Fig. 2

Unweighted UniFrac PCoA plots and differences in the relative abundance of specific bacteria at different time points and treatments (a). The T1–T2 PCoA plot (left) revealed the baseline differences between old and young mice (OC, old mice, control diet; OG, old mice, GOS diet; YC, young mice, control diet; YG, young mice, GOS diet). The middle panel shows the prebiotic impact on young (light purple) and old (pink) mice compared to the control diet (purple = young control, red = old control). The right panel shows the composed differences in relative abundances by age, diet, and time point. b The T2–T3 PCoA plot (left) and genus-level analysis (middle) showed the impact of the antibiotic treatment in water on both diet groups. Middle panel: control and GOS diets as before. Light blue dots represent no antibiotic treatment, and dark blue dots represent antibiotic treatment. c The T3–T4 PCoA plot (left) and genus-level analysis (middle) represent the samples immediately after clindamycin IP injection. The graphs did not show dramatic impacts to the microbiome, which were clearly visible in d the T4–T5 PCoA and taxa plots