Fig. 4

Several rejuvenation experiments induce changes in global microbial patterns. a Dynamics of dominant families and genera of colon microbiota composition during the rejuvenation procedure. For clarity, the bacterial taxa with an 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. b The relative abundance of the key prevalent microbial genera in the samples of aged mice during each rejuvenation procedure. ‘Young-specific’ indicates the increased abundance of bacterial taxa, such as Akkermansia, Parabacteroides, Anaerofustis, Desulfovibrio and Anaerostipes, in young mice (W20). ‘Aged-specific’ bacterial taxon indicates the increased abundance of bacterial taxa, such as Candidatus Arthromitus, AF12, Helicobacter, cc_115, Lactococcus, Streptococcus, Ruminococcus, Odoribacter, Bifidobacterium, Allobaculum, Prevotella, Turicibacter and Paraprevotella, in aged mice (W100). All data are means ± SEMs (Mann-Whitney U test; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001). c–e Logarithmic linear discriminant analysis (LDA) scores showing microbial genera that were significantly different in abundance between aged mice (W100) and c aged mice in the co-housing model, d aged mice in the parabiosis model or e aged mice in the serum injection model. Other pairwise LEfSe analyses are shown in Fig. S8. The blue and red genus names indicate enriched bacterial taxa in young mice (W20) and aged mice (W100), respectively. The threshold on the logarithmic LDA score was 2.0, and the Kruskal-Wallis test P < 0.05. f Relative abundance of the genus Akkermansia in colon microbiota during each rejuvenation procedure. All data are presented as means ± SEMs (Mann-Whitney U test; *P < 0.05; **P < 0.01). Each dot represents an individual mouse. g Comparison of the copy number of the AMUC_1100 gene in colon microbiota during each rejuvenation procedure. 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). All data are presented as the means ± SEMs (Mann-Whitney U test; *P < 0.05; **P < 0.01). Each dot represents an individual mouse. h LEfSe of metabolic pathways in the colon microbiota during each rejuvenation procedure. The two columns on the left indicate logarithmic LDA scores categorised by KEGG pathways, comparing the young group, Co-O, Iso-A, Hetero-A, iv 8 (Y→A) and iv 16 (Y→A) to the aged group. The last column on the right shows logarithmic LDA scores categorised by KEGG pathways, comparing Co-Y, Iso-Y, Hetero-Y, iv 8 (Y→Y) and iv 16 (Y→Y) to the young group. Only KEGG pathways that differed significantly between the young and aged groups are shown. Red and blue pathways indicate enriched metabolic pathways in young and aged mice, respectively. All KEGG pathways that differed significantly during the rejuvenation process are shown in Fig. S10. Co-Y young mice from co-housing experiments, Co-A aged mice from co-housing experiments, Hetero-Y young mice from heterochronic pairs, Hetero-A aged mice from heterochronic pairs, Iso-Y young mice from isochronic young pairs, Iso-A aged mice from isochronic aged pairs, iv 8 (Y→Y) young mice treated with serum isolated from young mice by intravenous injection into the tail vein 8 times, iv 16 (Y→Y) young mice treated with serum isolated from young mice by intravenous injection into the tail vein 16 times, iv 8 (Y→A) aged mice treated with serum isolated from young mice by intravenous injection into the tail vein 8 times, iv 16 (Y→A) aged mice treated with serum isolated from young mice by intravenous injection into the tail vein 16 times