Fig. 2: Infant’s gut microbiome during the first year of life and bacterial hosts of resistances.

A Alpha diversity of the mother-infant gut resistomes based on the 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. All samples represent independent biological replicates, derived from individual participants. Sample sizes per group are as follows: day 7 infants (N = 58), 1-month-old infants (N = 58), 6-month-old infants (N = 56), 12-month-old infants (N = 55), and mothers (N = 39). Asterisks indicate statistical significance: *p  <  0.05; **p  <  0.01; ***p  <  0.001; ****p  <  0.0001. B Microbial composition at the species level of infants gut over the first year of life. Samples are coloured according to infants’ age. Two-sided PERMANOVA on Bray-Curtis distances was applied to assess differences between timepoints. p = 0.05 for 7 days compared to older timepoints. C Microbial hosts of resistance during the first year of life. ARG-carrying contigs were detected within the bins. D Antibiotic resistance and their microbial hosts during the first year of life. E Relative abundance (%) of genus carrying ARGs and number of copies of these genes associated with a plasmid. FPA: Folate Pathway Antagonist; MLSB: Macrolide-Lincosamide-Streptogramin B. Source data are provided as a Source Data file.