Fold changes and relative abundances determined by 16S rRNA gene sequencing and qPCR. Columns show means with SEM (A-B) or box and whisker plots with full range (C-F) for Bifidobacteriaceae (dark grey) and Lactobacillacae (light gray) determined by high through-put sequencing (A,C & E) and for Bifidobacterium spp. (dark grey), Lactobacillus spp. (light gray) and Akkermansia muciniphilla (white), determined by qPCR (B,D and F). Akkermansia muciniphilla was not included in 16S sequencing due to low abundance. Analysis were performed on community DNA extracted from faecal samples (A-D) or caecum content (E-F). In panels A and B, significant differences from baseline are indicated with asterisks (p < 0.05). Observed differences between groups are indicated with P-values.