Extended Data Fig. 4: Age-dependent microbiome changes.

a MetaPhlAn4 derived species with significant changes in abundance with host age. The MetaPhlAn-based approach identified 335 bacteria at the species level of which 69 were found differentially abundant with age. The species Lactobacillus johnsonii matched the MAG based analysis (Fig. 4a). However, due to different taxonomic databases and methods of annotation the resulting species names might vary. On phylum level, the overall aging pattern of both MetaPhlAn and MAG-based taxonomic analysis yielded comparable results, which was a general decrease of Bacillota spec. and an increase of Bacteroidota spec. with host age. b Age-associated changes in metabolic fluxes within the community. c Comparison of community growth rates derived from FBA or PTR. d, e Change of microbiome community growth rate upon removal of a single MAG from the community. The y-axis shows the difference of community growth rate compared to the full community while the x-axis names the MAG that was removed in d or the age group of the host in e (p-values via FDR corrected Wilcoxon’s rank sum test). f Relative abundance of universal adaptive strategies in microbiome communities by age (p-values via FDR corrected Dunn’s test). Sample size for a-f: 30mo.: n = 12, all others n = 10. g Metabolomics derived D-galactose concentration in mouse feces increases with age (Spearman’s ρ = 0.22, unadjusted p = 0.04; Pairwise p-values via Dunn’s test with FDR correction; 3mo.: n = 15, 9mo.: n = 16, 15mo.: n = 15, 24mo.: n = 17, 28mo.: n = 18). Boxplot elements: center line, median; box limits, 25%–75% quantiles; whiskers, 1.5x IQR; points, outliers.