Immune cells harbor their own microbiome-derived metabolome: a new layer of immunometabolic regulation

Current models of microbiome, immune crosstalk center on extracellular receptor-mediated signaling, yet a critical observation challenges this paradigm: intracellular concentrations of gut-derived bacterial metabolites (GDBMs) in CD4⁺ T cells do not correlate with paired plasma levels, and it is intracellular, not circulating, GDBM burden that associates with metabolic pathway disruption and immune senescence. Here we propose the concept of an intracellular microbiome metabolome: a pool of aromatic GDBMs actively accumulated through carrier-mediated transport, retained through transcriptional suppression of efflux transporters, and integrated into host metabolic networks where metabolites directly engage intracellular senescence pathways. Using p-cresol sulfate (PCS) as a mechanistic prototype, we provide transcriptomic, proteomic, and metabolomic evidence implicating SLCO4A1/OATP4A1 as the primary entry transporter, whose suppression following PCS exposure creates a feed-forward intracellular retention loop. Once accumulated, PCS functions as a direct agonist of the aryl hydrocarbon receptor (AhR), engaging five downstream effector programs, TGF-β/SMAD signaling, Wnt/β-catenin reprogramming, Foxp3-dependent Treg induction, Notch dysregulation, and PTGS2/COX-2 induction with coordinate HPGD suppression driving PGE₂ excess via EP2/EP4/cAMP/CREM, that converge on mTOR suppression, glycolytic collapse, and mitochondrial dysfunction. This metabolic collapse in turn activates the integrated stress response (ISR) as a downstream consequence, driving p16/CDKN2A and p21/CDKN1A induction and the full immunometabolic signature of accelerated CD4⁺ T cell aging. The plasma intracellular dissociation explains why circulating GDBM levels have failed to predict immune outcomes in HIV-1 infection, chronic kidney disease, and aging, and positions intracellular GDBM quantification as the biologically relevant exposure metric. We discuss three therapeutic intervention layers: reduction of microbial metabolite production, blockade of SLCO4A1-mediated entry and efflux suppression, and targeting the AhR signaling axis with downstream metabolic and ISR consequences.