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The calories are irrelevant. If you have a snake that eats rodents, feed it rodents. If your snake will only eat lizards, then you are forced to feed it lizards.
The pathogen transmission potential from feeder reptiles outweighs anything else. Cost is the next downside to feeder geckos, and irregular availability (i.e. when geckos aren't available for months your snake starves) is downside number three. There are more downsides, but those are sufficient.
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