Figure 1

Treatment effects on ileal microbiota diversity and composition. Rarefaction curves, calculated at the lowest subsample size of 7,000 sequences per sample, show the effects of sequencing efforts on the observed number of OTUs at 97% sequence similarity (A) and phylogenetic diversity (whole tree) (B). Data are calculated at 3% distance. Error bars show standard deviation for each category. Principal component analysis (PCoA) of unweighted UniFrac distances from 24 ileal samples shows no difference in the community phylotype structure among treatments (C). Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify specific phylotypes that significantly associated with treatments. LDA more than 2 reflects significant difference between groups. LEfSe analysis provided the list of phylotypes that are differential among dietary supplementations with statistical and biological significance (D). The histograms indicated the increased relative abundance of the genera Propionibacterium (E) and Corynebacterium (F) in the ileal microbiota of chickens fed VIRG diet compared with other treatments. Each bar represents the relative abundance of the taxa in a sample at the age of 15 (red line), 25 (green line), and 35 days (blue line). The mean and median relative abundance are indicated with solid and dashed lines, respectively. CTL: control diet without any antibiotic or prebiotic; VIRG: control diet supplemented with 16.5 mg virginiamycin; LXOS: control diet supplemented with 1 g/kg xylo-oligosaccharides; HXOS: control diet supplemented with 2 g/kg xylo-oligosaccharides.