Fig. 4: Bifidobacterium abundance drives resistance load and composition.

A Antibiotic resistance load in the gut of infants during the first year of life, depending on their Bifidobacterium abundance (cluster High or Low), expressed as total CPM of ARGs per infant in each timepoint. ARG load was the summed abundance of all ARGs in a given sample. Significance values for ARG load were calculated using the pairwise rank-sum Wilcoxon test (Mann-Whitney U), two-sided. 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 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 Antibiotic resistance profiles in each group. ARGs have been grouped according to the resistance they confer. C Number of copies of ARGs associated with a plasmid in High- and Low-Bifidobacterium grouped infants. FPA: Folate Pathway Antagonist; MLSB: Macrolide-Lincosamide-Streptogramin B. Source data are provided as a Source Data file.