You wrote
"You are the nutrition you eat, not the psychological state of any animal that becomes your meat."
But it is known that for example stress in the animals before their get slaughtered affects it's flavor (I don't know if will affect the nutrition properties), it has to do with the lactic acid that gets released in the muscle fibers.
So in a sense their psychological state does affect what we eat!
RE: Microbiomes: I'll skip the chicken, but please pass me some cat poo!