They are kept in vinyl bubbles. The only things that enter the bubbles go through sterilization: a liquid sterilization for tubes/plasticware, etc., irradiation for food, autoclave sterilization for water and liquids. Germfree animals have been around for more than 70 years - they are actually not that hard to create in rats and mice because a fetus is sterile in utero.

> I can't help but think of a GI tract completely devoid of bacterial and fungal cells as being a massive power vacuum essentially

This is absolutely true for the right organisms. Surprisingly there are quite a few common human gut microbes that cannot colonize a germfree gut. Reasons are still not totally understood.

> I would love to see a study analyzing a germfree mouse, rat or pig that was kept germfree to full life as best as possible and then do an analysis on their microbiome to see if, in fact, they are germfree at the end of their life too. I'm not confident they would be.

This paper [0] from 1971 is a good review of the 40's and 50's work showing that germfree hosts are basically normal and can be easily maintained as sterile with proper procedure.

[0] Gordon and Pesti, The Gnotobiotic Animal as a Tool in the Study of Host Microbial Relationships, Bacteriological Reviews, 1971