Fig. 2

PCA of the profiling data from the intestinal microbiome. Microbiome analysis was performed using amplicon sequencing of the V1 and V2 regions of the 16S rRNA gene. Quantification of total bacterial was performed using real-time PCR. a Total bacterial numbers calculated using real-time PCR. b Rates of classifiable reads by RDP classifier. c PCA of classification data by RDP classifier. Differences between the antibiotic-treated and untreated groups in PC1 were recognized in the family- and genus-level analyses, although this was not recognized in the case of phylum, order, or class (d) PCA of family-, genus-, and species-level classification data after OTU-based analysis