Metabolic modeling reveals the aging-associated decline of host–microbiome metabolic interactions in mice

Aging is the predominant cause of morbidity and mortality in industrialized countries. The specific molecular mechanisms that drive aging are poorly understood, especially the contribution of the microbiota in these processes. Here, we combined multi-omics with metabolic modeling in mice to comprehensively characterize host–microbiome interactions and how they are affected by aging. Our findings reveal a complex dependency of host metabolism on microbial functions, including previously known as well as novel interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome, which we attribute to reduced beneficial interactions in the microbial community and a reduction in the metabolic output of the microbiome. These microbial changes coincided with a corresponding downregulation of key host pathways predicted by our model that are crucial for maintaining intestinal barrier function, cellular replication, and homeostasis. Our results elucidate potential microbiome–host interactions that may influence host aging processes, focusing on microbial nucleotide metabolism as a pivotal factor in aging dynamics. total-RNA with Illumina’s TruSeq stranded kit, with polyA enrichment, 100bp or 75bp paired end sequencing of 52 samples each from male mice’s (C57BL/6J/Ukj) colons, livers, brains at different ages: 2 (n = 10), 9 (n = 10), 15 (n = 10), 24 (n = 10), and 30 (n = 12) months.