mtDNA mutations regulates immunity via microbiota

Aging alters the gut microbiome and drives the accumulation of mitochondrial DNA (mtDNA) mutations, both contributors to senescence. The mechanism by which these mtDNA mutations affect host health via the microbiota is not yet defined. We utilized wild-type and polymerase gamma (POLG) mutator mice to model a spectrum of mtDNA mutation loads and conducted an integrated multi-omics profiling encompassing intestinal spatial transcriptomics, gut microbiome, and intestinal metabolomics. Spatial transcriptomics and 16S rRNA sequencing showed that mtDNA mutations drive cellular spatial disorganization, specifically the mislocalization of stem and Paneth cells to the mid-crypt, concurrent with lymphocyte depletion and gut microbiota remodeling. Mechanistically, elevated mtDNA mutations reduce intestinal L-citrulline levels, compromising MMP7-mediated antibacterial immunity; this permits expansion of acetate-producing bacteria, whose metabolite (serum acetate) directly diminishes B cell populations. Crucially, we identified parallel increases in acetic acid and its microbial producers during natural aging. Our work establishes a critical role for mitochondria-gut microbiota crosstalk in governing immunosenescence and identifies L-citrulline as a translatable therapeutic target.