times the interquartile range (IQR, 75^th–25^th percentile), plus or minus the 75^th and 25^th percentiles, respectively. (c) The sum of allergen–specific serum IgE concentrations measures at two–years of age (n = 130) is significantly higher in NGM3 versus NGM1 participants (Welch’s t–test; P = 0.034). Boxplots are constructed as defined in (b). (d) Taxonomic comparison of NGM3 with NGM1 subjects; taxa exhibiting significant difference (ZINB; Benjamini–Hochberg, q < 0.05) in mean relative abundance (natural log transformed for purposes of illustration) are shown. Bar height indicates the magnitude of between–group relative abundance delta. (e) Relative abundance of fungal genera differs across NGMs.