Yes, I do feed him in a separate plastic container. He eats fairly quickly but I let him sit in there a little longer just in case. My vet also suggested that leaving him in there 30 minutes or so more will maybe be better for his aspen ingesting (although he doesn't do it a lot). He's also pretty small at about 3-4 feet long, and when I transfer him back to his tank, I make sure to hold his whole body in a natural position so it doesn't mess with his digestion. I haven't had any problems with that as far as I know, and I didn't want him to ingest bedding or expect food every time I open the tank. He is very docile and sweet, and hardly bites even though he is not feeling good. I am going to call my vet once they open and see what they say.
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