Well, you've sort of left the field wide-open here, so-to-speak. In the scientific method, after the question has been narrowed down and asked, what is known as the hypothesis is put forth. The hypothesis is our best, educated, qualified guess as to what we think the answer to the question is going to be. It is not so important that we get the hyopothesis correct as it is to be able to explain why the experiment produced the results it did. Many important tenets of science have been discovered as hypotheses gone awry, not on target, not the result one would expect.
In the area of bacteria, one might hypothesize about the shape the bacterial cells present; they seem to occupy three general shapes, round, rod-like, and spiral. One might hypothesize about a specific bacterias ability to digest oil from an oil spill, such as recently occured in the Gulf of Mexico. One might hypothesize about the amount of intestinal gas produced from bacterial action in the large intestine, and the reliability of certain dietary products promising there will "be no gas" (Beano). So, as you see, it depends on what you are talking about, the specific aim of the question, as to what we want to put forth as our best, educated, hypothetical guess as to the logical outcome.