Figure 5. Rapamycin shifts aged oral microbiome towards young oral microbiome.

(A) Alpha diversity for all samples reveal significant differences between young (Y) and old (O) mice without rapamycin treatment (p<0.05). (B) Phylum level abundance using normalized agglomerated data show significant difference for the Bacteroidetes (p<0.001) in old (O) mice and old mice with rapamycin treatment (R) for all samples. Also, significant changes are observed in the Firmicutes (p<0.05) and Proteobacteria phylum (p<0.05, p<0.01) that is age and treatment dependent. (C) Principal coordinate analysis using weighted Unifrac distances reveal beta diversity in the rapamycin-treated old (R) groups clustered with the young (Y). (C, inner panel) A significant separation between old (O) and rapamycin-treated old (R) groups (p<0.01; Axis 1, 70.3%) was observed, but no significant difference between young (Y) and rapamycin-treated old (R) groups was observed. *p<0.05, **p<0.01,***p<0.001.

Figure 5—figure supplement 1. Independent Alpha Diversity Analysis for JAX and UW-NIA animals.

(A) Alpha Diversity measures for JAX Lab animals, including 6 month old (Y), 22 month old (O), and 22-month-old mice treated with rapamycin (R). (B) Alpha Diversity Measures for UW-NIA animals, including Y, O, and R mice. Significant differences between the different alpha diversity measures between Y and O mice, including Observed, Chao1, and Fisher, was observed among the JAX samples. No significant difference between taxonomic richness among Y and R mice was observed in Jax samples. This result was also observed independently in the UW-NIA animals. *p<0.05, **p<0.01.

Figure 5—figure supplement 2. Independent phylum level abundance analysis for JAX and UW-NIA animals.

Normalized agglomerated data were used to evaluate phylum level abundances using an amplicon sequence variant (ASV) approach for both JAX and UW-NIA animals independently. (A) Significant differences in Bacteroidetes, Firmicutes, and Proteobacteria was observed in JAX animals, including 6- month-old (Y), 22-month-old (O), and 22-month-old mice treated with rapamycin (R). (B) Significant differences in Bacteroidetes were observed in UW-NIA animals. *p<0.05, **p<0.01.

Figure 5—figure supplement 3. Independent beta diversity for JAX and UW-NIA animals by principal coordinate analysis using weighted unifrac distances.

(A) Beta diversity for only JAX samples there was significant separation between O and R (p<0.01; Axis 1, 69.8%) as well as between Y and O groups (p<0.05; Axis 2, 9.0%). (B) Beta diversity for only the UW samples also reveal significant difference between Y and O groups (p<0.05; Axis 1, 76.5%; p<0.05; Axis 2, 7.7%). *p<0.05, **p<0.01.

Figure 5—figure supplement 4. Combined beta diversity for JAX and NIA-UW animals by principal coordinate analysis using weighted unifrac distances by site location and group designation.

No distinct differences in clustering by site location was observed. A PERMANOVA (nperm = 999) analysis was performed using the Adonis package (v 2.5–6) as part of the R suite comparing site location (JAX, NIA-UW) and group designation (Y = Young, O = Old, R = Old + Rapa) between JAX and NIA-UW mice used in this study via Bray Curtis Distances (p=0.341).