Fig. 2
Antibiotic treatment affects microbiota in both treated dams and their pups. a Bacterial diversity in faecal/caecal content estimated as Shannon diversity index in dams n = 10 (CTR), n = 12 (AMX) and n = 11 (VAN) at the time of giving birth (D0W, faecal sample) and 4 weeks later (D4W, caecal sample) as well as pups at 2 days (P2D, intestinal sample), 2 weeks (P2W), 4 weeks (P4W) and 14 weeks (P14W) (all caecal samples) of age shown as box-plots with whisker indicating total range. b Boxplot of unweighted UniFrac distances calculated from caecal microbial composition within all groups (grey) and between groups (yellow) of dams (D0W and D4W) and pups (P2W, P4W and P14W) and c boxplot showing numbers of shared OTUs between animals within the CTR group and between the CTR and antibiotic treatment groups of pups at P2D, P4W and P14W. Whisker indicates total range. Principal coordinate analysis (PCoA) based on unweighted UniFrac distances of d faecal and caecal samples from dams (D0W and D4W) and e caecal samples from pups (P2W, P4W and P14W) coloured according to treatment group. f Bacterial composition in dams and pups shown as average relative abundance at the phylum level. g Heatmap depicting log10 relative abundance scores for faecal and caecal agglomerated genera present in >50% of samples. Results are shown for dams at delivery (D0W) and dams 4 weeks after delivery (D4W) as well as pups at different ages (P2D, P2W, P4W and P14W). In panels a, b and c: *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001 and in panel g FDR-corrected p values compared to the CTR group are shown *q < 0.05; **q < 0.01. The left-hand colour bar shows the taxonomic classification at the phylum level
