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Your metabolism is based on how efficiently your body tissues process nutrition and so your metabolism should be great. If you're asking about causality, running more can improve your metabolism, but having a high metabolism rate does not mean you will be an excellent runner. I am an endomorph and my metabolism is naturally really bad, but after a couple years of training, I've become a pretty good runner and my metabolism has improved. I have friends though who have excellent metabolism but are terrible runners. You need stamina to run, not a good metabolism.
My guess is: faster than the average person but much more slowly than a tuned runner. Phelps likely has similar, or better, aerobic capacity as tuned runners. But he doesnât have the training or muscle memory to run as fast as the best runners. I would bet, however, that if he spent a period of time training with a good coach he would become a very fast (though possibly not world-class) runner.