Here are some ideas regarding this topic:
First, agriculture and everything that requires it, should only be accessible to plant eating organisms. This is because meat will rarely be able to stay edible over long terms, and also animals are harder to grow and keep. Also, there should also always be a plant with grain-like seeds that can survive long periods of storage. No-one will want to have their game cut short because the game didn’t give them anything farmable. Animals should be domesticatible when the player’s tribe has enough food to feed a breeding population of the species. Domesticated organisms will be editable, but there will not be much mutation points. Also, symbiotes will be automatically domesticated when the awakening stage begins. The symbiote will be used like it was in the aware stage (phoresite hosts are used for riding, hematophage hosts are used for food).
What if cell farming could work? As in swarms of cells using smaller, more abundant cells as food, but in an organized way. Maybe using photosynthetic plants more since they would want to stand still to keep osmoregulation balanced. This would also seem to show cellular intelligence?
You are saying a player has to be a herbivore or omnivore? WHAT? Please don’t be that close-minded. I can easily imagine a herding civilization that doesn’t farm plants. There should be a grass analoge just lying around to feed them! Heck, some ants herd aphids and don’t farm plants. A carnivore can become civilized. I’m sorry but I just had to point this out. Also this topic might be a duplicate, I’d have to check.
Edit: yes the topic is a duplicate, and there are three topics on the topic. This one, this one and this one.