Fig. 3

A Composite plot of individual trajectories of longitudinal diversity progression during antibiotic administration (Group 2a) shown in thin grey lines, with weighted mean trajectory (thick black line). For comparative purposes, trajectory of diversity progression in Group 1 overlaid (thick green line). 95%CI for weighted mean trajectories denoted by dotted lines. For clarity and comparative purposes, the intercept of the two trajectories is plotted at the median intercept of the group on antibiotics. B Composite plot of individual trajectories of longitudinal Enterobacteriaceae relative abundance progression during antibiotic administration (Group 2a) shown in thin grey lines, with weighted median trajectory (thick black line). For comparative purposes, median trajectory of Enterobacteriaceae relative abundance progression in Group 1 overlaid (thick green line). 95%CI for weighted median trajectories denoted by dotted lines. For clarity and comparative purposes, the intercept of the two trajectories is plotted at the median intercept of the group on antibiotics. C Longitudinal taxonomic profiles of the majority taxa in babies during periods of receiving intravenous antibiotics (Group 2a). Red arrows indicate the sample taken prior to commencing antibiotics. Each panel represents the entire course of antibiotics. Antibiotic courses containing ceftazidime highlighted in blue. Days on antibiotics is indicated on the x-axis