Extended Data Fig. 6: Age-dependent shift in gut microbiota composition.

(a) PCA plot (beta-diversity) and (b) Shannon and Simpson alpha-diversity indices of gut microbiota. Non-parametric Mann-Whitney U-tests (two-sided) to compare alpha diversity between samples and Adonis from vegan package to assess the effects of groups for beta diversity. (c) Relative abundance of gut microbiota composition profiles at the phylum level in male mice at different ages (each color represents one bacterial phylum). (d) The average Firmicutes/Bacteroidetes ratio (F/R) in the cecal samples. (e) Relative abundance of the family Lachnospiraceae. (a-f) Data from young-adult and aged male mice, housed under SPF conditions (n = 5, 10). Each dot represents data from one animal. (d and e) Data are presented as mean values + SEM. (b and f) Box plots; centre = median, upper and lower “hinges” correspond to the first and third quartiles (the 25th and 75th percentiles), upper whisker extends from the hinge to the highest value that is within 1.5 * IQR of the hinge, and lower whisker extends from the hinge to the lowest value within 1.5 * IQR of the hinge, where IQR is the inter-quartile range, or distance between the first and third quartiles. (d and e) Statistics with Mann-Whitney U test (two-sided) (f) Relative abundance of differentially abundant genera in aging. Taxonomic differences at phylum and genus levels between tested groups were identified using the “multivariate analysis by linear models” (MaAsLin) R package.