Toilet water contains significant amounts of bacteria. One of the most common, C. difficile, causes significant amounts of diarrhea and vomiting and spews as high as a foot above the toilet seat when people flush while the lid is open, according to Prevention.
The toilet does not have to be in use for the bacteria to be present. Scientists from Leeds University found bacteria on the top and sides of the toilet and the floor, even when no one had flushed in a while. The bacteria levels are at their highest directly after flushing, but contaminated droplets appear on surfaces nearby even an hour or so after that last flush. Keeping the lid closed is a great way to control the spread of this bacteria.