ABSTRACT: Male reproductive aging involves coordinated changes in germ cells, the testicular niche, mitochondrial homeostasis and the gut microbial–metabolic environment, yet the temporal relationships among these processes remain poorly understood. Here, we profiled male mice at 5, 10, 15 and 20 months using testicular transcriptomics, total and mitochondrial-enriched proteomics, gut 16S rRNA gene sequencing, untargeted gut metabolomics and immune-factor profiling. Across molecular layers, the most pronounced remodeling occurred during late life, particularly between 15 and 20 months, with coordinated attenuation of meiotic, spermiogenic, mitochondrial-translation and respiratory-chain programs. In parallel, senescence-associated, macrophage-associated and inflammatory signals increased within the testicular niche. Mitochondrial-enriched proteomics further uncovered compartment-selective changes that were not consistently reflected at the RNA or total-proteome level. The gut microbial community and metabolic modules also underwent extensive late-life remodeling, and their age-associated patterns covaried with testicular oxidative-phosphorylation, fatty-acid-oxidation and mitochondrial quality-control programs. Collectively, these findings identify late life as a convergence window for spermatogenic, niche, mitochondrial and gut microbial–metabolic aging. By revealing coordinated remodeling across the gut microbial–metabolic environment and testicular mitochondrial programs, this study provides an integrative framework for investigating gut–testis communication and identifying microbial–metabolic processes relevant to male reproductive aging.
