Fig. 3: Bifidobacterium abundance drives microbial composition.

A Genus relative abundance over time, depending on the Bifidobacterium abundance-based clusters. Two distinct clusters (optimal number of clusters k  =  2) were identified via k-means clustering. Mann-Whitney U test revealed that statistically significant differences in relative abundance were found in the Bifidobacterium genus, in all timepoints, so clusters were named as High- and Low-Bifidobacterium. Upper boxplots represent alpha diversity of the mother-infant gut resistomes based on a two-sided Kruskal-Wallis test on the Shannon index. Box plots show the median (centre line), the first and third quartiles (bounds of the box). Whiskers are chosen to show the 1.5 of the IQR. Sample sizes per group and timepoint were as follows: day 7: High-Bifidobacterium N  =  23, Low-Bifidobacterium N  =  35; 1 month: High N  =  42, Low N  =  16; 6 months: High N  =  31, Low N  =  25; 12 months: High N  =  19, Low N  =  36. Asterisks denote statistical significance: *p  <  0.05; **p  <  0.01; ***p  <  0.001; ****p  <  0.0001. B Stability of the hierarchical clustering based on Bifidobacterium spp. abundance over the first year of life. C Relative abundance of Bifidobacterium species in each cluster during the first year of life. Only species with statistically different abundances at any time point are shown (Mann-Whitney U test, *p  <  0.05). Source data are provided as a Source Data file.