I raise chickens.
Some of them are Aracanas and Americanas, which lay eggs that are pale blue or green.
We joke about eating the green eggs with ham.
Chickens have a sac at the beginning of the digestive tract called a crop, where ruminant-like bacteria (lactobacilli, coliforms, and streptococci) help to digest food before it gets to the acidic stomach. At the other end of the digestive tract, they also have a caeca, where anaerobes live, just like in humans and cows.
Chickens only have one exit shared between the digestive system and the reproductive system. Thus the eggs pass through the same exit that the anaerobic microbes do.
Suppose someone were to feed the chicken some probiotic bacteria that expressed green or red fluorescent protein attached to a protein they excrete, so it attaches to the eggshell as it passes through. Now we get fluorescent green or red eggs.
The second idea is more practical, if less fun. Chickens are often fed foods high in omega-3 fatty acids, so that the eggs will also be rich in these beneficial fats. The sources of these fats are algae, which have the mechanisms for making them, which is why our main sources of DHA and EPA are fish oils, since the primary food source is algae.
Suppose someone engineered probiotic lactobacilli with a pathway for creating omega-3 fats stolen from marine algae, and we could feed this to chickens, so they produce their own omega-3 fats in their crop? This could dramatically lower the cost of omega-3 rich eggs, since the fats would not have to be added to the feed. It may also be possible to find a way to allow the original algae to grow in the crop, either by genetic modification or by changing the crop ecology so that other commensal organisms provide the nutrients the algae need to grow in the dark.
The nice thing about both of these modifications is that the chicken is not modified, and what we are feeding them has a friendly name -- "probiotics". These two things make it easier to market the resulting product.
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