Fig. 2

Metagenomic changes during the ageing process. a Schema of colon content collection during the ageing process. b Taxonomic composition for colon microbiota composition at the genus level, as determined with 16S rRNA sequencing. For clarity, the bacterial taxa with average abundance > 1% at each time point are shown. The taxonomic level is indicated as follows: ‘f’, family; ‘g’, genus. The unspecified ‘f__’ or ‘g__’ refer to OTUs without a specific family or genus name, respectively. c Principal coordinate analysis (PCoA) of β-diversity-based Jaccard distances (left panel) and Bray–Curtis dissimilarity metric (right panel) across five ageing groups (P = 0.001; permutational multivariate analysis of variance, PERMANOVA). Week-100 (W100, mice exhibit an aged phenotype) samples were significant different from week-4 (W4), week-20 (W20, mice exhibit a young phenotype) and week-50 (W50) samples (Table S2). d Linear discriminant analysis effect size (LEfSe) showing the taxonomic differences between young and aged mice at the genus level. Logarithmic linear discriminant analysis (LDA) score represents effect size associated with a bacterial taxon. Red and blue indicate significantly increased bacterial taxa in young mice (W20) and aged mice (W100), respectively. The asterisk indicates the bacterial taxa with average abundance > 1% at each time point. Threshold on the logarithmic LDA score was 2.0, and Kruskal-Wallis test P < 0.05. e Comparison of the AMUC_1100 gene abundance across five ageing groups. The copy number of AMUC_1100 was normalised with respect to the total number of genes in each metagenome (counts of AMUC_1100 / total number of ORFs × 1,000,000). Each value is the mean of biological replicate experiments, and error bars indicate ± SEM. Significance was assessed using the Mann-Whitney U test (*P < 0.05; **P < 0.01). f LEfSe identified the differentially abundant KEGG pathway between young and aged mice. Young- and aged-enriched pathways are indicated with a positive logarithmic LDA score (blue) and negative logarithmic LDA score (black), respectively. Threshold on the logarithmic LDA score was 2.0, and the Kruskal-Wallis test P < 0.05. The KEGG modules of oxidative phosphorylation (ko00190), histidine metabolism (ko00340), pentose and glucuronate interconversions (ko00040), benzoate degradation (ko00362), and lysine degradation (ko00310) were significantly (P < 0.01) abundant in the young groups, while those of carotenoid biosynthesis (ko00906), fatty acid biosynthesis (ko00061), butanoate metabolism (ko00650), glutathione metabolism (ko00480) and zeatin biosynthesis (ko00908) were significantly abundant in the aged mouse groups. Other results of LEfSe of metabolic pathways, comparing the 1-, 4- and 50-week-old groups to the 100-week-old group, are shown in Fig. S4a