Yes.
However, the bacteria are an essential part of the process when you are using maceration to clean bone. With out them it doesn't work well. So, you have to keep your skull container someplace where nothing will mess with it and someplace where the smell won't be a problem.
Sometimes the teeth come out and sometimes they don't. It seems like the little ones almost always come out. It helps to take a picture of the teeth before you start the process.