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I feel compelled to add though, the perspective that not all bacteria are harmful. Actually, most aren't, but many people still use the word "bacteria" as if it were "Satan." There are bacteria on EVERYTHING anyway, including your own body, the bulk weight of which is made up of microorganisms which colonize our insides and outsides, help keep our immune systems healthy, and help us to digest food, etc., and which we quite simply couldn't live without. Many types of bacteria are actually beneficial, if not essential to ingest--eating completely sterile food is, aside from being unrealistic, somewhat unhealthy. This is a fact of life, not just some crack-pot theory.
So it makes no sense to me to worry about the bacteria on an eggshell--especially when we are talking about feeding them to an animal that never bathes and regularly consumes traces of its own poop. Like us, chickens NEED some bacteria in their diet. And BTW mother hens often eat the shells after their babies hatch--and I'm sure they don't bake them in an oven first. IF the eggshells come from some unknown foreign source, especially a large-scale factory farm, then you might consider sterilizing them because those types of operations and their irresponsible practices are a hotbed of disease potential--although the odds of picking up something nasty even in these cases is pretty slim, especially since most large operations wash and sterilize their eggs before distribution. But I only feed my chickens the shells from their own eggs.
I have never baked eggshells to feed to the chickens (actually, not true, I tried once just to see if it would make them easier to crush and store, and finally dismissed it as being a waste of time and propane). Some things are worth worrying about, others aren't... If it works for you, then great. But IMO it's silly to do it purely out of an irrational and misplaced fear of germs....
And by the way I eat raw eggs, and homemade products with raw egg, from my own chickens from time to time too... I find them tasty and nourishing. Chance are that with all the exposure I've had to chickens and chicken manure over the years, I've already developed a resistence to any strains of salmonella that might be in the flock, and besides even so my chances of getting sick from this are much lower than my chances of dying in a car accident. Like I said, some things just aren't worth worrying about...