Fig. 5: The influence of environmental factors on shaping infant’s resistome during first year of life.

A Environmental factors driving infant’s resistome, ranked by effect size (‘envfit’ R2, false discovery rate (FDR)-corrected two-sided test, p < 0.05). B Antibiotic resistance load in the gut of infants of 7 days of age, depending on their mode of delivery (N = 40 vaginal, N = 26 C-section), expressed as total CPM of ARGs per infant in each timepoint. C Principal Coordinate Analysis (PCOA) of the composition of the resistome depending on the mode of delivery (vaginal or C-section) during the first 7 days and 1 month of life, based on Jaccard distances. Two-sided PERMANOVA on Jaccard distances was applied to assess differences between groups. D Antibiotic resistance load in the gut of infants of 1 month of age, depending on their diet (N = 40 breastfeeding, N = 4 formula feeding, N = 14 mixed), at each timepoint during the first year of life, expressed as total CPM of ARGs per infant in each timepoint. E Antibiotic resistance load in the gut of infants during the first month of life, depending on exclusive breastfeeding (N = 40 yes and N = 18 no), at each timepoint during the first year of life, expressed as total CPM of ARGs per infant in each timepoint. F Tendency of antibiotic resistance during the first year of life according to breastfeeding during the first month of life. The trajectory of the total load of ARGs was studied considering if the infant received exclusive breastfeeding during the first month of life. G ARGs differentially abundant due to breastfeeding in 6-month-old infants compared to non-breastfed infants, calculated using DESeq2 with the p-values attained by the Wald test corrected for multiple testing using the Benjamini-Hochberg method. H Antibiotic resistance load in the gut of infants during the first year of life, depending on the mode of delivery and if they were exclusively breastfed, at each timepoint during the first year of life, expressed as total CPM of ARGs per infant in each timepoint. I Multivariable association between factors and resistome composition using MaAsLin. Antibiotic resistance load was the summed abundance of all ARGs in a given sample. 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. Significance values for ARG load were calculated using the pairwise rank-sum Wilcoxon test (Mann-Whitney U), two-sided. Asterisks denote statistical significance: *p  <  0.05; **p  <  0.01; ***p  <  0.001; ****p  <  0.0001. kmeans_bifis: Bifidobacterium abundance-based clustering; AB_BB: infant’s antibiotic consumption; BF: breastfeeding; nBF_C: not exclusively breastfed infants born by C-section; nBF_V: not exclusively breastfed infants born vaginally; BF_C: exclusively breastfed infants born by C-section; BF_V: exclusively breastfed infants born vaginally. Source data are provided as a Source Data file.