Mechanistic details of mammalian metabolism in vivo and dynamic metabolic changes in intact organisms are difficult to monitor because of the lack of spatial, chemical, or temporal resolution when applying traditional analytical tools. These limitations can be addressed by sensitivity enhancement technology for fast in vivo NMR assays of enzymatic fluxes in tissues of interest. We apply this methodology to characterize organ-specific short chain fatty acid metabolism and the changes of carnitine and coenzyme A pools in ischemia reperfusion. This is achieved by assaying acetyl-CoA synthetase and acetyl-carnitine transferase catalyzed transformations in vivo. The fast and predominant flux of acetate and propionate signal into acyl-carnitine pools shows the efficient buffering of free CoA levels. Sizeable acetyl-carnitine formation from exogenous acetate is even found in liver, where acetyl-CoA synthetase and acetylcarnitine transferase activities have been assumed sequestered in different compartments. In vivo assays of altered acetate metabolism were applied to characterize pathological changes of acetate metabolism upon ischemia. Coenzyme pools in ischemic skeletal muscle are reduced in vivo even 1 h after disturbing muscle perfusion. Impaired mitochondrial metabolism and slow restoration of free CoA are corroborated by assays employing fumarate to show persistently reduced tricarboxylic acid (TCA) cycle activity upon ischemia. In the same animal model, anaerobic metabolism of pyruvate and tissue perfusion normalize faster than mitochondrial bioenergetics.Acetyl coenzyme A (acetyl-CoA) 2 is a central metabolite that connects metabolic paths such as fatty acid degradation and synthesis, cholesterol biosynthesis, glycolysis, and the TCA cycle (Fig. 1). Thus, acetyl-CoA is among the key molecules of energy and intermediary metabolism. Acetyl-CoA is generated by a number of enzymes in mammals including pyruvate dehydrogenase, -ketothiolase, and ATP citrate-lyase (1). A less well-explored metabolic pathway forming acetyl-CoA in mammals is the acetyl-CoA synthetase (AceCS)-catalyzed catabolism of acetate (Fig. 1), which accounts for up to 10% of the energy expenditure in humans (2).Esterification of carboxylic acids is a common means of generating activated molecules for entrance into metabolic pathways and renders the CoA-activated metabolite largely membrane impermeable. Pools of acyl-CoA esters in different cellular compartments require tight regulation because of their metabolic activity and because of the signaling function of some CoA esters (3). Under normal conditions, free CoA is regenerated by the metabolism esters, whereas large amounts of CoA esters may accumulate under stress conditions (4). Sufficient pools of free CoA are ensured under these conditions by buffering acyl-CoA:CoA ratios through transesterifications of acylCoA with carnitine. Carnitine also provides a shuttle for the flux of CoA-activated metabolites between intracellular compartments (5). Transesterification between CoA and carnitine est...