Age-dependent remodeling of gut microbiome and host serum metabolome in mice

Abstract

The interplay between microbiota and host metabolism plays an important role in health. Here, we examined the relationship between age, gut microbiome and host serum metabolites in male C57BL/6J mice. Fecal microbiome analysis of 3, 6, 18, and 28 months (M) old mice showed that the Firmicutes/Bacteroidetes ratio was highest in the 6M group; the decrease of Firmicutes in the older age groups suggests a reduced capacity of gut microflora to harvest energy from food. We found age-dependent increase in Proteobacteria, which may lead to altered mucus structure more susceptible to bacteria penetration and ultimately increased intestinal inflammation. Metabolomic profiling of polar serum metabolites at fed state in 3, 12, 18 and 28M mice revealed age-associated changes in metabolic cascades involved in tryptophan, purine, amino acids, and nicotinamide metabolism. Correlation analyses showed that nicotinamide decreased with age, while allantoin and guanosine, metabolites in purine metabolism, increased with age. Notably, tryptophan and its microbially derived compounds indole and indole-3-lactic acid significantly decreased with age, while kynurenine increased with age. Together, these results suggest a significant interplay between bacterial and host metabolism, and gut dysbiosis and altered microbial metabolism contribute to aging.

Keywords: aging; gut microbiome; metabolism; serum metabolome.

Conflict of interest statement

CONFLICTS OF INTEREST: The authors declare no conflicts of interest.

Figures

Figure 1

Alteration in gut microbiota diversity and composition at different ages. Mice at 3-, 6-, 18- and 28 months of age (3M, 6M, 18M, 28M) were used (n=8, 9, 10 and 6, respectively). (A) Box-and-whisker plot showing the bacterial α-diversity measurements, including richness (observed species and chao1), and overall sample diversity measured according to Shannon metrics. One-way ANOVA with age as an independent factor. (B) PCoA analysis plot representing microbial β-diversity. (C) Microbiome composition at the level of major phyla. (D) Correlation analysis of the abundance of the major phyla with age. Heatmap shows the abundance-fold-change of bacteria with age. In red: bacteria which are more abundant, in blue: bacteria which are less abundant. Scale: Log2 (Fold change) = -1 (blue) < 0 (white) < 1 (red).

Figure 2

Taxonomic distribution of fecal microbiome by genera. (A) Microbiome composition at the level of genera. (B) The left histogram shows the Linear discriminant analysis (LDA) effect size (Lefse) scores computed for features (on the OTU level) differentially abundant between the different age groups. The right heatmap shows the relative abundance (log10 transformation) of OTUs. “unc”: unclassified.

Figure 3

Fed-state serum metabolome and enriched pathways impacted by aging. Serum samples from 3-, 12-, 18- and 28 months old (3M, 12M, 18M and 28M) mice at the fed state were analyzed (n=4, 5, 4 and 4, respectively). (A) PCA analysis shows the grouped discriminations of the different age groups. 12M and 18M groups clustered together on the PC1 axis. (B) Mummichog pathway analysis plot, using peaks-to-pathway analysis module in MetaboAnalyst 4.0. The color and size of each circle corresponds to its p-value and enrichment factor, respectively. The enrichment factor of a pathway is calculated as the ratio between the number of significant pathway hits and the expected number of compound hits within the pathway [69]. The corresponding pathways are listed in Table 1.

Figure 4

Top metabolic alterations in aging. (A, B) Guanosine and allantoin, metabolites in the purine metabolism pathway. (C, D) Hydroxyproline and N-acetylornithine, metabolites in the arginine and proline metabolism pathway. (E, F) Erythrose phosphate and nicotinamide, metabolites in the pentose phosphate and nicotinamide pathways, respectively. n=4, 5, 4 and 4 for the 3-, 12-, 18- and 28 months old (3M, 12M, 18M, 28M) groups, respectively.

Figure 5

Tryptophan metabolism was altered in aging. (A) Tryptophan and (B) L-kynurenine, metabolite from tryptophan catabolism by host. (C, D) indole and indole-3-lactic acid, metabolites from tryptophan catabolism by gut bacteria. n=4, 5, 4 and 4 for the 3-, 12-, 18- and 28 months old (3M, 12M, 18M, 28M) groups, respectively.