Systems analysis reveals alternate metabolic states adopted by Mycobacterium tuberculosis across species

Mycobacterium tuberculosis (Mtb) persists within macrophages, yet how different host species shape bacterial state remains poorly understood. Here, we directly compared the intracellular transcriptome of Mtb during infection of human and mouse macrophages, revealing distinct host-imposed microenvironments that drive the pathogen into separable metabolic states. Lipid metabolism and regulatory circuits were prominently remodeled, with mouse macrophages inducing iron- and oxidative-stress responses while human macrophages promoted fatty acid import programs. Using fluorescent fatty acid tracing, we uncovered a striking species-specific phenotype: Mtb forms intracellular lipid inclusions (ILIs) in murine macrophages but not in human macrophages. This phenotype was independent of culture media, macrophage ontogeny, or host antimicrobial factors such as nitric oxide and itaconate. Access of Mtb to host-derived lipids required the ESX-1 secretion system and was inversely correlated with host triacylglycerol (TAG) synthesis. Inhibition of TAG formation in human macrophages partially restored Mtb ILI formation, revealing a metabolic gate that governs lipid flow between host lipid droplets and intracellular Mtb. Together, these findings establish a cross-species framework for decoding host-driven bacterial metabolic states and identify a key barrier limiting Mtb’s access to host lipid stores in human macrophages.