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Here's one possible design:

Currently the immune system prevents bacteria from living too close to the cells of the intestines (they have to stay in the mucus).

Setup a signaling system where bacteria that make vitamin C are permitted to stay close, and are shielded from the actions of the immune system. This lets you selectively host those bacteria, and it puts the vitamin C right where it can be immediately absorbed before other bacteria can get to it.

It also punished cheaters, since without the vitamin C the immune system would attack them and force them to stay farther from the food.

It's not much father from there to a dedicated organelle (or cells) the specifically host desired bacteria and all others are killed by the immune system.

And from there the host might incorporate the genes from the bacteria in the same way mitochondria are setup.




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