Fig. 3: Richness and abundance of ARG-harbouring bacterial species during early life.

a Histogram of ARG richness per metagenome-assembled genome (MAG). b Number of ARG-harbouring MAGs 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 mothers 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 8. 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. c ARG and virulence gene richness per MAG. The top 25 MAGs with the highest number of ARGs are coloured according to species name. The size of the dots reflects the number of clinically relevant ARGs per MAG. d Absolute abundance of the top 25 MAGs with the highest number of ARGs in faecal samples at the given time points during early life. N as in b. Colours refer to species names (see legend for c). Source data are provided as a Source Data file.