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This is spot-on. Killing off the common bacteria can cause the bacteria to mutate and become more resilient. Also, since you've raised him and been around him all this time, you have already been exposed to (and have antibodies for) any bacteria the rooster may have. Because of these things, home-raised meat birds are safer to eat than those from a strange farm or even the grocery store. Just make sure you still use safe storing/ handling/ cooking practices, as with any raw meat.