Fig. 2: Interindividual ARG diversity in early life.

a ARG Shannon diversity in faecal samples at the given time points during early childhood, 3–6 d (n = 51), 3w (n = 52), 2 m (n = 55), 6 m (n = 55), 12 m (n = 56), 18 m (n = 55), 24 m (n = 56), 60 m (n = 55), and in mother during the 3rd pregnancy trimester (M-preg 3tr, n = 56), and at 2 months postpartum (M-2m pp, n = 56). Differences between time points were tested with a two-sided Dunn’s test. Stars represent significance compared to the 6 months samples according to the following FDR-adjusted P values, *, Padj < 0.05, **, Padj < 0.01, ***, Padj < 0.001. Exact Padj values can be found in Supplementary Table 5. Horizontal lines indicate the median; box boundaries indicate the interquartile range; whiskers represent values within 1.5× the interquartile range of the first and third quartiles. Dots represent the individual data points. b Non-metric multidimensional scaling (NMDS) plot of ARG β-diversity calculated using Bray–Curtis dissimilarity. Individual taxa were fitted on the NMDS plot based on their relative abundance. Taxa with a squared correlation coefficient > 0.15 and a Padj < 0.01 are displayed (1: Alistipes putredinis, 2–4: Fusicatenibacter saccharivorans, 5: Gemmiger qucibialis, 6: Odoribacter splanchnicus, 7: Alistipes communis, 8: Barnesiella intestinihominis). c Perinatal variables associated with ARG β-diversity based on sex, birth mode and family lifestyle adjusted PERMANOVA. Size of the dot depicts the R-squared (R2), and colour depicts the significant FDR-adjusted P value (Padj). Non-significant conditions are depicted in grey. FDR adjustment was done per time point. N is provided in Supplementary Table 7. Source data are provided as a Source Data file.