Reducing activity of the INDY gene—a citrate transporter—in fruit flies significantly lowers bacterial load while increasing microbiome diversity during aging compared to controls. This genetic manipulation also suppresses JAK/STAT signaling ligands Upd3 and Upd2 in young flies, preserving intestinal stem cell homeostasis and extending lifespan. The microbiome itself wasn't required for lifespan extension, though its removal amplified INDY's longevity benefits. This finding illuminates a crucial mechanistic pathway where metabolic regulation directly influences gut microbial ecology to promote healthy aging. The INDY gene's mammalian counterpart, SLC13A5, suggests these mechanisms may translate to human longevity interventions. What makes this particularly significant is the demonstration that a single metabolic gene can orchestrate both cellular signaling and microbial community structure—two previously separate aging mechanisms. However, the fly model limits immediate clinical relevance, and the preprint status means peer review validation is pending. This work represents an important conceptual advance in understanding how metabolic genes integrate multiple aging pathways, potentially opening new therapeutic targets that simultaneously address cellular metabolism and microbiome dysbiosis.