What something like E. Coli can do in a well bioreactor is the ideal case, and even then most of what they produce is the bacteria themselves. On Earth this isn’t a problem at all, but as a means of husbanding every joule because you don’t know when or where the next one is coming from, I think it might matter.

It’s also probably a genuinely hard problem keeping your organisms viable without a constant supply of food, a means to get rid of mutants, or some hitherto unknown means of preservation that could handle the extreme time spans involved between “awakenings”.